changeset 8:8fa3254cfa53 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bubbles_v9_NSAF_natural_log.R	Tue Mar 15 15:19:21 2016 -0400
@@ -0,0 +1,233 @@
+rm(list=ls())
+###################################################################################################
+# R-code: Multi-bubble graph generation from SAINTexpress output
+# Author: Brent Kuenzi
+###################################################################################################
+library(dplyr); library(tidyr); library(ggplot2)
+###################################################################################################
+### Run program ###
+
+## REQUIRED INPUT ##
+# 1) listfile: SAINTexpress generated "list.txt" file
+# 2) preyfile: SAINT pre-processing generated "prey.txt" file used to run SAINTexpress
+## OPTIONAL INPUT ##
+# 3) crapome: raw output from crapome Workflow 1 query (http://www.crapome.org)
+# 4) color: bubble color (default = "red")
+#     - color= "crapome": color bubbles based on Crapome(%)
+#     - Also recognizes any color within R's built-in colors() vector
+# 5) label: Adds gene name labels to bubbles within the "zoomed in" graphs (default = FALSE)
+# 6) cutoff: Saintscore cutoff to be assigned for filtering the "zoomed in" graphs (default = 0.8)
+###################################################################################################
+main <- function(listfile, preyfile , crapome=FALSE, color="red", label=FALSE, cutoff=0.8, type="SC", inc_file = "None", exc_file = "None" ) {
+  cutoff_check(cutoff)
+  listfile <- list_type(listfile, inc_file, exc_file)
+  if(type == "SC") {
+    df <- merge_files_sc(listfile, preyfile, crapome)
+  }
+  if(type == "MQ") {
+    df <- merge_files_mq(listfile, preyfile, crapome)
+  }
+  bubble_NSAF(df,color)
+  bubble_SAINT(df,color)
+  bubble_zoom_SAINT(df, color, label, cutoff)
+  bubble_zoom_NSAF(df, color, label, cutoff)
+  write.table(df,"output.txt",sep="\t",quote=FALSE, row.names=FALSE)
+}
+
+list_type <- function(df, inc_file, exc_file) {
+  Saint <- read.delim(df, stringsAsFactors=FALSE)
+  if (inc_file != "None") {
+    if (exc_file == "None"){
+      inc_prots <- read.delim(inc_file, sep='\t', header=FALSE, stringsAsFactors=FALSE)
+      filtered_df = subset(Saint, Saint$Prey == inc_prots[,1])
+    }
+    else {
+      inc_prots <- read.delim(inc_file, sep='\t', header=FALSE, stringsAsFactors=FALSE)
+      exc_prots <- read.delim(exc_file, sep='\t', header=FALSE, stringsAsFactors=FALSE)
+      filtered_df = subset(Saint, Saint$Prey == inc_prots[,1])
+      filtered_df = subset(filtered_df, filtered_df$Prey != exc_prots[,1])
+    }
+  }
+  else if (exc_file != "None") {
+    exc_prots <- read.delim(exc_file, sep='\t', header=FALSE, stringsAsFactors=FALSE)
+    filtered_df = subset(Saint, Saint$Prey != exc_prots[,1])
+  }
+  else {
+    filtered_df = Saint
+  }
+  return(filtered_df)
+  
+}
+###################################################################################################
+# Merge input files and caculate Crapome(%) and NSAF for each protein for each bait
+###################################################################################################
+merge_files_mq <- function(SAINT, prey_DF, crapome=FALSE) {
+  #SAINT <- read.table(SAINT_DF, sep='\t', header=TRUE)
+  prey <- read.table(prey_DF, sep='\t', header=FALSE); colnames(prey) <- c("Prey", "Length", "PreyGene")
+  DF <- merge(SAINT,prey)
+  DF$SpecSum <- log2(DF$SpecSum)
+  
+  if(crapome!=FALSE) {
+    crapome <- read.table(crapome, sep='\t', header=TRUE)
+    colnames(crapome) <- c("Prey", "Symbol", "Num.of.Exp", "Ave.SC", "Max.SC")
+    DF1 <- merge(DF, crapome); as.character(DF1$Num.of.Exp); DF1$Symbol <- NULL;
+                    DF1$Ave.SC <- NULL; DF1$Max.SC <- NULL #remove unnecessary columns
+    DF1$Num.of.Exp <- sub("^$", "0 / 1", DF1$Num.of.Exp ) #replace blank values with 0 / 1
+    DF <- DF1 %>% separate(Num.of.Exp, c("NumExp", "TotalExp"), " / ") #split into 2 columns
+    DF$CrapomePCT <- 100 - (as.integer(DF$NumExp) / as.integer(DF$TotalExp) * 100) #calculate crapome %
+  }
+  DF$SAF <- DF$AvgSpec / DF$Length
+  DF2 = DF %>% group_by(Bait) %>% mutate(NSAF = SAF/sum(SAF))
+  DF$NSAF = DF2$NSAF
+  return(DF)
+}
+
+merge_files_sc <- function(SAINT, prey_DF, crapome=FALSE) {
+  #SAINT <- read.table(SAINT_DF, sep='\t', header=TRUE)
+  prey <- read.table(prey_DF, sep='\t', header=FALSE); colnames(prey) <- c("Prey", "Length", "PreyGene")
+  DF <- merge(SAINT,prey)
+  
+  if(crapome!=FALSE) {
+    crapome <- read.table(crapome, sep='\t', header=TRUE)
+    colnames(crapome) <- c("Prey", "Symbol", "Num.of.Exp", "Ave.SC", "Max.SC")
+    DF1 <- merge(DF, crapome); as.character(DF1$Num.of.Exp); DF1$Symbol <- NULL;
+                    DF1$Ave.SC <- NULL; DF1$Max.SC <- NULL #remove unnecessary columns
