From 37d5d6cec7defa61ee750b637c5cfcd4a342950e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 21 Mar 2019 11:14:58 -0500
Subject: [PATCH] Reconfigure for Astrocyte
---
.gitlab-ci.yml | 12 +
astrocyte_pkg.yml | 94 +
docs/index.md | 3 +
vizapp/server.R | 517 +
vizapp/tcga_genes.txt | 20530 ++++++++++++++++++++++++++++++++++
vizapp/ui.R | 36 +
workflow/conf/.gitkeep | 0
workflow/conf/biohpc.config | 32 +
workflow/main.nf | 27 +
workflow/nextflow.config | 5 +
workflow/scripts/.gitkeep | 0
11 files changed, 21256 insertions(+)
create mode 100755 .gitlab-ci.yml
create mode 100755 astrocyte_pkg.yml
create mode 100644 docs/index.md
create mode 100644 vizapp/server.R
create mode 100755 vizapp/tcga_genes.txt
create mode 100644 vizapp/ui.R
create mode 100644 workflow/conf/.gitkeep
create mode 100755 workflow/conf/biohpc.config
create mode 100755 workflow/main.nf
create mode 100644 workflow/nextflow.config
create mode 100644 workflow/scripts/.gitkeep
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100755
index 0000000..08bb4e9
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,12 @@
+before_script:
+ - module load python/3.6.1-2-anaconda
+ - module load nextflow/0.27.6
+ - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_count/*fastq.gz test_data/
+
+stages:
+ - integration
+
+simple_test:
+ stage: integration
+ script:
+ - nextflow run workflow/main.nf
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
new file mode 100755
index 0000000..4fe26b8
--- /dev/null
+++ b/astrocyte_pkg.yml
@@ -0,0 +1,94 @@
+#
+# metadata for the Astrocyte CellRanger mkfastq workflow package
+#
+
+# -----------------------------------------------------------------------------
+# BASIC INFORMATION
+# -----------------------------------------------------------------------------
+
+# A unique identifier for the workflow package, text/underscores only
+name: 'tcga_shiny'
+# Who wrote this?
+author: 'Spencer Barnes, Gervaise Henry and Venkat Malladi'
+# A contact email address for questions
+email: 'bicf@utsouthwestern.edu'
+# A more informative title for the workflow package
+title: 'BICF TCGA Shiny Workflow'
+# A summary of the workflow package in plain text
+description: |
+ This is a workflow package for the exploration of TCGA data.
+
+# -----------------------------------------------------------------------------
+# DOCUMENTATION
+# -----------------------------------------------------------------------------
+
+# A list of documentation file in .md format that should be viewable from the
+# web interface. These files are in the 'docs' subdirectory. The first file
+# listed will be used as a documentation index and is index.md by convention
+documentation_files:
+ - 'index.md'
+
+# -----------------------------------------------------------------------------
+# NEXTFLOW WORKFLOW CONFIGURATION
+# -----------------------------------------------------------------------------
+
+# Remember - The workflow file is always named 'workflow/main.nf'
+# The workflow must publish all final output into $baseDir
+
+# A list of cluster environment modules that this workflow requires to run.
+# Specify versioned module names to ensure reproducability.
+workflow_modules:
+ - 'R'
+
+# A list of parameters used by the workflow, defining how to present them,
+# options etc in the web interface. For each parameter:
+#
+# REQUIRED INFORMATION
+# id: The name of the parameter in the NEXTFLOW workflow
+# type: The type of the parameter, one of:
+# string - A free-format string
+# integer - An integer
+# real - A real number
+# file - A single file from user data
+# files - One or more files from user data
+# select - A selection from a list of values
+# required: true/false, must the parameter be entered/chosen?
+# description: A user friendly description of the meaning of the parameter
+#
+# OPTIONAL INFORMATION
+# default: A default value for the parameter (optional)
+# min: Minium value/characters/files for number/string/files types
+# max: Maxumum value/characters/files for number/string/files types
+# regex: A regular expression that describes valid entries / filenames
+#
+# SELECT TYPE
+# choices: A set of choices presented to the user for the parameter.
+# Each choice is a pair of value and description, e.g.
