Adding DEG Type prefix to output karyplot to prevent race conditions

CCBR · Jun 27, 2019 · 7b33da1 · 7b33da1
1 parent 4090cba
commit 7b33da1
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Showing 4 changed files with 17 additions and 14 deletions.
diff --git a/Results-template/Scripts/Deseq2Report.Rmd b/Results-template/Scripts/Deseq2Report.Rmd
@@ -72,7 +72,7 @@ sessionInfo()
 
 ## **Count Distribution** {.tabset}
 
-### Before Normalization
+### **Before Normalization**
 
 ```{r before_hist, echo=FALSE, warning=FALSE,message=FALSE,webgl=TRUE}
 
@@ -411,7 +411,7 @@ for(i in seq(1, length(contras), by = 2)) {
     }
 
     if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
-      system(paste0("cd ",getwd(),";/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/r_env/bin/Rscript ../Scripts/karyoploter.R -d DESeq2_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt -c ", params$karyotext, " -g ", SPECIES))
+      system(paste0("cd ",getwd(),";/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/r_env/bin/Rscript ../Scripts/karyoploter.R -o deseq2 -d DESeq2_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt -c ", params$karyotext, " -g ", SPECIES))
     }
 }
 
@@ -424,7 +424,7 @@ res=as.data.frame(cbind(mfc,mpval))
 rownames(res)=rownames(res1)
 write.table(res,file="DESeq2_res_all_contrasts.txt",sep="\t",col.names=NA)
 #DT::datatable(res, caption=htmltools::tags$caption("DEG for contrast",style="color:grey; font-size: 18px" ))
-DT::datatable(deseq2out, extensions = 'Buttons', options = list(dom = 'Bfrtip', buttons = c('colvis','excel', 'csv')))
+DT::datatable(deseq2out, extensions = 'Buttons', options = list(dom = 'Bfrtip', buttons = c('colvis','excel', 'csv'), pageLength = 15))
 ```
 
 
@@ -448,7 +448,7 @@ v_fdr
 
 ```{r, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
 if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
-  cat("![](karyoplot1.png)")
+  cat("![](deseq2_karyoplot1.png)")
 } else {
   cat("Genome Not Supported")
 }
@@ -459,7 +459,7 @@ if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECI
 
 ```{r, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
 if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
-  cat("![](karyoplot2.png)")
+  cat("![](deseq2_karyoplot2.png)")
 } else {
   cat("Genome Not Supported")
 }

diff --git a/Results-template/Scripts/EdgerReport.Rmd b/Results-template/Scripts/EdgerReport.Rmd
@@ -468,7 +468,7 @@ for(i in 1:nb){
   }
 
   if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ) {
-    system(paste0("cd ",getwd(),";/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/r_env/bin/Rscript ../Scripts/karyoploter.R -d edgeR_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt -c ", params$karyotext, " -g ", SPECIES))
+    system(paste0("cd ",getwd(),";/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/r_env/bin/Rscript ../Scripts/karyoploter.R -o edgeR -d edgeR_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt -c ", params$karyotext, " -g ", SPECIES))
   }
 }
 
@@ -483,7 +483,7 @@ rownames(res)=rownames(res1)
 write.table(res,file="edgeR_res_all_contrasts.txt",sep="\t",col.names=NA)
 #DT::datatable(res, caption=htmltools::tags$caption("DEG for all contrasts",style="color:blue; font-size: 18px"))
 
-DT::datatable(edgerout, extensions = 'Buttons', options = list(dom = 'Bfrtip', buttons = c('colvis','excel', 'csv')))
+DT::datatable(edgerout, extensions = 'Buttons', options = list(dom = 'Bfrtip', buttons = c('colvis','excel', 'csv'), pageLength = 15))
 ```
 
 ## **Volcano Plots** {.tabset}
@@ -506,7 +506,7 @@ v_fdr
 
 ```{r de_karyo1, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
 if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
-  cat("![](karyoplot1.png)")
+  cat("![](edgeR_karyoplot1.png)")
 } else {
   cat("Genome Not Supported")
 }
@@ -517,7 +517,7 @@ if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECI
 
 ```{r de_karyo2, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
 if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
-  cat("![](karyoplot2.png)")
+  cat("![](edgeR_karyoplot2.png)")
 } else {
   cat("Genome Not Supported")
 }
@@ -566,4 +566,4 @@ if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
 } else {
   cat("Genome Not Supported")
 }
-```
+```
diff --git a/Results-template/Scripts/LimmaReport.Rmd b/Results-template/Scripts/LimmaReport.Rmd
@@ -434,7 +434,7 @@ for (i in 1:nb) {
   }
   
   if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ) {
-    system(paste0("cd ",getwd(),";/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/r_env/bin/Rscript ../Scripts/karyoploter.R -d limma_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt -c ", params$karyotext, " -g ", SPECIES))
+    system(paste0("cd ",getwd(),";/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/r_env/bin/Rscript ../Scripts/karyoploter.R -o limma -d limma_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt -c ", params$karyotext, " -g ", SPECIES))
   }
   
 }
@@ -473,7 +473,7 @@ v_fdr
 
 ```{r karyo_gene1, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
 if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
-  cat("![](karyoplot1.png)")
+  cat("![](limma_karyoplot1.png)")
 } else {
   cat("Genome Not Supported")
 }
@@ -484,7 +484,7 @@ if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECI
 
 ```{r karyo_gene2, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
 if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
-  cat("![](karyoplot2.png)")
+  cat("![](limma_karyoplot2.png)")
 } else {
   cat("Genome Not Supported")
 }

diff --git a/Results-template/Scripts/karyoploter.R b/Results-template/Scripts/karyoploter.R
@@ -9,6 +9,9 @@ parser$add_argument("-g", "--genome", type="character", required=TRUE,
                     help="Genome .. either hg19/hg38/mm9/mm10/Mmul8.0.1/canFam3")
 parser$add_argument("-f", "--fdr", type="double", default=0.05,
                     help="FDR cutoff to use")
+parser$add_argument("-o", "--outfileprefix", type="character", required=TRUE,
+                    help="DEG type output file prefix: limma/edgeR/DESeq2")
+
 args <- parser$parse_args()
 
 
@@ -92,7 +95,7 @@ if (nrow(neg_strand_down_triangle)>0) {neg_strand_down_triangle$log2fc=neg_scale
 
 for (i in seq(1,length(chrs_subsets))) {
   chrs2=unlist(chrs_subsets[i])
-  png(paste("karyoplot",i,".png",sep=""), width = 10, height = 6, units = 'in', res = 1600)
+  png(paste(args$outfileprefix,"_karyoplot",i,".png",sep=""), width = 10, height = 6, units = 'in', res = 1600)
   kp <- plotKaryotype(genome=genome, plot.type=2, chromosomes = chrs2)
 
   kpDataBackground(kp, data.panel = 1, r0=0, r1=0.9)