Last updated: 2019-04-25
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Knit directory: apaQTL/analysis/
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In this analysis I will look at correlations heatmaps for the counts of all of the inidividuals.
library(tidyverse)
── Attaching packages ──────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0 ✔ purrr 0.3.2
✔ tibble 2.1.1 ✔ dplyr 0.8.0.1
✔ tidyr 0.8.3 ✔ stringr 1.3.1
✔ readr 1.3.1 ✔ forcats 0.3.0
── Conflicts ─────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
library(workflowr)
This is workflowr version 1.3.0
Run ?workflowr for help getting started
library(reshape2)
Attaching package: 'reshape2'
The following object is masked from 'package:tidyr':
smiths
library(gplots)
Attaching package: 'gplots'
The following object is masked from 'package:stats':
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library(gdata)
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: 'gdata'
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Load metadata:
metadata=read.table("../data/MetaDataSequencing.txt",header = T)
meta_T=metadata %>% filter(grepl("T", Sample_ID)) %>% mutate(samp=paste("X", Sample_ID, sep=""))
meta_N=metadata %>% filter(grepl("N", Sample_ID)) %>% mutate(samp=paste("X", Sample_ID, sep=""))
totCount=read.table("../data/peakCoverage/APAPeaks.ALLChrom.Filtered.Named.GeneLocAnnoPARSED.Total.Quant.Fixed.fc", stringsAsFactors = F,header=T) %>% select(-Geneid, -Chr, -Start, -End, -Strand, -Length)
Correlation:
totCount_corr= round(cor(totCount),2)
totCount_corr_melt=melt(totCount_corr)
Plot heatmap:
ggplot(data = totCount_corr_melt, aes(x=Var1, y=Var2, fill=value)) +
geom_tile() +theme(axis.text.x = element_text(angle = 90))
Version | Author | Date |
---|---|---|
8837331 | brimittleman | 2019-04-25 |
Use heatmap2.
meta_TBatch=meta_T %>% select(samp,batch)
target=colnames(totCount_corr)
meta_TBatch$samp <- reorder.factor(meta_TBatch$samp, new.order=target)
meta_TBatch_order=meta_TBatch %>% arrange(samp)
meta_TBatch_order = meta_TBatch_order %>% mutate(color=ifelse(batch=="1", "green", ifelse(batch=="2", "blue", ifelse(batch=="3", "purple", "pink"))))
heatmap.2(as.matrix(totCount_corr),trace="none", dendrogram =c("col"), ColSideColors =meta_TBatch_order$color, key=T)
Version | Author | Date |
---|---|---|
8837331 | brimittleman | 2019-04-25 |
nucCount=read.table("../data/peakCoverage/APAPeaks.ALLChrom.Filtered.Named.GeneLocAnnoPARSED.Nuclear.Quant.Fixed.fc", stringsAsFactors = F,header=T) %>% select(-Geneid, -Chr, -Start, -End, -Strand, -Length)
Correlation:
nucCount_corr= round(cor(nucCount),2)
nucCount_corr_melt=melt(nucCount_corr)
Plot heatmap:
ggplot(data = nucCount_corr_melt, aes(x=Var1, y=Var2, fill=value)) +
geom_tile() +theme(axis.text.x = element_text(angle = 90))
Version | Author | Date |
---|---|---|
8837331 | brimittleman | 2019-04-25 |
meta_NBatch=meta_N %>% select(samp,batch)
target=colnames(nucCount_corr)
meta_NBatch$samp <- reorder.factor(meta_NBatch$samp, new.order=target)
meta_NBatch_order=meta_NBatch %>% arrange(samp)
meta_NBatch_order = meta_NBatch_order %>% mutate(color=ifelse(batch=="1", "green", ifelse(batch=="2", "blue", ifelse(batch=="3", "purple", "pink"))))
heatmap.2(as.matrix(nucCount_corr),trace="none", dendrogram =c("col"), ColSideColors =meta_NBatch_order$color, key=T)
totUsage=read.table("../data/phenotype_5perc/APApeak_Phenotype_GeneLocAnno.Total.5perc.CountsNumeric", stringsAsFactors = F,header=F, col.names = colnames(totCount))
Correlation:
totUsage_corr= round(cor(totUsage),2)
totUsage_corr_melt=melt(totUsage_corr)
Plot heatmap:
ggplot(data = totUsage_corr_melt, aes(x=Var1, y=Var2, fill=value)) +
geom_tile() +theme(axis.text.x = element_text(angle = 90))
nucUsage=read.table("../data/phenotype_5perc/APApeak_Phenotype_GeneLocAnno.Nuclear.5perc.CountsNumeric", stringsAsFactors = F,header=F, col.names = colnames(nucCount))
Correlation:
nucUsage_corr= round(cor(nucUsage),2)
nucUsage_corr_melt=melt(nucUsage_corr)
Plot heatmap:
ggplot(data = nucUsage_corr_melt, aes(x=Var1, y=Var2, fill=value)) +
geom_tile() +theme(axis.text.x = element_text(angle = 90))
Version | Author | Date |
---|---|---|
8837331 | brimittleman | 2019-04-25 |
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gdata_2.18.0 gplots_3.0.1 reshape2_1.4.3 workflowr_1.3.0
[5] forcats_0.3.0 stringr_1.3.1 dplyr_0.8.0.1 purrr_0.3.2
[9] readr_1.3.1 tidyr_0.8.3 tibble_2.1.1 ggplot2_3.1.0
[13] tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] gtools_3.8.1 tidyselect_0.2.5 haven_1.1.2
[4] lattice_0.20-38 colorspace_1.3-2 generics_0.0.2
[7] htmltools_0.3.6 yaml_2.2.0 rlang_0.3.1
[10] pillar_1.3.1 glue_1.3.0 withr_2.1.2
[13] modelr_0.1.2 readxl_1.1.0 plyr_1.8.4
[16] munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0
[19] rvest_0.3.2 caTools_1.17.1.1 evaluate_0.12
[22] labeling_0.3 knitr_1.20 broom_0.5.1
[25] Rcpp_1.0.0 KernSmooth_2.23-15 scales_1.0.0
[28] backports_1.1.2 jsonlite_1.6 fs_1.2.6
[31] hms_0.4.2 digest_0.6.18 stringi_1.2.4
[34] grid_3.5.1 rprojroot_1.3-2 cli_1.0.1
[37] tools_3.5.1 bitops_1.0-6 magrittr_1.5
[40] lazyeval_0.2.1 crayon_1.3.4 whisker_0.3-2
[43] pkgconfig_2.0.2 xml2_1.2.0 lubridate_1.7.4
[46] assertthat_0.2.0 rmarkdown_1.10 httr_1.3.1
[49] rstudioapi_0.10 R6_2.3.0 nlme_3.1-137
[52] git2r_0.23.0 compiler_3.5.1