Results DESeq2 per species

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Last updated: 2024-11-04

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Knit directory: locust-comparative-genomics/

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Load the libraries

We start by loading all the required R packages.

#(install first from CRAN or Bioconductor)
library("DESeq2")
library("tximport")
library("txdbmaker")
library("knitr")
library("rmdformats")
library("tidyverse")
library("data.table")
library("DT")  # for making interactive search table
library("plotly") # for interactive plots
library("ggthemes") # for theme_calc
library("reshape2")
library("ComplexHeatmap")
library("RColorBrewer")
library("circlize")
library("apeglm")
library("ggpubr")
library("ggplot2")
library("ggrepel")
library("EnhancedVolcano")
library("SARTools")
library("pheatmap")
library("clusterProfiler")
library("sva")
library("cowplot")
library("ashr")
library("vsn")
library("ggdist")
library("ggConvexHull")
library("kableExtra")
library("plotly")

# Path for all species
workDir <- "/Users/maevatecher/Library/Mobile Documents/com~apple~CloudDocs/Documents/GitHub/locust-comparative-genomics/data"

## PARAMETERS for running DEseq2
tresh_logfold <- 1                    # Treshold for log2(foldchange) in final DE-files
tresh_padj <- 0.05                    # Treshold for adjusted p-valued in final DE-files
alpha_DEseq2 <- 0.05                  # threshold of statistical significance
pAdjustMethod_DEseq2 <- "BH"          # p-value adjustment method: "BH" (default) or "BY"
featuresToRemove <- c(NULL)           # names of the features to be removed, NULL if none or if using Idxstats
varInt <- "RearingCondition"          # factor of interest
condRef <- "Isolated"                 # reference biological condition
batch <- NULL                         # blocking factor: NULL (default) or "batch" for example  
fitType <- "parametric"               # mean-variance relationship: "parametric" (default) or "local"
cooksCutoff <- TRUE                   # TRUE/FALSE to perform the outliers detection (default is TRUE)
independentFiltering <- TRUE          # TRUE/FALSE to perform independent filtering (default is TRUE)
typeTrans <- "rlog"                   # transformation for PCA/clustering: "VST" or "rlog"
locfunc <- "median"

STRATEGY 1: One genome S. gregaria

1. DEGs in bulk Head tissues

piceifrons

cancellata

americana

cubense

nitens

2. DEGs in bulk Head tissues

piceifrons

cancellata

americana

cubense

nitens

STRATEGY 2: Own RefSeq genome

STAR + featurecounts + DEseq2 {.tabset .tabset-fade}

3. DEGs in bulk Head tissues

This follows the same code as for STRATEGY 1 except that we will change the RefSeq to the transcript species genome path.

gregaria

rawDir <- file.path(workDir, "03-gregaria-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "gregaria"
targetFile <- file.path(workDir, "list", paste0("Head", "_", species, ".txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 5697

A total of 5,697 genes out of the pre-filtered 16,305 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 16305 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 2709, 17%
LFC < 0 (down)     : 2988, 18%
outliers [1]       : 99, 0.61%
low counts [2]     : 0, 0%
(mean count < 1)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "gregaria2 plot-1.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "gregaria2 plot-2.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "gregaria2 plot-3.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "gregaria2 plot-4.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "gregaria2 plot-5.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "gregaria2 plot-6.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. gregaria","Isolated S. gregaria"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. gregaria Head tissues", subtitle = "rlog transformation") 

Past versions of "gregaria2 plot-7.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. gregaria","Isolated S. gregaria"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. gregaria Head tissues", subtitle = "vst transformation") 

Past versions of "gregaria2 plot-8.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "gregaria2 plot-9.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "gregaria2 plot-10.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "gregaria2 plot-11.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "gregaria2 plot-12.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "gregaria2 plot-13.png"

Version	Author	Date
f01f1cf	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Head tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Head S. gregaria", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

piceifrons

rawDir <- file.path(workDir, "03-piceifrons-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "piceifrons"
targetFile <- file.path(workDir, "list", paste0("Head", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 1053

A total of 1,053 genes out of the pre-filtered 13,527 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 13527 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 538, 4%
LFC < 0 (down)     : 518, 3.8%
outliers [1]       : 43, 0.32%
low counts [2]     : 525, 3.9%
(mean count < 5)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "piceifrons2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "piceifrons2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "piceifrons2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "piceifrons2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "piceifrons2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "piceifrons2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. piceifrons","Isolated S. piceifrons"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. piceifrons Head tissues", subtitle = "rlog transformation") 