+#
+# choices:
+# - [ 'myval', 'The first option']
+# - [ 'myval', 'The second option']
+#
+# NOTE - All parameters are passed to NEXTFLOW as strings... but they
+# are validated by astrocyte using the information provided above
+
+workflow_parameters: []
+# -----------------------------------------------------------------------------
+# SHINY APP CONFIGURATION
+# -----------------------------------------------------------------------------
+
+# Remember - The vizapp is always 'vizapp/server.R' 'vizapp/ui.R'
+# The workflow must publish all final output into $baseDir
+
+# Name of the R module that the vizapp will run against
+vizapp_r_module: 'R/3.2.1-intel'
+
+# List of any CRAN packages, not provided by the modules, that must be made
+# available to the vizapp
+vizapp_cran_packages:
+ - shiny
+ - ggplot2
+ - shinyjs
+ - survival
+ - survminer
+
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..77b73f3
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,3 @@
+# Astrocyte TCGA Shiny Workflow Package
+
+## Workflow SOP
diff --git a/vizapp/server.R b/vizapp/server.R
new file mode 100644
index 0000000..c62a923
--- /dev/null
+++ b/vizapp/server.R
@@ -0,0 +1,517 @@
+library(ggplot2)
+library(shiny)
+library(shinyjs)
+library("survival")
+library("survminer")
+
+cat("reading in gene list...")
+all.genes<-read.table("tcga_genes.txt",sep = "\t",header = FALSE)
+all.genes<-as.character(all.genes[,1])
+cat("done\n")
+get.filt<-function(var){
+ if(var$operation=="Boxplot"){
+ return(
+ list(
+ operation=var$operation,
+ gene=var$gene,
+ cancer.list=var$cancerType
+ )
+ )
+ }else{
+ if(var$operation2 == "Manual"){
+ return(
+ list(
+ operation=var$operation,
+ operation2=var$operation2,
+ gene=var$gene2,
+ cancer=var$cancerType2,
+ cutoff=var$cut.off
+ )
+ )
+ }else if(var$operation2 == "Automatic"){
+ return(
+ list(
+ operation=var$operation,
+ operation2=var$operation2,
+ gene=var$gene2,
+ cancer=var$cancerType2
+ )
+ )
+ }
+ }
+}
+
+shinyServer(
+ function(input,output,session){
+
+ vars<-eventReactive(input$go,{
+ get.filt(input)
+ })
+
+ output$myPlot <- renderPlot({
+ #PANCAN BOX PLOT
+ withProgress(message = 'Making plot', value = 0,{
+ if(vars()$operation=="Boxplot"){
+
+ gene<-toupper(gsub("\\s", "", as.character(vars()$gene)))
+ cancer.list<-as.character(vars()$cancer.list)
+ if(!(gene %in% all.genes)){
+ showNotification(paste0("SORRY! ", gene, " is not a valid gene!"), duration = 8, type = "error")
+ }else{
+ data <- data.frame(value=as.numeric(),type=as.character(),cancer=as.character(),pval=as.numeric())
+ pval <- NULL
+ count <- 1
+ n = length(cancer.list) + 1
+ for(i in cancer.list){
+ incProgress(1/n, detail = paste0("collating data ", count, " of ", length(cancer.list)))
+ if(!file.exists(paste0("../Expression/out_genes/",gene,"/",i,".txt"))){
+ cat("File not present\n")
+ if(!dir.exists(paste0("../Expression/out_genes/",gene))){
+ system(paste0("mkdir ../Expression/out_genes/",gene))
+ cat("Made directory\n")
+ }
+ system(paste0("ls ../Expression/*",i,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../Expression/out_genes/",
+ gene,"/","$fname; grep -wi ",gene," $line >> ../Expression/out_genes/",gene,"/","$fname;done"))
+ cat("creating data\n")
+
+ }
+ temp <- as.data.frame(t(read.table(paste("../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$type))<2){
+ if(length(cancer.list) > 1){
+ showNotification(paste0("WARNING! Project ", i, " does not have normal tissue data! Skipping..."), duration = 8, type = "warning")
+ next
+ }else{
+ showNotification(paste0("SORRY! Project ", i, " does not have normal tissue data! Choose another project."), duration = 8, type = "error")
+ break
+ }
+
+ }else{
+ colnames(temp) <- c("value","type","cancer")
+ print(i)
+ pval <- c(pval,signif(kruskal.test(value~type,temp)$p.value,2))
+ data <- rbind(data,temp)
+ }
+ count <- count + 1
+ }
+
+ if(nrow(data)==0){
+ return()
+ }else{
+ data$value <- 2^data$value
+ p <- ggplot(data = data, aes(x=type, y=value)) + geom_boxplot(aes(fill=type),outlier.size = 0.2,outlier.alpha=0.8) + scale_y_continuous(limits = c(0, 2000)) +
+ geom_text(data=data.frame(x=1.5,y=1800,labels=pval,cancer=unique(data$cancer)),aes(x,y,label=labels),size=3 , inherit.aes=FALSE) +
+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
+ panel.background = element_blank(), axis.line = element_line(colour = "black"))
+ #cat("printing",gene,"\n")
+ print(p + facet_wrap( ~ cancer, scales="free") + ggtitle(gene) + theme(plot.title = element_text(hjust = 0.5)))
+ incProgress(1/n, detail = paste0("printing plot!"))
