First attempt at script-run-workflow
This commit is contained in:
765
workflow/templates/qhtcp/Code/TSHeatmaps5dev2.R
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765
workflow/templates/qhtcp/Code/TSHeatmaps5dev2.R
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library("ontologyIndex")
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library("ggplot2")
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library("RColorBrewer")
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library("grid")
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library("ggthemes")
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#library("plotly")
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#library("htmlwidgets")
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library("extrafont")
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library("stringr")
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library("org.Sc.sgd.db")
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library("ggrepel")
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library(gplots)
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Wstudy=getwd()
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inputFile= 'asdf'
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inputFile[1] <- "../Exp1/ZScores/ZScores_Interaction.csv" #paste0(Wstudy,"/Exp1/ZScores/ZScores_Interaction.csv")
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inputFile[2] <- "../Exp2/ZScores/ZScores_Interaction.csv"
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inputFile[3] <- "../Exp3/ZScores/ZScores_Interaction.csv"
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inputFile[4] <- "../Exp4/ZScores/ZScores_Interaction.csv"
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inputFile[5] <- "../Exp5/ZScores/ZScores_Interaction.csv"
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#labels <- read.delim("ExpLabels.txt",skip=0,as.is=T,row.names=1,strip.white=TRUE)
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#labels <- read.delim("StudyInfo.csv",skip=0,as.is=T,row.names=1,strip.white=TRUE)
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labels<- read.csv(file= "StudyInfo.csv",stringsAsFactors = FALSE)
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lstExpNum= 'asdf'
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a=0
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#R can't index data.frame's so some stupid nasty code must be implemented
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if (file.exists(inputFile[1])){
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X1 <- (read.csv(file = inputFile[1],stringsAsFactors=FALSE,header = TRUE))
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a=a+1
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lstExpNum[a]= 1
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Name1 <- labels[1,2]} #ssArg2 These are now supplied by Code/ExpLabels.txt which is user edited
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if (file.exists(inputFile[2])){
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X2 <- (read.csv(file = inputFile[2],stringsAsFactors=FALSE,header = TRUE))
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a=a+1
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lstExpNum[a]= 2
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Name2 <- labels[2,2]}
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if (file.exists(inputFile[3])){
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X3 <- (read.csv(file = inputFile[3],stringsAsFactors=FALSE,header = TRUE))
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a=a+1
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lstExpNum[a]= 3
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Name3 <- labels[3,2]} #ssArg2 These are now supplied by Code/ExpLabels.txt which is user edited
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if (file.exists(inputFile[4])){
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X4 <- (read.csv(file = inputFile[4],stringsAsFactors=FALSE,header = TRUE))
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a=a+1
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lstExpNum[a]= 4
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Name4 <- labels[4,2]}
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if (file.exists(inputFile[5])){
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X5 <- (read.csv(file = inputFile[5],stringsAsFactors=FALSE,header = TRUE))
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a=a+1
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lstExpNum[a]= 5
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Name5 <- labels[5,2]}
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#--------------------------Standard Names-------------------------------------------------------
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#ExpNames= c('Exp1','Exp2','Exp3','Exp4','Exp5')
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#expNumber1<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[1]))
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#expNumber2<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[2]))
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#expNumber3<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[3]))
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#expNumber4<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[4]))
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#Name1= ExpNames[1]
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#Name2= ExpNames[2]
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#Name3= ExpNames[3]
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#Name4= ExpNames[4]
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#Name5= ExpNames[5]
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print('52')
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#----------------------TABLES------------------------------------------------------------
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#import standard tables used in Sean's code That should be copied to each ExpStudy
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ontology_obo_input <- "gene_ontology_edit.obo" #paste0(Wstudy,"/Code/gene_ontology_edit.obo") # Args[5]
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GOtermstab_file <- "go_terms.tab"