Past versions of "piceifrons2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. piceifrons","Isolated S. piceifrons"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. piceifrons Head tissues", subtitle = "vst transformation") 

Past versions of "piceifrons2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "piceifrons2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "piceifrons2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "piceifrons2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "piceifrons2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "piceifrons2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Head tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Head S. piceifrons", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

cancellata

rawDir <- file.path(workDir, "03-cancellata-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "cancellata"
targetFile <- file.path(workDir, "list", paste0("Head", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 1628

A total of 1,628 genes out of the pre-filtered 13,547 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 13547 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 751, 5.5%
LFC < 0 (down)     : 877, 6.5%
outliers [1]       : 26, 0.19%
low counts [2]     : 263, 1.9%
(mean count < 4)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "cancellata2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "cancellata2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "cancellata2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "cancellata2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "cancellata2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "cancellata2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. cancellata","Isolated S. cancellata"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. cancellata Head tissues", subtitle = "rlog transformation") 

Past versions of "cancellata2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. cancellata","Isolated S. cancellata"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. cancellata Head tissues", subtitle = "vst transformation") 

Past versions of "cancellata2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "cancellata2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "cancellata2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "cancellata2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "cancellata2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "cancellata2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Head tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Head S. cancellata", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

americana

rawDir <- file.path(workDir, "03-americana-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "americana"
targetFile <- file.path(workDir, "list", paste0("Head", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 1413

A total of 1,413 genes out of the pre-filtered 13,764 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 13764 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 802, 5.8%
LFC < 0 (down)     : 619, 4.5%
outliers [1]       : 57, 0.41%
low counts [2]     : 534, 3.9%
(mean count < 5)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "americana2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "americana2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "americana2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "americana2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "americana2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "americana2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. americana","Isolated S. americana"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. americana Head tissues", subtitle = "rlog transformation") 

Past versions of "americana2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. americana","Isolated S. americana"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. americana Head tissues", subtitle = "vst transformation") 

Past versions of "americana2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "americana2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "americana2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "americana2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "americana2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "americana2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Head tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Head S. americana", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

cubense

rawDir <- file.path(workDir, "03-cubense-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "cubense"
targetFile <- file.path(workDir, "list", paste0("Head", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 105

A total of 105 genes out of the pre-filtered 14,328 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 14328 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 49, 0.34%
LFC < 0 (down)     : 56, 0.39%
outliers [1]       : 173, 1.2%
low counts [2]     : 0, 0%
(mean count < 2)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "cubense2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "cubense2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "cubense2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "cubense2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "cubense2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "cubense2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. cubense","Isolated S. cubense"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. cubense Head tissues", subtitle = "rlog transformation") 

Past versions of "cubense2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. cubense","Isolated S. cubense"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. cubense Head tissues", subtitle = "vst transformation") 

Past versions of "cubense2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "cubense2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "cubense2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "cubense2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "cubense2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "cubense2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Head tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Head S. cubense", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

nitens

rawDir <- file.path(workDir, "03-nitens-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "nitens"
targetFile <- file.path(workDir, "list", paste0("Head", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 540

A total of 540 genes out of the pre-filtered 13,510 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 13510 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 233, 1.7%
LFC < 0 (down)     : 314, 2.3%
outliers [1]       : 124, 0.92%
low counts [2]     : 524, 3.9%
(mean count < 5)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "nitens2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "nitens2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "nitens2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "nitens2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "nitens2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "nitens2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. nitens","Isolated S. nitens"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. nitens Head tissues", subtitle = "rlog transformation") 

Past versions of "nitens2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. nitens","Isolated S. nitens"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. nitens Head tissues", subtitle = "vst transformation") 

Past versions of "nitens2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "nitens2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "nitens2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "nitens2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "nitens2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Head tissue heatmap distance matrix, rlog transformation")

Past versions of "nitens2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Head tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Head S. nitens", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

4. DEGs in bulk Thorax tissues

gregaria

rawDir <- file.path(workDir, "03-gregaria-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "gregaria"
targetFile <- file.path(workDir, "list", paste0("Thorax", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 5442