+ }
+ }
+ #SURVIVAL PLOTS
+ }else if(vars()$operation=="Survival"){
+ #Define Cancer & Gene
+ oldw <- getOption("warn")
+ options(warn = -1)
+ cat("Survival plot\n")
+ cancer <- vars()$cancer
+ gene<-toupper(gsub("\\s", "", as.character(vars()$gene)))
+ cat(paste0(cancer," ",gene,"\n"))
+ if(!(gene %in% all.genes)){
+ showNotification(paste0("SORRY! ", gene, " is not a valid gene!"), duration = 8, type = "error")
+ }else{
+ n <- 4
+ incProgress(1/n, detail = "Getting expression data")
+ #Import Expression and Clinical Data
+ cat(paste0("going to read expression ",cancer,"\n"))
+ if(!file.exists(paste0("../Expression/out_genes/",gene,"/",cancer,".txt"))){
+ cat("File not present\n")
+ if(!dir.exists(paste0("../Expression/out_genes/",gene))){
+ system(paste0("mkdir ../Expression/out_genes/",gene))
+ cat("Made directory\n")
+ }
+ system(paste0("ls ../Expression/*",cancer,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../Expression/out_genes/",
+ gene,"/","$fname; grep -wi ",gene," $line >> ../Expression/out_genes/",gene,"/","$fname;done"))
+ cat("creating data\n")
+
+ }
+ exp <- read.table(paste0("../Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F)
+ #exp <- read.table(paste0("../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("../Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
+
+
+ #Process Clinical
+ # get the columns that contain data we can use: days to death, new tumor event, last day contact to....
+ ind_keep <- grep("days_to_new_tumor_event_after_initial_treatment",colnames(clinical))
+
+ # this is a bit tedious, since there are numerous follow ups, let's collapse them together and keep the first value (the higher one) if more than one is available
+ new_tum <- as.matrix(clinical[,ind_keep])
+ new_tum_collapsed <- c()
+ for (i in 1:dim(new_tum)[1]){
+ if(sum(is.na(new_tum[i,])) < dim(new_tum)[2]){
+ m <- min(new_tum[i,],na.rm=T)
+ new_tum_collapsed <- c(new_tum_collapsed,m)
+ } else {
+ new_tum_collapsed <- c(new_tum_collapsed,"NA")
+ }
+ }
+
+ # do the same to death
+ ind_keep <- grep("days_to_death",colnames(clinical))
+ death <- as.matrix(clinical[,ind_keep])
+ death_collapsed <- c()
+ for (i in 1:dim(death)[1]){
+ if(sum(is.na(death[i,])) < dim(death)[2]){
+ m <- max(death[i,],na.rm=T)
+ death_collapsed <- c(death_collapsed,m)
+ } else {
+ death_collapsed <- c(death_collapsed,"NA")
+ }
+ }
+
+ # and days last follow up here we take the most recent which is the max number
+ ind_keep <- grep("days_to_last_followup",colnames(clinical))
+ fl <- as.matrix(clinical[,ind_keep])
+ fl_collapsed <- c()
+ for (i in 1:dim(fl)[1]){
+ if(sum(is.na(fl[i,])) < dim(fl)[2]){
+ m <- max(fl[i,],na.rm=T)
+ fl_collapsed <- c(fl_collapsed,m)
+ } else {
+ fl_collapsed <- c(fl_collapsed,"NA")
+ }
+ }
+
+ # and put everything together
+ all_clin <- data.frame(new_tum_collapsed,death_collapsed,fl_collapsed)
+ colnames(all_clin) <- c("new_tumor_days", "death_days", "followUp_days")
+
+ # create vector with time to new tumor containing data to censor for new_tumor
+ all_clin$new_time <- c()
+ for (i in 1:length(as.numeric(as.character(all_clin$new_tumor_days)))){
