Last updated: 2019-02-27
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Knit directory: threeprimeseq/analysis/
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Modified: code/Snakefile
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | c583588 | Briana Mittleman | 2019-02-27 | add res and plots |
html | dd8d988 | Briana Mittleman | 2019-02-21 | Build site. |
Rmd | d210987 | Briana Mittleman | 2019-02-21 | add res and plots |
html | 4ea438e | Briana Mittleman | 2019-02-18 | Build site. |
Rmd | bcb2f86 | Briana Mittleman | 2019-02-18 | add qtl by per and diff iso |
library(tidyverse)
── Attaching packages ───────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.0.0 ✔ purrr 0.2.5
✔ tibble 1.4.2 ✔ dplyr 0.7.6
✔ tidyr 0.8.1 ✔ stringr 1.4.0
✔ readr 1.1.1 ✔ forcats 0.3.0
Warning: package 'stringr' was built under R version 3.5.2
── Conflicts ──────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
library(workflowr)
This is workflowr version 1.2.0
Run ?workflowr for help getting started
library(reshape2)
Attaching package: 'reshape2'
The following object is masked from 'package:tidyr':
smiths
Leafcutter environment: module unload Anaconda3 module load Anaconda3/5.3.0 conda activate leafcutter
awk '{if(NR>1)print}' /project2/gilad/briana/threeprimeseq/data/diff_iso_processed_GeneLocAnno/TN_diff_isoform_GeneLocAnno_chr*.txt_effect_sizes.txt > /project2/gilad/briana/threeprimeseq/data/diff_iso_processed_GeneLocAnno/TN_diff_isoform_GeneLocAnno_AllChrom.txt_effect_sizes.txt
awk '{if(NR>1)print}' /project2/gilad/briana/threeprimeseq/data/diff_iso_processed_GeneLocAnno/TN_diff_isoform_GeneLocAnno_chr*cluster_significance.txt > /project2/gilad/briana/threeprimeseq/data/diff_iso_processed_GeneLocAnno/TN_diff_isoform_GeneLocAnno_AllChrom.txt_cluster_significance.txt
diffIso=read.table("../data/diff_iso_GeneLocAnno/TN_diff_isoform_GeneLocAnno_AllChrom.txt_cluster_significance.txt", header = F,col.names = c("status", "loglr", "df", "p", "cluster", "p.adjust"),stringsAsFactors = F,sep="\t") %>% filter(status == "Success")
diffIso$p.adjust=as.numeric(as.character(diffIso$p.adjust))
Make plot
png("../output/plots/DiffIsoQQplot.png")
qqplot(-log10(runif(nrow(diffIso))), -log10(diffIso$p.adjust),ylab="-log10 Total Adjusted Leafcutter pvalue", xlab="-log 10 Uniform expectation", main="Leafcutter differencial isoform analysis between fractions")
abline(0,1)
dev.off()
quartz_off_screen
2
diffIso_10FDR=diffIso %>% filter(-log10(p.adjust)>1)
diffIso_10FDR_genes=diffIso_10FDR %>% separate(cluster, into = c("chr", "gene"), sep=":") %>% group_by(gene) %>% tally()
nrow(diffIso_10FDR_genes)
[1] 8227
There are 8227 significant genes
effectsize=read.table("../data/diff_iso_GeneLocAnno/TN_diff_isoform_GeneLocAnno_AllChrom.txt_effect_sizes.txt", stringsAsFactors = F, col.names=c('intron', 'logef' ,'Nuclear', 'Total','deltapsi'))
effectsize$deltapsi=as.numeric(as.character(effectsize$deltapsi))
Warning: NAs introduced by coercion
effectsize$logef=as.numeric(as.character(effectsize$logef))
Warning: NAs introduced by coercion
plot(sort(effectsize$deltapsi),main="Leafcutter delta PSI", ylab="Delta PSI", xlab="Peak Index")
Version | Author | Date |
---|---|---|
dd8d988 | Briana Mittleman | 2019-02-21 |
effectsize_dpsi= effectsize %>% filter(abs(deltapsi) > .2)
effectsize_dpsi_gene= effectsize %>% filter(abs(deltapsi) > .2) %>% separate(intron, into=c("chr", 'start', 'end','gene'), sep=":") %>% group_by(gene) %>% tally()
nrow(effectsize_dpsi)
[1] 2574
nrow(effectsize_dpsi_gene)
[1] 1983
inboth=effectsize_dpsi_gene %>% inner_join(diffIso_10FDR_genes, by="gene")
nrow(inboth)
[1] 1983
There are 1983 genes that are significant at 10 FDR with peaks with delta psi > .2. There are 2574 peaks in this set.