A total of 5,442 genes out of the pre-filtered 16,613 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 16613 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 2751, 17%
LFC < 0 (down)     : 2691, 16%
outliers [1]       : 112, 0.67%
low counts [2]     : 0, 0%
(mean count < 2)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "thoraxgregaria2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "thoraxgregaria2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "thoraxgregaria2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "thoraxgregaria2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "thoraxgregaria2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "thoraxgregaria2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. gregaria","Isolated S. gregaria"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. gregaria Thorax tissues", subtitle = "rlog transformation") 

Past versions of "thoraxgregaria2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. gregaria","Isolated S. gregaria"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. gregaria Thorax tissues", subtitle = "vst transformation") 

Past versions of "thoraxgregaria2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "thoraxgregaria2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "thoraxgregaria2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "thoraxgregaria2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxgregaria2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxgregaria2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Thorax tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Thorax S. gregaria", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

piceifrons

rawDir <- file.path(workDir, "03-piceifrons-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "piceifrons"
targetFile <- file.path(workDir, "list", paste0("Thorax", "_", species, ".txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 3002

A total of 3,002 genes out of the pre-filtered 13,527 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 13253 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 1641, 12%
LFC < 0 (down)     : 1361, 10%
outliers [1]       : 36, 0.27%
low counts [2]     : 0, 0%
(mean count < 2)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "thoraxpiceifrons2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "thoraxpiceifrons2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "thoraxpiceifrons2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "thoraxpiceifrons2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "thoraxpiceifrons2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "thoraxpiceifrons2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. piceifrons","Isolated S. piceifrons"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. piceifrons Thorax tissues", subtitle = "rlog transformation") 

Past versions of "thoraxpiceifrons2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. piceifrons","Isolated S. piceifrons"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. piceifrons Thorax tissues", subtitle = "vst transformation") 

Past versions of "thoraxpiceifrons2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "thoraxpiceifrons2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "thoraxpiceifrons2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "thoraxpiceifrons2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxpiceifrons2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxpiceifrons2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Thorax tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Thorax S. piceifrons", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

cancellata

rawDir <- file.path(workDir, "03-cancellata-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "cancellata"
targetFile <- file.path(workDir, "list", paste0("Thorax", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 1475

A total of 1,475 genes out of the pre-filtered 13,557 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 13557 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 734, 5.4%
LFC < 0 (down)     : 738, 5.4%
outliers [1]       : 37, 0.27%
low counts [2]     : 526, 3.9%
(mean count < 6)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "thoraxcancellata2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "thoraxcancellata2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "thoraxcancellata2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "thoraxcancellata2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "thoraxcancellata2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "thoraxcancellata2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. cancellata","Isolated S. cancellata"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. cancellata Thorax tissues", subtitle = "rlog transformation") 

Past versions of "thoraxcancellata2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. cancellata","Isolated S. cancellata"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. cancellata Thorax tissues", subtitle = "vst transformation") 

Past versions of "thoraxcancellata2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "thoraxcancellata2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "thoraxcancellata2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "thoraxcancellata2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxcancellata2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxcancellata2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Thorax tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Thorax S. cancellata", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

americana

rawDir <- file.path(workDir, "03-americana-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "americana"
targetFile <- file.path(workDir, "list", paste0("Thorax", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 1264

A total of 1,264 genes out of the pre-filtered 13,764 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 13520 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 460, 3.4%
LFC < 0 (down)     : 798, 5.9%
outliers [1]       : 48, 0.36%
low counts [2]     : 0, 0%
(mean count < 2)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "thoraxamericana2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "thoraxamericana2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "thoraxamericana2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "thoraxamericana2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "thoraxamericana2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "thoraxamericana2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. americana","Isolated S. americana"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. americana Thorax tissues", subtitle = "rlog transformation") 

Past versions of "thoraxamericana2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. americana","Isolated S. americana"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. americana Thorax tissues", subtitle = "vst transformation") 

Past versions of "thoraxamericana2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "thoraxamericana2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "thoraxamericana2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "thoraxamericana2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxamericana2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxamericana2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Thorax tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Thorax S. americana", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

cubense

rawDir <- file.path(workDir, "03-cubense-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "cubense"
targetFile <- file.path(workDir, "list", paste0("Thorax", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 368