+ all_clin$new_time[i] <- ifelse(is.na(as.numeric(as.character(all_clin$new_tumor_days))[i]),
+ as.numeric(as.character(all_clin$followUp_days))[i],as.numeric(as.character(all_clin$new_tumor_days))[i])
+ }
+
+ # create vector time to death containing values to censor for death
+ all_clin$new_death <- c()
+ for (i in 1:length(as.numeric(as.character(all_clin$death_days)))){
+ all_clin$new_death[i] <- ifelse(is.na(as.numeric(as.character(all_clin$death_days))[i]),
+ as.numeric(as.character(all_clin$followUp_days))[i],as.numeric(as.character(all_clin$death_days))[i])
+ }
+
+ all_clin$death_event <- ifelse(clinical$vital_status == "LIVING", 0,1)
+ row.names(all_clin) <- row.names(clinical)
+ colnames(exp) <- gsub("01A","01",colnames(exp))
+ gene.exp <- t(exp[gene,])
+ colnames(gene.exp) <- "gene"
+
+ #Fork for Manual vs Automatic selection
+ if(vars()$operation2 == "Manual"){
+ cutoff <- as.numeric(vars()$cutoff)
+ #Setup Data
+
+ colnames(exp) <- gsub("01A","01",colnames(exp))
+ gene.exp <- t(exp[gene,])
+ colnames(gene.exp) <- "gene"
+ data <- merge(all_clin,gene.exp,by="row.names")
+ data$event_rna <- ifelse(data$gene > quantile(as.numeric(data$gene),1-cutoff),1,0)
+ data <- data[which(data$gene > quantile(as.numeric(data$gene),1-cutoff) | data$gene < quantile(as.numeric(data$gene),cutoff)),]
+ # run survival analysis
+ s <- surv_fit(Surv(as.numeric(as.character(data$new_death)),data$death_event)~event_rna,data)
+ incProgress(1/n, detail = "Printing plot")
+ p<-ggsurvplot(s,conf.int=F,xlab="Time(days)",pval=T,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ print(p+ggtitle(paste(cancer, gene,"cutoff: ", cutoff)))
+ options(warn = oldw)
+ }else{
+ cutoff.vals=c(.10, .15, .20, .25, .30, .35, .40, .45, .50)
+ incProgress(1/n, detail = "Checking Cutoffs")
+ for(cutoff in cutoff.vals){
+ cat("\tchecking cutoff value:",cutoff,"\n") ###add status update here
+ data <- merge(all_clin,gene.exp,by="row.names")
+ if(is.na(data$gene)[1]){
+ showNotification(paste0("SORRY! No data for gene ", gene,"!"), duration = 8, type = "error")
+ break
+ }
+ data$event_rna <- ifelse(data$gene > quantile(as.numeric(data$gene),1-cutoff),1,0)
+ data <- data[which(data$gene > quantile(as.numeric(data$gene),1-cutoff) | data$gene < quantile(as.numeric(data$gene),cutoff)),]
+ # run survival analysis
+ if(length(unique(data$event_rna)) < 2){
+ next
+ }
+
+ cat("done!\n")
+ if(cutoff == 0.10){
+ cat("first run\n")
+ best.data <- data
+ best.res <- surv_fit(Surv(as.numeric(as.character(best.data$new_death)),best.data$death_event)~event_rna,best.data)
+ p<-ggsurvplot(best.res,conf.int=F,xlab="Time(days)",pval=TRUE,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),
+ legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ best.cutoff <- cutoff
+ }else{
+ s <- surv_fit(Surv(as.numeric(as.character(data$new_death)),data$death_event)~event_rna,data)
+ p<-ggsurvplot(s,conf.int=F,xlab="Time(days)",pval=TRUE,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),
+ legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ if((as.numeric(surv_pvalue(s)[2]) < as.numeric(surv_pvalue(best.res)[2])) & (p$table$data$n.risk[1] > 10) & (p$table$data$n.risk[6] > 10)){