+    DF1$Num.of.Exp <- sub("^$", "0 / 1", DF1$Num.of.Exp ) #replace blank values with 0 / 1
+    DF <- DF1 %>% separate(Num.of.Exp, c("NumExp", "TotalExp"), " / ") #split into 2 columns
+    DF$CrapomePCT <- 100 - (as.integer(DF$NumExp) / as.integer(DF$TotalExp) * 100) #calculate crapome %
+  }
+  DF$SAF <- DF$AvgSpec / DF$Length
+  DF2 = DF %>% group_by(Bait) %>% mutate(NSAF = SAF/sum(SAF))
+  DF$NSAF = DF2$NSAF
+  return(DF)
+}
+###################################################################################################
+# Plot all proteins for each bait by x=ln(NSAF), y=Log2(FoldChange)
+###################################################################################################
+bubble_NSAF <- function(data, color) {
+    if(color=="crapome") {
+      a <- subset(data, CrapomePCT <80, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait))
+      b <- subset(data, CrapomePCT>=80, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait))
+      p <- qplot(x=log(NSAF), y=log2(FoldChange), data=a, colour=I("tan"),size=SpecSum) + scale_size(range=c(1,10)) + 
+        geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=a)
+      if(length(levels(a$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")} # multiple graphs if multiple baits
+      p <- p + geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum, color=CrapomePCT), data=b) + 
+        scale_colour_gradient(limits=c(80, 100), low="tan", high="red") + 
+        labs(colour="CRAPome Probability \nof Specific Interaction (%)", x="ln(NSAF)") + 
+        geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=b)
+      return(ggsave(p, width=8,height=4,filename = "bubble_NSAF.png"))
+    }
+   if(color != "crapome") {
+      p <- qplot(x=log(NSAF), y=log2(FoldChange), data=data, colour=I(color),size=SpecSum) + scale_size(range=c(1,10)) + 
+        geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=data) + # add bubble outlines
+          labs(x="ln(NSAF)")
+        if(length(levels(data$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}
+      return(ggsave(p, width=8,height=4,filename = "bubble_NSAF.png"))
+    }
+  }
+###################################################################################################
+# Plot all proteins for each bait by x=Saintscore, y=Log2(FoldChange)
+###################################################################################################
+bubble_SAINT <- function(data, color) {
+    if(color=="crapome") {
+      a <- subset(data, CrapomePCT <80, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait)) #filter on CRAPome
+      b <- subset(data, CrapomePCT >=80, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait))
+      p <- qplot(x=SaintScore, y=log2(FoldChange), data=a, colour=I("tan"),size=SpecSum) + 
+        scale_size(range=c(1,10)) + geom_point(aes(x=SaintScore,y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=a)
+      if(length(levels(a$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}
+      p <- p + geom_point(aes(x=SaintScore,y=log2(FoldChange), size=SpecSum, color=CrapomePCT), data=b) + 
+        scale_colour_gradient(limits=c(80, 100), low="tan", high="red") + 
+        labs(colour="CRAPome Probability \nof Specific Interaction (%)") +
+        geom_point(aes(x=SaintScore,y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=b)
+      return(ggsave(p, width=8,height=4,filename = "bubble_SAINT.png"))
+    }
+    if(color != "crapome") {
+      p <- qplot(x=SaintScore, y=log2(FoldChange), data=data, colour=I(color),size=SpecSum) +
+        scale_size(range=c(1,10)) + geom_point(aes(x=SaintScore,y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=data)
+      if(length(levels(data$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}
+      return(ggsave(p, width=8,height=4,filename = "bubble_SAINT.png"))
+    }
+  }
+###################################################################################################
+# Filter proteins on Saintscore cutoff and plot for each bait x=Saintscore, y=Log2(FoldChange)
+###################################################################################################
+bubble_zoom_SAINT <- function(data, color, label=FALSE, cutoff=0.8) {
+  if(color=="crapome") {
+    a <- subset(data, CrapomePCT <80 & SaintScore>=cutoff, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait, PreyGene))
+    b <- subset(data, CrapomePCT >=80 & SaintScore >=cutoff, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait, PreyGene))
+    p <- qplot(x=SaintScore, y=log2(FoldChange), data=a, colour=I("tan"),size=SpecSum) + 
+      scale_size(range=c(1,10)) + ggtitle("Filtered on SAINT score")+geom_point(aes(x=SaintScore,y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=a)
+    if(label==TRUE & length(a$NSAF!=0)) {