A total of 368 genes out of the pre-filtered 14,328 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 13909 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 127, 0.91%
LFC < 0 (down)     : 251, 1.8%
outliers [1]       : 137, 0.98%
low counts [2]     : 1079, 7.8%
(mean count < 7)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
brock_df <- as.data.frame(brock)
datatable(brock_df, options = list(
  pageLength = 10,       # Set initial page length
  scrollX = TRUE,        # Enable horizontal scrolling
  autoWidth = TRUE,      # Adjust column width automatically
  searchHighlight = TRUE # Highlight search matches
))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "thoraxcubense2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "thoraxcubense2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "thoraxcubense2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "thoraxcubense2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "thoraxcubense2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "thoraxcubense2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. cubense","Isolated S. cubense"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. cubense Thorax tissues", subtitle = "rlog transformation") 

Past versions of "thoraxcubense2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. cubense","Isolated S. cubense"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. cubense Thorax tissues", subtitle = "vst transformation") 

Past versions of "thoraxcubense2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "thoraxcubense2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "thoraxcubense2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "thoraxcubense2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxcubense2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxcubense2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

The following plots are interactive and we can hover or Zoom on the locus of interest.

# Ma plot parameters after shrinkage
de_shrink <- lfcShrink(dds = shigeru, coef="RearingCondition_Crowded_vs_Isolated", type="apeglm")
#head(de_shrink)
maplot <-ggmaplot(de_shrink, fdr = 0.05, fc = 1, size = 1, palette = c("#B31B21", "#1465AC", "darkgray"), genenames = as.vector(rownames(de_shrink$name)), top = 0,legend="top",label.select = NULL) +
  coord_cartesian(xlim = c(0, 20)) + 
  scale_y_continuous(limits=c(-12, 12)) + 
  theme(axis.text.x = element_text(size=12),axis.text.y = element_text(size=12),axis.title.x = element_text(size=14),axis.title.y = element_text(size=14),axis.line = element_line(size = 1, colour="gray20"),axis.ticks = element_line(size = 1, colour="gray20")) +
  guides(color = guide_legend(override.aes = list(size = c(3,3,3)))) + 
  theme(legend.position = c(0.70, 0.12),legend.text=element_text(size=14,face="bold"),legend.background = element_rect(fill="transparent")) +
  theme(plot.title = element_text(size=18, colour="gray30", face="bold",hjust=0.06, vjust=-5)) +
  labs(title="MA-plot for the shrunken log2 fold changes in the Thorax tissues")
interactive_maplot <- ggplotly(maplot)
interactive_maplot

#Volcano plot
keyvals <-ifelse( 
  res_shigeru$log2FoldChange >= 1 & res_shigeru$padj <= 0.05, '#B31B21', 
  ifelse(res_shigeru$log2FoldChange <= -1 & res_shigeru$padj <= 0.05, '#1465AC', 'darkgray')) 

keyvals[is.na(keyvals)] <-'lightgray' 
names(keyvals)[keyvals == "#B31B21"] <-'Upregulated' 
names(keyvals)[keyvals == "#1465AC"] <-'Downregulated' 
names(keyvals)[keyvals == 'darkgray'] <-'NS'

res_shigeru$color <- keyvals
volcano_plot <- ggplot(res_shigeru, aes(x = log2FoldChange, y = -log10(padj), 
                                        color = color,  # Use the color column with keyvals
                                        text = rownames(res_shigeru))) +
  geom_point(size = 3, alpha = 0.8) +
  scale_color_identity() +  # Directly use the color values from `keyvals`
  guides(color = "none") +  # Hide the color legend
  labs(title = "Volcano Plot DEG Thorax S. cubense", x = "log2 Fold Change", y = "-log10 Adjusted P-Value") +
  theme_minimal()

# Convert to interactive plot with hover text for gene names
interactive_volcano <- ggplotly(volcano_plot, tooltip = "text") %>%
  layout(hoverlabel = list(namelength = -1))

# Display the interactive plot
interactive_volcano

nitens

rawDir <- file.path(workDir, "03-nitens-DESeq2") 

# Path and name of targetfile containing conditions and file names
species <- "nitens"
targetFile <- file.path(workDir, "list", paste0("Thorax", "_", species, "_nooutliers.txt")) 

sampletable <- fread(targetFile)
rownames(sampletable) <- sampletable$SampleName
sampletable$RearingCondition <- as.factor(sampletable$RearingCondition)
sampletable$Tissue <- as.factor(sampletable$Tissue)