+ best.data <- data
+ best.res <- surv_fit(Surv(as.numeric(as.character(best.data$new_death)),best.data$death_event)~event_rna,best.data)
+ p<-ggsurvplot(best.res,conf.int=F,xlab="Time(days)",pval=TRUE,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),
+ legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ best.cutoff <- cutoff
+ }
+ }
+
+ }
+ incProgress(1/n, detail = "Printing plot")
+ p <- ggsurvplot(best.res,conf.int=F,xlab="Time(days)",pval=TRUE,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),
+ legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ print(p+ggtitle(paste(cancer, "cutoff: ", best.cutoff)))
+
+ }
+ }
+ }
+ })
+
+ })
+
+ plotInput = function(){
+ if(vars()$operation=="Boxplot"){
+
+ gene<-toupper(gsub("\\s", "", as.character(vars()$gene)))
+ cancer.list<-as.character(vars()$cancer.list)
+ if(!(gene %in% all.genes)){
+ #showNotification(paste0("SORRY! ", gene, " is not a valid gene!"), duration = 8, type = "error")
+ }else{
+ data <- data.frame(value=as.numeric(),type=as.character(),cancer=as.character(),pval=as.numeric())
+ pval <- NULL
+ count <- 1
+ n = length(cancer.list) + 1
+ for(i in cancer.list){
+ #incProgress(1/n, detail = paste0("collating data ", count, " of ", length(cancer.list)))
+ if(!file.exists(paste0("../Expression/out_genes/",gene,"/",i,".txt"))){
+ cat("File not present\n")
+ if(!dir.exists(paste0("../Expression/out_genes/",gene))){
+ system(paste0("mkdir ../Expression/out_genes/",gene))
+ cat("Made directory\n")
+ }
+ system(paste0("ls ../Expression/*",i,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../Expression/out_genes/",
+ gene,"/","$fname; grep -wi ",gene," $line >> ../Expression/out_genes/",gene,"/","$fname;done"))
+ cat("creating data\n")
+
+ }
+ temp <- as.data.frame(t(read.table(paste("../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$type))<2){
+ if(length(cancer.list) > 1){
+ #showNotification(paste0("WARNING! Project ", i, " does not have normal tissue data! Skipping..."), duration = 8, type = "warning")
+ next
+ }else{
+ #showNotification(paste0("SORRY! Project ", i, " does not have normal tissue data! Choose another project."), duration = 8, type = "error")
+ break
+ }
+
+ }else{
+ colnames(temp) <- c("value","type","cancer")
+ print(i)
+ pval <- c(pval,signif(kruskal.test(value~type,temp)$p.value,2))
+ data <- rbind(data,temp)
+ }
+ count <- count + 1
+ }
+
+ if(nrow(data)==0){
+ return()
+ }else{
+ data$value <- 2^data$value
+ p <- ggplot(data = data, aes(x=type, y=value)) + geom_boxplot(aes(fill=type),outlier.size = 0.2,outlier.alpha=0.8) + scale_y_continuous(limits = c(0, 2000)) +
+ geom_text(data=data.frame(x=1.5,y=1800,labels=pval,cancer=unique(data$cancer)),aes(x,y,label=labels),size=3 , inherit.aes=FALSE) +
+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
+ panel.background = element_blank(), axis.line = element_line(colour = "black"))
+ #cat("printing",gene,"\n")
+ print(p + facet_wrap( ~ cancer, scales="free") + ggtitle(gene) + theme(plot.title = element_text(hjust = 0.5)))
+ #incProgress(1/n, detail = paste0("printing plot!"))