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GO_ID_Arg <-"All_SGD_GOTerms_for_QHTCPtk.csv" #All_SGD_GOTerms.csv #Args[7]
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Ontology <- get_ontology(file=ontology_obo_input,propagate_relationships = "is_a",extract_tags = "minimal")
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GO2ALLORFs <- as.list(org.Sc.sgdGO2ALLORFS) #all ORFs associated with GO term
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Terms <- read.delim(file=GOtermstab_file,header=FALSE,quote = "",col.names = c("GO_ID","GO_Term","GO_Aspect","GO_Term_Definition"))
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#----------------------------------------------------------------------------
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#The directory to put the results into. Sean puts this in the 'Home' directory
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subDir <- "../TermSpecificHeatmaps"
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if (file.exists(subDir)){
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outputpath <- subDir
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} else {
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dir.create(file.path(subDir))
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}
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outputpath <- "../TermSpecificHeatmaps/" #paste0(Wstudy,"/TermSpecificHeatmaps/")
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print(outputpath)
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print('73')
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#-----------------------------------------------------------------------------------
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XX3 <- read.csv(file = GO_ID_Arg,stringsAsFactors=FALSE,header = TRUE)
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XX3[,1] <- paste("GO:",formatC(XX3[,1],width=7,flag="0"),sep="")
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XX3[,2] <- gsub(pattern = " ",replacement = "_",x = XX3[,2])
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XX3[,2] <- gsub(pattern = "/",replacement = "_",x = XX3[,2])
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print('80')
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#rm(X,)
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#Exp1--------------------------------------------------
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if (file.exists(inputFile[1])){
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print('84')
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X1$ORF <- X1$OrfRep
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X1$ORF <- gsub("_1","",x=X1$ORF)
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X1$ORF <- gsub("_2","",x=X1$ORF)
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X1$ORF <- gsub("_3","",x=X1$ORF)
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X1$ORF <- gsub("_4","",x=X1$ORF)
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X1$Score_L <- "No Effect"
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try(X1[is.na(X1$Z_lm_L),]$Score_L <- "No Growth")
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try(X1[!is.na(X1$Z_lm_L) & X1$Z_lm_L >= 2,]$Score_L <- "Deletion Enhancer")
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try(X1[!is.na(X1$Z_lm_L) & X1$Z_lm_L <= -2,]$Score_L <- "Deletion Suppressor")
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X1$Score_K <- "No Effect"
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try(X1[is.na(X1$Z_lm_K),]$Score_K <- "No Growth")
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try(X1[!is.na(X1$Z_lm_K) & X1$Z_lm_K >= 2,]$Score_K <- "Deletion Suppressor")
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try(X1[!is.na(X1$Z_lm_K) & X1$Z_lm_K <= -2,]$Score_K <- "Deletion Enhancer")
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#express the na data as 0.001 in X1 for K and L
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X1[is.na(X1$Z_lm_L),]$Z_lm_L <- 0.001
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X1[is.na(X1$Z_lm_K),]$Z_lm_K <- 0.001
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X1$Rank_L <- rank(X1$Z_lm_L)
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X1$Rank_K <- rank(X1$Z_lm_K)
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X1 <- X1[order(X1$OrfRep,decreasing = FALSE),]
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colnames(X1) <- paste(colnames(X1),"_X1",sep="")
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print('110')
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}
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print('112')
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#Exp2------------------------------------------------------------------------
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if (file.exists(inputFile[2])){
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X2$ORF <- X2$OrfRep
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X2$ORF <- gsub("_1","",x=X2$ORF)
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X2$ORF <- gsub("_2","",x=X2$ORF)
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X2$ORF <- gsub("_3","",x=X2$ORF)
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X2$ORF <- gsub("_4","",x=X2$ORF)
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X2$Score_L <- "No Effect"
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try(X2[is.na(X2$Z_lm_L),]$Score_L <- "No Growth")
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try(X2[!is.na(X2$Z_lm_L) & X2$Z_lm_L >= 2,]$Score_L <- "Deletion Enhancer")
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try(X2[!is.na(X2$Z_lm_L) & X2$Z_lm_L <= -2,]$Score_L <- "Deletion Suppressor")
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X2$Score_K <- "No Effect"
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try(X2[is.na(X2$Z_lm_K),]$Score_K <- "No Growth")
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try(X2[!is.na(X2$Z_lm_K) & X2$Z_lm_K >= 2,]$Score_K <- "Deletion Suppressor")
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try(X2[!is.na(X2$Z_lm_K) & X2$Z_lm_K <= -2,]$Score_K <- "Deletion Enhancer")
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#express the na data as 0.001 in X2
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X2[is.na(X2$Z_lm_L),]$Z_lm_L <- 0.001
