From c5e18c46d34c673c84e9dd30393de9fb3b9cac4e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 10 Apr 2019 23:10:29 -0500
Subject: [PATCH] Try to pull out dir into vizapp
---
vizapp/server.R | 33 +++++++++++++++++----------------
vizapp/ui.R | 8 ++++----
2 files changed, 21 insertions(+), 20 deletions(-)
diff --git a/vizapp/server.R b/vizapp/server.R
index 5d01361..0221b88 100644
--- a/vizapp/server.R
+++ b/vizapp/server.R
@@ -44,6 +44,7 @@ get.filt<-function(var){
shinyServer(
function(input,output,session){
+ data.dir <- Sys.getenv('outputDir')
vars<-eventReactive(input$go,{
get.filt(input)
})
@@ -64,9 +65,9 @@ shinyServer(
n = length(cancer.list) + 1
for(i in cancer.list){
incProgress(1/n, detail = paste0("collating data ", count, " of ", length(cancer.list)))
- if(!file.exists(paste0("../output/Expression/out_genes/",gene,"/",i,".txt"))){
+ if(!file.exists(paste0(data.dir,"Expression/out_genes/",gene,"/",i,".txt"))){
cat("File not present\n")
- if(!dir.exists(paste0("../output/Expression/out_genes/",gene))){
+ if(!dir.exists(paste0(data.dir,"Expression/out_genes/",gene))){
system(paste0("mkdir ../output/Expression/out_genes/",gene))
cat("Made directory\n")
}
@@ -75,7 +76,7 @@ shinyServer(
cat("creating data\n")
}
- temp <- as.data.frame(t(read.table(paste("../output/Expression/out_genes/",gene,"/",i,".txt",sep=""),header=T,sep="\t",row.names=1)))
+ temp <- as.data.frame(t(read.table(paste(data.dir,"Expression/out_genes/",gene,"/",i,".txt",sep=""),header=T,sep="\t",row.names=1)))
temp$type <- as.factor(ifelse(grepl("11",row.names(temp)),"Normal","Tumor"))
temp$cancer <- rep(i,nrow(temp))
if(ncol(temp)<3 | length(unique(temp$type))<2){
@@ -125,9 +126,9 @@ shinyServer(
incProgress(1/n, detail = "Getting expression data")
#Import Expression and Clinical Data
cat(paste0("going to read expression ",cancer,"\n"))
- if(!file.exists(paste0("../output/Expression/out_genes/",gene,"/",cancer,".txt"))){
+ if(!file.exists(paste0(data.dir,"Expression/out_genes/",gene,"/",cancer,".txt"))){
cat("File not present\n")
- if(!dir.exists(paste0("../output/Expression/out_genes/",gene))){
+ if(!dir.exists(paste0(data.dir,"Expression/out_genes/",gene))){
system(paste0("mkdir ../output/Expression/out_genes/",gene))
cat("Made directory\n")
}
@@ -136,11 +137,11 @@ shinyServer(
cat("creating data\n")
}
- exp <- read.table(paste0("../output/Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F)
- #exp <- read.table(paste0("../output/Expression/",cancer,".txt"),header=T,row.names=1,check.names=F) #Instead of importing entire expression matrix should import single gene.
+ exp <- read.table(paste0(data.dir,"Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F)
+ #exp <- read.table(paste0(data.dir,"Expression/",cancer,".txt"),header=T,row.names=1,check.names=F) #Instead of importing entire expression matrix should import single gene.