+ }
+ }
+ #SURVIVAL PLOTS
+ }else if(vars()$operation=="Survival"){
+ #Define Cancer & Gene
+ oldw <- getOption("warn")
+ options(warn = -1)
+ cat("Survival plot\n")
+ cancer <- vars()$cancer
+ gene<-toupper(gsub("\\s", "", as.character(vars()$gene)))
+ cat(paste0(cancer," ",gene,"\n"))
+ if(!(gene %in% all.genes)){
+ #showNotification(paste0("SORRY! ", gene, " is not a valid gene!"), duration = 8, type = "error")
+ }else{
+ n <- 4
+ #incProgress(1/n, detail = "Getting expression data")
+ #Import Expression and Clinical Data
+ cat(paste0("going to read expression ",cancer,"\n"))
+ if(!file.exists(paste0("../Expression/out_genes/",gene,"/",cancer,".txt"))){
+ cat("File not present\n")
+ if(!dir.exists(paste0("../Expression/out_genes/",gene))){
+ system(paste0("mkdir ../Expression/out_genes/",gene))
+ cat("Made directory\n")
+ }
+ system(paste0("ls ../Expression/*",cancer,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../Expression/out_genes/",
+ gene,"/","$fname; grep -wi ",gene," $line >> ../Expression/out_genes/",gene,"/","$fname;done"))
+ cat("creating data\n")
+
+ }
+ exp <- read.table(paste0("../Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F)
+ #exp <- read.table(paste0("../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("../Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
+
+
+ #Process Clinical
+ # get the columns that contain data we can use: days to death, new tumor event, last day contact to....
+ ind_keep <- grep("days_to_new_tumor_event_after_initial_treatment",colnames(clinical))
+
+ # this is a bit tedious, since there are numerous follow ups, let's collapse them together and keep the first value (the higher one) if more than one is available
+ new_tum <- as.matrix(clinical[,ind_keep])
+ new_tum_collapsed <- c()
+ for (i in 1:dim(new_tum)[1]){
+ if(sum(is.na(new_tum[i,])) < dim(new_tum)[2]){
+ m <- min(new_tum[i,],na.rm=T)
+ new_tum_collapsed <- c(new_tum_collapsed,m)
+ } else {
+ new_tum_collapsed <- c(new_tum_collapsed,"NA")
+ }
+ }
+
+ # do the same to death
+ ind_keep <- grep("days_to_death",colnames(clinical))
+ death <- as.matrix(clinical[,ind_keep])
+ death_collapsed <- c()
+ for (i in 1:dim(death)[1]){
+ if(sum(is.na(death[i,])) < dim(death)[2]){
+ m <- max(death[i,],na.rm=T)
+ death_collapsed <- c(death_collapsed,m)
+ } else {
+ death_collapsed <- c(death_collapsed,"NA")
+ }
+ }
+
+ # and days last follow up here we take the most recent which is the max number
+ ind_keep <- grep("days_to_last_followup",colnames(clinical))
+ fl <- as.matrix(clinical[,ind_keep])
+ fl_collapsed <- c()
+ for (i in 1:dim(fl)[1]){
+ if(sum(is.na(fl[i,])) < dim(fl)[2]){
+ m <- max(fl[i,],na.rm=T)
+ fl_collapsed <- c(fl_collapsed,m)
+ } else {
+ fl_collapsed <- c(fl_collapsed,"NA")
+ }
+ }
+
+ # and put everything together
+ all_clin <- data.frame(new_tum_collapsed,death_collapsed,fl_collapsed)
+ colnames(all_clin) <- c("new_tumor_days", "death_days", "followUp_days")
+
+ # create vector with time to new tumor containing data to censor for new_tumor
+ all_clin$new_time <- c()
+ for (i in 1:length(as.numeric(as.character(all_clin$new_tumor_days)))){
+ all_clin$new_time[i] <- ifelse(is.na(as.numeric(as.character(all_clin$new_tumor_days))[i]),
+ as.numeric(as.character(all_clin$followUp_days))[i],as.numeric(as.character(all_clin$new_tumor_days))[i])
+ }
+
+ # create vector time to death containing values to censor for death
+ all_clin$new_death <- c()