## Import count files
satoshi <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
                        directory = rawDir,
                        design = ~ RearingCondition )
#satoshi

smallestGroupSize <- 3
keep <- rowSums(counts(satoshi) >= 5) >= smallestGroupSize
satoshi <- satoshi[keep,]
#nrow(satoshi)
satoshi$RearingCondition <- relevel(satoshi$RearingCondition, ref = "Isolated")

# Fit the statistical model
shigeru <- DESeq(satoshi)
#cbind(resultsNames(shigeru))
res_shigeru <- results(shigeru)
sum(res_shigeru$padj < tresh_padj, na.rm = TRUE)

[1] 0

A total of 0 genes out of the pre-filtered 13,510 features were showing significant differences in expression levels. The summary below showed how many were upregulated and downregulated in crowded compared to isolated it is possible to scroll it.

brock <- results(shigeru, name = "RearingCondition_Crowded_vs_Isolated", alpha = alpha_DEseq2)
summary(brock)

out of 13168 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 0, 0%
LFC < 0 (down)     : 0, 0%
outliers [1]       : 132, 1%
low counts [2]     : 0, 0%
(mean count < 2)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

#mcols(brock)$description
#head(brock)
#brock_df <- as.data.frame(brock)
#datatable(brock_df, options = list(
#  pageLength = 10,       # Set initial page length
#  scrollX = TRUE,        # Enable horizontal scrolling
#  autoWidth = TRUE,      # Adjust column width automatically
#  searchHighlight = TRUE # Highlight search matches
#))

Now we will make the different plots: PCA, MA and Volcano.

# Try with the data transformation
shigeru_vst <- vst(shigeru)
shigeru_rlog <- rlog(shigeru)
shigeru_ntd <- normTransform(shigeru)
itadori <- meanSdPlot(assay(shigeru_ntd))

Past versions of "thoraxnitens2 plot-1.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

itadori2 <- itadori$gg + ggtitle("Transformation with ntd")
itadori2

Past versions of "thoraxnitens2 plot-2.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi <- meanSdPlot(assay(shigeru_vst))

Past versions of "thoraxnitens2 plot-3.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

megumi2 <- megumi$gg + ggtitle("Transformation with vst")
megumi2

Past versions of "thoraxnitens2 plot-4.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara <- meanSdPlot(assay(shigeru_rlog))

Past versions of "thoraxnitens2 plot-5.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

nobara2 <-nobara$gg + ggtitle("Transformation with rlog")
nobara2

Past versions of "thoraxnitens2 plot-6.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# Create the pca on the defined groups
pcaData1 <- plotPCA(object = shigeru_rlog, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData1, "percentVar"))
pcaData1$RearingCondition<-factor(pcaData1$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. nitens","Isolated S. nitens"))
#levels(pcaData1$RearingCondition)
p1 <- ggplot(pcaData1, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p1 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. nitens Thorax tissues", subtitle = "rlog transformation") 

Past versions of "thoraxnitens2 plot-7.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pcaData2 <- plotPCA(object = shigeru_vst, intgroup = c("RearingCondition"),returnData=TRUE)
percentVar <- round(100 * attr(pcaData2, "percentVar"))
pcaData2$RearingCondition<-factor(pcaData2$RearingCondition,levels=c("Crowded","Isolated"), labels=c("Crowded S. nitens","Isolated S. nitens"))
#levels(pcaData2$RearingCondition)
p2 <-ggplot(pcaData2, aes(PC1, PC2, color= RearingCondition)) +
  geom_point(size=6) +
  xlab(paste0("PC1: ", percentVar[1], "% variance")) +
  ylab(paste0("PC2: ", percentVar[2], "% variance")) + 
  scale_color_manual(values = c("blue", "red")) +
  #coord_fixed() +
  theme_bw() +
  theme(legend.title = element_blank()) + 
  theme(legend.text = element_text(face="bold", size=16)) +
  theme(axis.text = element_text(size=14)) +
  theme(axis.title = element_text(size=14))
p2 + geom_convexhull(aes(fill = RearingCondition, color = RearingCondition), alpha = 0.5) +
    scale_fill_manual(values = c("blue", "red"))+ 
    ggtitle("PCA on S. nitens Thorax tissues", subtitle = "vst transformation") 