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X2[is.na(X2$Z_lm_K),]$Z_lm_K <- 0.001
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X2$Rank_L <- rank(X2$Z_lm_L)
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X2$Rank_K <- rank(X2$Z_lm_K)
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X2 <- X2[order(X2$OrfRep,decreasing = FALSE),]
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colnames(X2) <- paste(colnames(X2),"_X2",sep="")
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X <- cbind(X1,X2)
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print('file2-140')
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}
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print('142')
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#Exp3--------------------------------------------------------------
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if (file.exists(inputFile[3])){
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X3$ORF <- X3$OrfRep
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X3$ORF <- gsub("_1","",x=X3$ORF)
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X3$ORF <- gsub("_2","",x=X3$ORF)
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X3$ORF <- gsub("_3","",x=X3$ORF)
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X3$ORF <- gsub("_4","",x=X3$ORF)
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X3$Score_L <- "No Effect"
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try(X3[is.na(X3$Z_lm_L),]$Score_L <- "No Growth")
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try(X3[!is.na(X3$Z_lm_L) & X3$Z_lm_L >= 2,]$Score_L <- "Deletion Enhancer")
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try(X3[!is.na(X3$Z_lm_L) & X3$Z_lm_L <= -2,]$Score_L <- "Deletion Suppressor")
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X3$Score_K <- "No Effect"
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try(X3[is.na(X3$Z_lm_K),]$Score_K <- "No Growth")
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try(X3[!is.na(X3$Z_lm_K) & X3$Z_lm_K >= 2,]$Score_K <- "Deletion Suppressor")
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try(X3[!is.na(X3$Z_lm_K) & X3$Z_lm_K <= -2,]$Score_K <- "Deletion Enhancer")
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#express the na data as 0.001 in X3
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X3[is.na(X3$Z_lm_L),]$Z_lm_L <- 0.001
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X3[is.na(X3$Z_lm_K),]$Z_lm_K <- 0.001
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X3$Rank_L <- rank(X3$Z_lm_L)
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X3$Rank_K <- rank(X3$Z_lm_K)
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X3 <- X3[order(X3$OrfRep,decreasing = FALSE),]
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colnames(X3) <- paste(colnames(X3),"_X3",sep="")
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X <- cbind(X,X3)
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}
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#Exp4
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if (file.exists(inputFile[4])){
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X4$ORF <- X4$OrfRep
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X4$ORF <- gsub("_1","",x=X4$ORF)
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X4$ORF <- gsub("_2","",x=X4$ORF)
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X4$ORF <- gsub("_3","",x=X4$ORF)
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X4$ORF <- gsub("_4","",x=X4$ORF)
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X4$Score_L <- "No Effect"
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try(X4[is.na(X4$Z_lm_L),]$Score_L <- "No Growth")
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try(X4[!is.na(X4$Z_lm_L) & X4$Z_lm_L >= 2,]$Score_L <- "Deletion Enhancer")
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try(X4[!is.na(X4$Z_lm_L) & X4$Z_lm_L <= -2,]$Score_L <- "Deletion Suppressor")
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X4$Score_K <- "No Effect"
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try(X4[is.na(X4$Z_lm_K),]$Score_K <- "No Growth")
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try(X4[!is.na(X4$Z_lm_K) & X4$Z_lm_K >= 2,]$Score_K <- "Deletion Suppressor")
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try(X4[!is.na(X4$Z_lm_K) & X4$Z_lm_K <= -2,]$Score_K <- "Deletion Enhancer")
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#express the na data as 0.001 in X4
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X4[is.na(X4$Z_lm_L),]$Z_lm_L <- 0.001
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X4[is.na(X4$Z_lm_K),]$Z_lm_K <- 0.001
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X4$Rank_L <- rank(X4$Z_lm_L)
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X4$Rank_K <- rank(X4$Z_lm_K)
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X4 <- X4[order(X4$OrfRep,decreasing = FALSE),]
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colnames(X4) <- paste(colnames(X4),"_X4",sep="")
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X <- cbind(X,X4)
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}
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#Exp5--------------------------------------------------------------
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if (file.exists(inputFile[5])){
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X5$ORF <- X5$OrfRep
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X5$ORF <- gsub("_1","",x=X5$ORF)
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X5$ORF <- gsub("_2","",x=X5$ORF)
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X5$ORF <- gsub("_3","",x=X5$ORF)
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X5$ORF <- gsub("_4","",x=X5$ORF)
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X5$Score_L <- "No Effect"
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try(X5[is.na(X5$Z_lm_L),]$Score_L <- "No Growth")
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try(X5[!is.na(X5$Z_lm_L) & X5$Z_lm_L >= 2,]$Score_L <- "Deletion Enhancer")
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try(X5[!is.na(X5$Z_lm_L) & X5$Z_lm_L <= -2,]$Score_L <- "Deletion Suppressor")
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X5$Score_K <- "No Effect"
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try(X5[is.na(X5$Z_lm_K),]$Score_K <- "No Growth")