+ for (i in 1:length(as.numeric(as.character(all_clin$death_days)))){
+ all_clin$new_death[i] <- ifelse(is.na(as.numeric(as.character(all_clin$death_days))[i]),
+ as.numeric(as.character(all_clin$followUp_days))[i],as.numeric(as.character(all_clin$death_days))[i])
+ }
+
+ all_clin$death_event <- ifelse(clinical$vital_status == "LIVING", 0,1)
+ row.names(all_clin) <- row.names(clinical)
+ colnames(exp) <- gsub("01A","01",colnames(exp))
+ gene.exp <- t(exp[gene,])
+ colnames(gene.exp) <- "gene"
+
+ #Fork for Manual vs Automatic selection
+ if(vars()$operation2 == "Manual"){
+ cutoff <- as.numeric(vars()$cutoff)
+ #Setup Data
+
+ colnames(exp) <- gsub("01A","01",colnames(exp))
+ gene.exp <- t(exp[gene,])
+ colnames(gene.exp) <- "gene"
+ data <- merge(all_clin,gene.exp,by="row.names")
+ data$event_rna <- ifelse(data$gene > quantile(as.numeric(data$gene),1-cutoff),1,0)
+ data <- data[which(data$gene > quantile(as.numeric(data$gene),1-cutoff) | data$gene < quantile(as.numeric(data$gene),cutoff)),]
+ # run survival analysis
+ s <- surv_fit(Surv(as.numeric(as.character(data$new_death)),data$death_event)~event_rna,data)
+ #incProgress(1/n, detail = "Printing plot")
+ p<-ggsurvplot(s,conf.int=F,xlab="Time(days)",pval=T,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ print(p+ggtitle(paste(cancer, gene,"cutoff: ", cutoff)))
+ options(warn = oldw)
+ }else{
+ cutoff.vals=c(.10, .15, .20, .25, .30, .35, .40, .45, .50)
+ #incProgress(1/n, detail = "Checking Cutoffs")
+ for(cutoff in cutoff.vals){
+ cat("\tchecking cutoff value:",cutoff,"\n") ###add status update here
+ data <- merge(all_clin,gene.exp,by="row.names")
+ if(is.na(data$gene)[1]){
+ showNotification(paste0("SORRY! No data for gene ", gene,"!"), duration = 8, type = "error")
+ break
+ }
+ data$event_rna <- ifelse(data$gene > quantile(as.numeric(data$gene),1-cutoff),1,0)
+ data <- data[which(data$gene > quantile(as.numeric(data$gene),1-cutoff) | data$gene < quantile(as.numeric(data$gene),cutoff)),]
+ # run survival analysis
+ if(length(unique(data$event_rna)) < 2){
+ next
+ }
+
+ cat("done!\n")
+ if(cutoff == 0.10){
+ cat("first run\n")
+ best.data <- data
+ best.res <- surv_fit(Surv(as.numeric(as.character(best.data$new_death)),best.data$death_event)~event_rna,best.data)
+ p<-ggsurvplot(best.res,conf.int=F,xlab="Time(days)",pval=TRUE,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),
+ legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ best.cutoff <- cutoff
+ }else{
+ s <- surv_fit(Surv(as.numeric(as.character(data$new_death)),data$death_event)~event_rna,data)
+ p<-ggsurvplot(s,conf.int=F,xlab="Time(days)",pval=TRUE,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),
+ legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ if((as.numeric(surv_pvalue(s)[2]) < as.numeric(surv_pvalue(best.res)[2])) & (p$table$data$n.risk[1] > 10) & (p$table$data$n.risk[6] > 10)){
+ best.data <- data
+ best.res <- surv_fit(Surv(as.numeric(as.character(best.data$new_death)),best.data$death_event)~event_rna,best.data)
+ p<-ggsurvplot(best.res,conf.int=F,xlab="Time(days)",pval=TRUE,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),
+ legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ best.cutoff <- cutoff
+ }
+ }
+
+ }
+ #incProgress(1/n, detail = "Printing plot")
+ p <- ggsurvplot(best.res,conf.int=F,xlab="Time(days)",pval=TRUE,pval.coord=c(1000,0.3),risk.table=TRUE,legend.title="",legend=c(0.8,0.8),
+ legend.labs = c( paste(gene,"LOW",sep=" "), paste(gene,"HIGH",sep=" ")))