arrange(effectsize_dpsi,deltapsi) %>% head()
intron logef Nuclear
1 chr1:151134497:151134579:TNFAIP8L2 -1.531127 0.78054161651153
2 chr21:43762910:43762982:TFF2 -1.292723 0.7517177403328
3 chr3:23306502:23306675:UBE2E2 -1.576854 0.689518624324535
4 chr14:67029307:67029417:GPHN -1.178720 0.79525048466399
5 chr6:84007319:84007404:ME1 -1.941535 0.637895884685942
6 chr7:73885912:73885994:GTF2IRD1 -1.094156 0.803004504625396
Total deltapsi
1 0.142652878646319 -0.6378887
2 0.185782405086405 -0.5659353
3 0.152772791233433 -0.5367458
4 0.268829380937913 -0.5264211
5 0.115849020504727 -0.5220469
6 0.313645034829832 -0.4893595
How many total genes tested:
diffIsoGene=diffIso %>% separate(cluster, into=c("chrom", "gene"), sep = ":")
length(unique(diffIsoGene$gene))
[1] 9790
We tested 9790 genes and 8227 are significant at FDR 10%
I can make a plot that separates genes into tested, if passes has fdr 10%, if it has a peak greater than .2 delta psi.
sigandPSIGene=effectsize_dpsi_gene$gene
SiggenesDF=diffIso_10FDR %>% separate(cluster, into=c("chrom", "gene"), sep = ":") %>% select(gene)
Siggenes = SiggenesDF$gene
LCgeneDF=diffIsoGene %>% select(gene)
LCgene=LCgeneDF$gene
type=c("NotSig", "Sig", "SigHighDPAU")
nGenes=c(1563, 6244,1983)
nGenesProp=c(1563/9790, 6244/9790, 1983/9790)
LCDF=data.frame(cbind(type, nGenes, nGenesProp))
LCDF$nGenesProp=as.numeric(as.character(LCDF$nGenesProp))
labT=paste("Genes =", "1563", sep=" ")
labS=paste("Genes =", "6244", sep=" ")
labD=paste("Genes =", "1983", sep=" ")
LCResplot=ggplot(LCDF, aes(x=" ", y=nGenesProp, fill=type))+ geom_bar(stat="identity") + labs(x="Total Genes = 9790", y="Proportion of Genes", title="Proportion of Genes \nby Differencial PAU Test Result") + annotate("text", x=" ", y= .1, label=labT) + annotate("text", x=" ", y= .5, label=labS) + annotate("text", x=" ", y= .9, label=labD) + scale_fill_brewer(palette="RdYlBu")
LCResplot
Version | Author | Date |
---|---|---|
dd8d988 | Briana Mittleman | 2019-02-21 |
ggsave(LCResplot, file="../output/plots/LCResPlot.png",height=8, width=5)
As a boxplot:
LCResplotpie=ggplot(LCDF, aes(x=" ", y=nGenesProp, fill=type))+ geom_bar(stat="identity") + labs(x="Total Genes = 9790", y="Proportion of Genes", title="Proportion of Genes \nby Differencial PAU Test Result") + scale_fill_brewer(palette="RdYlBu")+ coord_polar("y")
LCResplotpie
Version | Author | Date |
---|---|---|
dd8d988 | Briana Mittleman | 2019-02-21 |
ggsave(LCResplotpie, file="../output/plots/LCResBoxPie.png")
Saving 7 x 5 in image
Look at examples:
arrange(effectsize_dpsi,deltapsi) %>% head(n=15)
intron logef Nuclear
1 chr1:151134497:151134579:TNFAIP8L2 -1.5311270 0.78054161651153
2 chr21:43762910:43762982:TFF2 -1.2927231 0.7517177403328