Past versions of "thoraxnitens2 plot-8.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

select <- order(rowMeans(counts(shigeru,normalized=TRUE)),
                decreasing=TRUE)[1:12]
df <- as.data.frame(colData(shigeru)[,c("RearingCondition","Tissue")])


# Count matrix
pheatmap(assay(shigeru_ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after norm transformation")

Past versions of "thoraxnitens2 plot-9.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_vst)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after vst transformation")

Past versions of "thoraxnitens2 plot-10.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

pheatmap(assay(shigeru_rlog)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df, main = "Count Matrix after rlog transformation")

Past versions of "thoraxnitens2 plot-11.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

# calculate between-sample distance matrix
metadata <- sampletable[,c("RearingCondition", "Tissue")]
rownames(metadata) <- sampletable$SampleName
sampleDistMatrix.rlog <- as.matrix(dist(t(assay(shigeru_rlog))))
pheatmap(sampleDistMatrix.rlog, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxnitens2 plot-12.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

sampleDistMatrix.vst<- as.matrix(dist(t(assay(shigeru_vst))))
pheatmap(sampleDistMatrix.vst, annotation_col=metadata, main = "Thorax tissue heatmap distance matrix, rlog transformation")

Past versions of "thoraxnitens2 plot-13.png"

Version	Author	Date
200db58	Maeva TECHER	2024-11-01

Session information

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] ggConvexHull_0.1.0          ggdist_3.3.2               
 [3] vsn_3.72.0                  cowplot_1.1.3              
 [5] sva_3.52.0                  BiocParallel_1.38.0        
 [7] genefilter_1.86.0           mgcv_1.9-1                 
 [9] nlme_3.1-166                clusterProfiler_4.12.6     
[11] pheatmap_1.0.12             SARTools_1.8.1             
[13] kableExtra_1.4.0            edgeR_4.2.2                
[15] limma_3.60.6                ashr_2.2-63                
[17] EnhancedVolcano_1.22.0      ggrepel_0.9.6              
[19] ggpubr_0.6.0                apeglm_1.26.1              
[21] circlize_0.4.16             RColorBrewer_1.1-3         
[23] ComplexHeatmap_2.20.0       reshape2_1.4.4             
[25] ggthemes_5.1.0              plotly_4.10.4              
[27] DT_0.33                     data.table_1.16.2          
[29] lubridate_1.9.3             forcats_1.0.0              
[31] stringr_1.5.1               dplyr_1.1.4                
[33] purrr_1.0.2                 readr_2.1.5                
[35] tidyr_1.3.1                 tibble_3.2.1               
[37] ggplot2_3.5.1               tidyverse_2.0.0            
[39] rmdformats_1.0.4            knitr_1.48                 
[41] txdbmaker_1.0.1             GenomicFeatures_1.56.0     
[43] AnnotationDbi_1.66.0        tximport_1.32.0            
[45] DESeq2_1.44.0               SummarizedExperiment_1.34.0
[47] Biobase_2.64.0              MatrixGenerics_1.16.0      
[49] matrixStats_1.4.1           GenomicRanges_1.56.2       
[51] GenomeInfoDb_1.40.1         IRanges_2.38.1             
[53] S4Vectors_0.42.1            BiocGenerics_0.50.0        