+ print(p+ggtitle(paste(cancer, "cutoff: ", best.cutoff)))
+
+ }
+ }
+ }
+ }
+
+ output$downloadplot <- downloadHandler(
+ filename = function() { paste0("plot", '.pdf') },
+ content = function(file) {
+ #ggsave(file = file, plot = plotInput(), device = "pdf")
+ pdf(file)
+ plotInput()
+ dev.off()
+ }
+ )
+
+
+ }
+)
diff --git a/vizapp/tcga_genes.txt b/vizapp/tcga_genes.txt
new file mode 100755
index 0000000..8645a50
--- /dev/null
+++ b/vizapp/tcga_genes.txt
@@ -0,0 +1,20530 @@
+?|100130426
+?|100133144
+?|100134869
+?|10357
+?|10431
+?|136542
+?|155060
+?|26823
+?|280660
+?|317712
+?|340602
+?|388795
+?|390284
+?|391343
+?|391714
+?|404770
+?|441362
+?|442388
+?|553137
+?|57714
+?|645851
+?|652919
+?|653553
+?|728045
+?|728603
+?|728788
+?|729884
+?|8225
+?|90288
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diff --git a/vizapp/ui.R b/vizapp/ui.R
new file mode 100644
index 0000000..4db5af6
--- /dev/null
+++ b/vizapp/ui.R
@@ -0,0 +1,36 @@
+shinyUI(
+ fluidPage(
+ headerPanel("TCGA Analysis"),
+ sidebarLayout(
+ sidebarPanel(
+ 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("../Expression/",pattern=".txt"),1,
+ nchar(list.files("../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("../Expression/",pattern=".txt"),1,
+ nchar(list.files("../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"))
+
+ ),
+ conditionalPanel(condition="input.operation2=='Manual' & input.operation=='Survival'",
+ sliderInput("cut.off","Select a cutoff value",min = .10,max=.50,step = .05,value = .25)
+ ),
+ actionButton("go","GO")
+
+ ),
+ mainPanel(
+ plotOutput("myPlot"),
+ downloadButton('downloadplot',"Download Figure")
+ )
+
+ )
+ )
+)
+
diff --git a/workflow/conf/.gitkeep b/workflow/conf/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
new file mode 100755
index 0000000..0b515ec
--- /dev/null
+++ b/workflow/conf/biohpc.config
@@ -0,0 +1,32 @@
+process {
+ executor = 'slurm'
+ queue='super'
+
+ // Process specific configuration
+ $checkDesignFile {
+ module = ['python/3.6.1-2-anaconda']
+ executor = 'local'
+ }
+ $count2 {
+ module = ['cellranger/2.1.1']
+ }
+ $count3 {
+ module = ['cellranger/3.0.1']
+ }
+}
+
+trace {
+ enabled = true
+ file = 'pipeline_trace.txt'
+ fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
+}
+
+timeline {
+ enabled = true
+ file = 'timeline.html'
+}
+
+report {
+ enabled = true
+ file = 'report.html'
+}
diff --git a/workflow/main.nf b/workflow/main.nf
new file mode 100755
index 0000000..d352fb2
--- /dev/null
+++ b/workflow/main.nf
@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+// Path to an input file, or a pattern for multiple inputs
+// Note - $baseDir is the location of this workflow file main.nf
+
+// Define Input variables
+params.run = "TRUE"
+
+process copy {
+
+ publishDir "$baseDir/output", mode: 'copy'
+
+ input:
+
+ params.run
+
+ output:
+
+ file("**/Clinical/**") into outPathClinical
+ file("**/Expression/**") into outPathExpression
+
+ script:
+
+ """
+ cp -r /project/shared/bicf_workflow_ref/tcga_shiny_app_data/* .
+ """
+}
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
new file mode 100644
index 0000000..30e47ea
--- /dev/null
+++ b/workflow/nextflow.config
@@ -0,0 +1,5 @@
+profiles {
+ standard {
+ includeConfig 'conf/biohpc.config'
+ }
+}
diff --git a/workflow/scripts/.gitkeep b/workflow/scripts/.gitkeep
new file mode 100644
index 0000000..e69de29
--
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