3 chr3:23306502:23306675:UBE2E2 -1.5768538 0.689518624324535
4 chr14:67029307:67029417:GPHN -1.1787199 0.79525048466399
5 chr6:84007319:84007404:ME1 -1.9415348 0.637895884685942
6 chr7:73885912:73885994:GTF2IRD1 -1.0941563 0.803004504625396
7 chr10:76217704:76217788:ADK -2.3345121 0.514019809620595
8 chr13:76202828:76202942:LMO7-AS1 -0.9814079 0.72785023020159
9 chr11:10415338:10415423:CAND1.11 -0.9620970 0.664450041884926
10 chr3:52434425:52434511:DNAH1 -0.9754214 0.643269826767032
11 chr11:61518275:61518363:DKFZP434K028 -0.9377435 0.715454168470806
12 chr1:246336771:246336983:SMYD3 -1.3736073 0.493768702856053
13 chr1:52550381:52550450:BTF3L4 -1.5857042 0.542706568051568
14 chr13:99716094:99716178:DOCK9 -1.9875150 0.479993274419107
15 chr1:234519189:234519278:COA6 -1.4539240 0.535470572408034
Total deltapsi
1 0.142652878646319 -0.6378887
2 0.185782405086405 -0.5659353
3 0.152772791233433 -0.5367458
4 0.268829380937913 -0.5264211
5 0.115849020504727 -0.5220469
6 0.313645034829832 -0.4893595
7 0.0448511480538154 -0.4691687
8 0.273075759544 -0.4547745
9 0.224261076041106 -0.4401890
10 0.204035877067268 -0.4392339
11 0.278188768939522 -0.4372654
12 0.0588483217543034 -0.4349204
13 0.108088063042586 -0.4346185
14 0.0504035538093602 -0.4295897
15 0.110557031548937 -0.4249135
Stuck on visualization
peak5329- that is the QTL peak for dock7
test=read.table("../data/PeakUsage_noMP_GeneLocAnno/filtered_APApeaks_merged_allchrom_refseqGenes.GeneLocAnno.NoMP_sm_quant.Total_fixed.pheno.5percPeaks.txt")
testN=read.table("../data/PeakUsage_noMP_GeneLocAnno/filtered_APApeaks_merged_allchrom_refseqGenes.GeneLocAnno.NoMP_sm_quant.Nuclear_fixed.pheno.5percPeaks.txt")
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bindrcpp_0.2.2 reshape2_1.4.3 workflowr_1.2.0 forcats_0.3.0
[5] stringr_1.4.0 dplyr_0.7.6 purrr_0.2.5 readr_1.1.1
[9] tidyr_0.8.1 tibble_1.4.2 ggplot2_3.0.0 tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] tidyselect_0.2.4 haven_1.1.2 lattice_0.20-35
[4] colorspace_1.3-2 htmltools_0.3.6 yaml_2.2.0
[7] rlang_0.2.2 pillar_1.3.0 glue_1.3.0
[10] withr_2.1.2 RColorBrewer_1.1-2 modelr_0.1.2
[13] readxl_1.1.0 bindr_0.1.1 plyr_1.8.4
[16] munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0
[19] rvest_0.3.2 evaluate_0.13 labeling_0.3
[22] knitr_1.20 broom_0.5.0 Rcpp_0.12.19
[25] scales_1.0.0 backports_1.1.2 jsonlite_1.6
[28] fs_1.2.6 hms_0.4.2 digest_0.6.17
[31] stringi_1.2.4 grid_3.5.1 rprojroot_1.3-2
[34] cli_1.0.1 tools_3.5.1 magrittr_1.5
[37] lazyeval_0.2.1 crayon_1.3.4 whisker_0.3-2
[40] pkgconfig_2.0.2 xml2_1.2.0 lubridate_1.7.4
[43] assertthat_0.2.0 rmarkdown_1.11 httr_1.3.1
[46] rstudioapi_0.9.0 R6_2.3.0 nlme_3.1-137
[49] git2r_0.24.0 compiler_3.5.1