loaded via a namespace (and not attached):
  [1] fs_1.6.5                 bitops_1.0-9             enrichplot_1.24.4       
  [4] httr_1.4.7               doParallel_1.0.17        numDeriv_2016.8-1.1     
  [7] tools_4.4.1              backports_1.5.0          utf8_1.2.4              
 [10] R6_2.5.1                 lazyeval_0.2.2           GetoptLong_1.0.5        
 [13] withr_3.0.2              prettyunits_1.2.0        GGally_2.2.1            
 [16] gridExtra_2.3            preprocessCore_1.66.0    cli_3.6.3               
 [19] scatterpie_0.2.4         labeling_0.4.3           sass_0.4.9              
 [22] SQUAREM_2021.1           mvtnorm_1.3-1            mixsqp_0.3-54           
 [25] Rsamtools_2.20.0         systemfonts_1.1.0        yulab.utils_0.1.7       
 [28] gson_0.1.0               DOSE_3.30.5              svglite_2.1.3           
 [31] R.utils_2.12.3           invgamma_1.1             bbmle_1.0.25.1          
 [34] rstudioapi_0.17.1        RSQLite_2.3.7            gridGraphics_0.5-1      
 [37] generics_0.1.3           shape_1.4.6.1            BiocIO_1.14.0           
 [40] crosstalk_1.2.1          distributional_0.5.0     car_3.1-3               
 [43] GO.db_3.19.1             Matrix_1.7-1             fansi_1.0.6             
 [46] abind_1.4-8              R.methodsS3_1.8.2        lifecycle_1.0.4         
 [49] whisker_0.4.1            yaml_2.3.10              carData_3.0-5           
 [52] qvalue_2.36.0            SparseArray_1.4.8        BiocFileCache_2.12.0    
 [55] blob_1.2.4               promises_1.3.0           crayon_1.5.3            
 [58] bdsmatrix_1.3-7          lattice_0.22-6           annotate_1.82.0         
 [61] KEGGREST_1.44.1          pillar_1.9.0             fgsea_1.30.0            
 [64] rjson_0.2.23             codetools_0.2-20         fastmatch_1.1-4         
 [67] glue_1.8.0               ggfun_0.1.7              treeio_1.28.0           
 [70] vctrs_0.6.5              png_0.1-8                gtable_0.3.6            
 [73] emdbook_1.3.13           cachem_1.1.0             xfun_0.49               
 [76] S4Arrays_1.4.1           tidygraph_1.3.1          coda_0.19-4.1           
 [79] survival_3.7-0           iterators_1.0.14         statmod_1.5.0           
 [82] ggtree_3.12.0            bit64_4.5.2              progress_1.2.3          
 [85] filelock_1.0.3           rprojroot_2.0.4          bslib_0.8.0             
 [88] affyio_1.74.0            irlba_2.3.5.1            colorspace_2.1-1        
 [91] DBI_1.2.3                tidyselect_1.2.1         bit_4.5.0               
 [94] compiler_4.4.1           curl_5.2.3               git2r_0.35.0            
 [97] httr2_1.0.5              xml2_1.3.6               ggdendro_0.2.0          
[100] DelayedArray_0.30.1      shadowtext_0.1.4         bookdown_0.41           
[103] rtracklayer_1.64.0       scales_1.3.0             hexbin_1.28.4           
[106] affy_1.82.0              rappdirs_0.3.3           digest_0.6.37           
[109] rmarkdown_2.28           XVector_0.44.0           htmltools_0.5.8.1       
[112] pkgconfig_2.0.3          highr_0.11               dbplyr_2.5.0            
[115] fastmap_1.2.0            rlang_1.1.4              GlobalOptions_0.1.2     
[118] htmlwidgets_1.6.4        UCSC.utils_1.0.0         farver_2.1.2            
[121] jquerylib_0.1.4          jsonlite_1.8.9           GOSemSim_2.30.2         
[124] R.oo_1.26.0              RCurl_1.98-1.16          magrittr_2.0.3          
[127] ggplotify_0.1.2          Formula_1.2-5            GenomeInfoDbData_1.2.12 
[130] patchwork_1.3.0          munsell_0.5.1            Rcpp_1.0.13             
[133] ape_5.8                  viridis_0.6.5            stringi_1.8.4           
[136] ggraph_2.2.1             zlibbioc_1.50.0          MASS_7.3-61             
[139] plyr_1.8.9               ggstats_0.7.0            parallel_4.4.1          
[142] graphlayouts_1.2.0       Biostrings_2.72.1        splines_4.4.1           
[145] hms_1.1.3                locfit_1.5-9.10          igraph_2.1.1            
[148] ggsignif_0.6.4           biomaRt_2.60.1           XML_3.99-0.17           
[151] evaluate_1.0.1           BiocManager_1.30.25      tweenr_2.0.3            
[154] tzdb_0.4.0               foreach_1.5.2            httpuv_1.6.15           
[157] polyclip_1.10-7          clue_0.3-65              ggforce_0.4.2           
[160] broom_1.0.7              xtable_1.8-4             restfulr_0.0.15         
[163] tidytree_0.4.6           rstatix_0.7.2            later_1.3.2             
[166] viridisLite_0.4.2        truncnorm_1.0-9          aplot_0.2.3             
[169] memoise_2.0.1            GenomicAlignments_1.40.0 cluster_2.1.6           
[172] workflowr_1.7.1          timechange_0.3.0