+      p <- p + geom_text(data=a, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black")
+    }
+    if(length(levels(a$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}
+    p <- p + geom_point(aes(x=SaintScore,y=log2(FoldChange), size=SpecSum, color=CrapomePCT), data=b) + 
+      scale_colour_gradient(limits=c(80, 100), low="tan", high="red") + 
+      labs(colour="CRAPome Probability \nof Specific Interaction (%)") + 
+      geom_point(aes(x=SaintScore,y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=b)
+    if(label==TRUE & length(b$NSAF!=0)) {
+      p <- p + geom_text(data=b, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black", show_guide=FALSE)
+    }
+    return(ggsave(p, width=8,height=4,filename = "bubble_zoom_SAINT.png"))
+  }
+  if(color != "crapome") {
+    a <- subset(data, SaintScore>=cutoff, select = c(NSAF,SpecSum, FoldChange, SaintScore, Bait, PreyGene))
+    p <- qplot(x=SaintScore, y=log2(FoldChange), data=a, colour=I(color),size=SpecSum) +
+      scale_size(range=c(1,10)) + ggtitle("Filtered on SAINT score") + 
+      geom_point(aes(x=SaintScore,y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=a)
+    if(label==TRUE & length(a$NSAF!=0)) {
+      p <- p + geom_text(data=a, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black", show_guide=FALSE)
+    }
+    if(length(levels(data$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}
+    return(ggsave(p, width=8,height=4,filename = "bubble_zoom_SAINT.png"))
+  }
+}
+###################################################################################################
+# Filter proteins on Saintscore cutoff and plot for each bait x=log(NSAF), y=Log2(FoldChange)
+###################################################################################################
+bubble_zoom_NSAF <- function(data, color, label=FALSE, cutoff=0.8) {
+  if(color=="crapome") {
+    a <- subset(data, CrapomePCT <80 & SaintScore>=cutoff, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait, PreyGene))
+    b <- subset(data, CrapomePCT >=80 & SaintScore >=cutoff, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait, PreyGene))
+    p <- qplot(x=log(NSAF), y=log2(FoldChange), data=a, colour=I("tan"),size=SpecSum) + 
+      scale_size(range=c(1,10)) + ggtitle("Filtered on SAINT score") + 
+      geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=a)
+    if(label==TRUE & length(a$NSAF!=0)) {
+      p <- p + geom_text(data=a, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black")
+    }
+    if(length(levels(a$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}
+    p <- p + geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum, color=CrapomePCT), data=b) + 
+      scale_colour_gradient(limits=c(80, 100), low="tan", high="red") + 
+      labs(colour="CRAPome Probability \nof Specific Interaction (%)", x="ln(NSAF)") + 
+      geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=b)
+    if(label==TRUE & length(b$NSAF!=0)) {
+      p <- p + geom_text(data=b, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black", show_guide=FALSE)
+    }
+    return(ggsave(p, width=8,height=4,filename = "bubble_zoom_NSAF.png"))
+  }
+  if(color != "crapome") {
+    a <- subset(data, SaintScore>=cutoff, select = c(NSAF,SpecSum, FoldChange, SaintScore, Bait, PreyGene))
+    p <- qplot(x=log(NSAF), y=log2(FoldChange), data=a, colour=I(color), size=SpecSum) +
+      scale_size(range=c(1,10)) + ggtitle("Filtered on SAINT score") + 
+      geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=a) + 
+      labs(x="ln(NSAF)")
+    if(label==TRUE & length(a$NSAF!=0)) {
+      p <- p + geom_text(data=a, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black", show_guide=FALSE)
+    }
+    if(length(levels(data$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}
+    return(ggsave(p, width=8,height=4,filename = "bubble_zoom_NSAF.png"))
+  }
+}
+###################################################################################################
+# Check Saintscore cutoff and stop program if not between 0 and 1
+###################################################################################################
+cutoff_check <- function(cutoff){
+  if( any(cutoff < 0 | cutoff > 1) ) stop('SAINT score cutoff not between 0 and 1. Please correct and try again')
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+main(args[1],args[2],args[3],args[4],args[5],args[6],args[7],args[8],args[9])
+
+#main("test_list.txt", "preytest.txt", crapome="craptest.txt", color="crapome", label=TRUE)
+#main("Crizo_list.txt", "prey_cr.txt", crapome = "crizo_crap.txt", color="crapome", label=TRUE, cutoff=0.7)
+#main("test_list.txt", "preytest.txt", crapome=FALSE, color="magenta", label=FALSE, cutoff=1.1)
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