cat("going to read clinical data\n")
incProgress(1/n, detail = "Getting clinical data")
- clinical <- read.table(paste("../output/Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
+ clinical <- read.table(paste(data.dir,"Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
#Process Clinical
@@ -291,9 +292,9 @@ shinyServer(
n = length(cancer.list) + 1
for(i in cancer.list){
#incProgress(1/n, detail = paste0("collating data ", count, " of ", length(cancer.list)))
- if(!file.exists(paste0("../output/Expression/out_genes/",gene,"/",i,".txt"))){
+ if(!file.exists(paste0(data.dir,"Expression/out_genes/",gene,"/",i,".txt"))){
cat("File not present\n")
- if(!dir.exists(paste0("../output/Expression/out_genes/",gene))){
+ if(!dir.exists(paste0(data.dir,"Expression/out_genes/",gene))){
system(paste0("mkdir ../output/Expression/out_genes/",gene))
cat("Made directory\n")
}
@@ -302,7 +303,7 @@ shinyServer(
cat("creating data\n")
}
- temp <- as.data.frame(t(read.table(paste("../output/Expression/out_genes/",gene,"/",i,".txt",sep=""),header=T,sep="\t",row.names=1)))
+ temp <- as.data.frame(t(read.table(paste(data.dir,"Expression/out_genes/",gene,"/",i,".txt",sep=""),header=T,sep="\t",row.names=1)))
temp$type <- as.factor(ifelse(grepl("11",row.names(temp)),"Normal","Tumor"))
temp$cancer <- rep(i,nrow(temp))
if(ncol(temp)<3 | length(unique(temp$type))<2){
@@ -352,9 +353,9 @@ shinyServer(
#incProgress(1/n, detail = "Getting expression data")
#Import Expression and Clinical Data
cat(paste0("going to read expression ",cancer,"\n"))
- if(!file.exists(paste0("../output/Expression/out_genes/",gene,"/",cancer,".txt"))){
+ if(!file.exists(paste0(data.dir,"Expression/out_genes/",gene,"/",cancer,".txt"))){
cat("File not present\n")
- if(!dir.exists(paste0("../output/Expression/out_genes/",gene))){
+ if(!dir.exists(paste0(data.dir,"Expression/out_genes/",gene))){
system(paste0("mkdir ../output/Expression/out_genes/",gene))
cat("Made directory\n")
}
@@ -363,11 +364,11 @@ shinyServer(
cat("creating data\n")
}
- exp <- read.table(paste0("../output/Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F)
- #exp <- read.table(paste0("../output/Expression/",cancer,".txt"),header=T,row.names=1,check.names=F) #Instead of importing entire expression matrix should import single gene.
+ exp <- read.table(paste0(data.dir,"Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F)
+ #exp <- read.table(paste0(data.dir,"Expression/",cancer,".txt"),header=T,row.names=1,check.names=F) #Instead of importing entire expression matrix should import single gene.
cat("going to read clinical data\n")
#incProgress(1/n, detail = "Getting clinical data")
- clinical <- read.table(paste("../output/Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
+ clinical <- read.table(paste(data.dir,"Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
#Process Clinical
diff --git a/vizapp/ui.R b/vizapp/ui.R
index cb396b0..93fb612 100644
--- a/vizapp/ui.R
+++ b/vizapp/ui.R
@@ -6,15 +6,15 @@ shinyUI(
selectInput("operation","Select Plot Type",choices = c("Boxplot","Survival")),
conditionalPanel(condition = "input.operation=='Boxplot'",
selectInput("cancerType","Select one or more cancer types",
- choices = substr(list.files("../output/Expression/",pattern=".txt"),1,
- nchar(list.files("../output/Expression/",pattern=".txt"))-4),
+ choices = substr(list.files(data.dir,"Expression/",pattern=".txt"),1,
+ nchar(list.files(data.dir,"Expression/",pattern=".txt"))-4),
multiple = TRUE),
textInput("gene","Please input one gene of interest",placeholder = "Gene name ie TRIM21")
),
conditionalPanel(condition="input.operation=='Survival'",
selectInput("cancerType2","Select a cancer type",
- choices = substr(list.files("../output/Expression/",pattern=".txt"),1,
- nchar(list.files("../output/Expression/",pattern=".txt"))-4)),
+ choices = substr(list.files(data.dir,"Expression/",pattern=".txt"),1,
+ nchar(list.files(data.dir,"Expression/",pattern=".txt"))-4)),
textInput("gene2","Please input one gene of interest",placeholder = "Gene name ie BRCA1"),
selectInput("operation2","Select automatic or manual cutoff", choices = c("Automatic", "Manual"))
--
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