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try(X5[!is.na(X5$Z_lm_K) & X5$Z_lm_K >= 2,]$Score_K <- "Deletion Suppressor")
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try(X5[!is.na(X5$Z_lm_K) & X5$Z_lm_K <= -2,]$Score_K <- "Deletion Enhancer")
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#express the na data as 0.001 in X5
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X5[is.na(X5$Z_lm_L),]$Z_lm_L <- 0.001
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X5[is.na(X5$Z_lm_K),]$Z_lm_K <- 0.001
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X5$Rank_L <- rank(X5$Z_lm_L)
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X5$Rank_K <- rank(X5$Z_lm_K)
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X5 <- X5[order(X5$OrfRep,decreasing = FALSE),]
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colnames(X5) <- paste(colnames(X5),"_X5",sep="")
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X <- cbind(X,X5)
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}
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print('after5-229')
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X$ORF <- X$OrfRep_X1
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part1=1
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if (file.exists(inputFile[1])& file.exists(inputFile[2])){
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print('234 ifFile2')
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X$ORF <- gsub("_1","",x=X$ORF)
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try(X[X$Gene_X1 == "",]$Gene_X1 <- X[X$Gene_X1 == "",]$OrfRep_X1)
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try(X[X$Gene_X2 == "",]$Gene_X2 <- X[X$Gene_X2 == "",]$OrfRep_X2)
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X_heatmap <- X[colnames(X) == "ORF" | colnames(X) == "Gene_X1" |
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colnames(X) == "Z_Shift_K_X1" | colnames(X) == "Z_lm_K_X1" |
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colnames(X) == "Z_Shift_K_X2" | colnames(X) == "Z_lm_K_X2" |
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colnames(X) == "Z_Shift_L_X1" | colnames(X) == "Z_lm_L_X1" |
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colnames(X) == "Z_Shift_L_X2" | colnames(X) == "Z_lm_L_X2" ]
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X_heatmap <- X_heatmap[,c(10,1,4,5,8,9,2,3,6,7)]
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colnames(X_heatmap) <- gsub(pattern = "X1",replacement = Name1,colnames(X_heatmap))
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colnames(X_heatmap) <- gsub(pattern = "X2",replacement = Name2,colnames(X_heatmap))
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colnames(X_heatmap)[2] <- "Gene"
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}
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if (file.exists(inputFile[3])){
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X$ORF <- gsub("_1","",x=X$ORF)
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X$ORF <- gsub("_2","",x=X$ORF)
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try(X[X$Gene_X1 == "",]$Gene_X1 <- X[X$Gene_X1 == "",]$OrfRep_X1)
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try(X[X$Gene_X2 == "",]$Gene_X2 <- X[X$Gene_X2 == "",]$OrfRep_X2)
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try(X[X$Gene_X3 == "",]$Gene_X3 <- X[X$Gene_X3 == "",]$OrfRep_X3)
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X_heatmap <- X[colnames(X) == "ORF" | colnames(X) == "Gene_X1" |
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colnames(X) == "Z_Shift_K_X1" | colnames(X) == "Z_lm_K_X1" |
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colnames(X) == "Z_Shift_K_X2" | colnames(X) == "Z_lm_K_X2" |
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colnames(X) == "Z_Shift_K_X3" | colnames(X) == "Z_lm_K_X3" |
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colnames(X) == "Z_Shift_L_X1" | colnames(X) == "Z_lm_L_X1" |
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colnames(X) == "Z_Shift_L_X2" | colnames(X) == "Z_lm_L_X2" |
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colnames(X) == "Z_Shift_L_X3" | colnames(X) == "Z_lm_L_X3" ]
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#Reorder columns
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X_heatmap <- X_heatmap[,c(14,1,4,5,8,9,12,13,2,3,6,7,10,11)] #Three
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colnames(X_heatmap) <- gsub(pattern = "X1",replacement = Name1,colnames(X_heatmap))
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colnames(X_heatmap) <- gsub(pattern = "X2",replacement = Name2,colnames(X_heatmap))
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colnames(X_heatmap) <- gsub(pattern = "X3",replacement = Name3,colnames(X_heatmap))
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colnames(X_heatmap)[2] <- "Gene"
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}
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if (file.exists(inputFile[4])){
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X$ORF <- gsub("_1","",x=X$ORF)
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X$ORF <- gsub("_2","",x=X$ORF)
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X$ORF <- gsub("_3","",x=X$ORF)
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try(X[X$Gene_X1 == "",]$Gene_X1 <- X[X$Gene_X1 == "",]$OrfRep_X1)
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try(X[X$Gene_X2 == "",]$Gene_X2 <- X[X$Gene_X2 == "",]$OrfRep_X2)
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try(X[X$Gene_X3 == "",]$Gene_X3 <- X[X$Gene_X3 == "",]$OrfRep_X3)
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try(X[X$Gene_X4 == "",]$Gene_X4 <- X[X$Gene_X4 == "",]$OrfRep_X4)
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X_heatmap <- X[colnames(X) == "ORF" | colnames(X) == "Gene_X1" |
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colnames(X) == "Z_Shift_K_X1" | colnames(X) == "Z_lm_K_X1" |
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colnames(X) == "Z_Shift_K_X2" | colnames(X) == "Z_lm_K_X2" |
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colnames(X) == "Z_Shift_K_X3" | colnames(X) == "Z_lm_K_X3" |
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colnames(X) == "Z_Shift_K_X4" | colnames(X) == "Z_lm_K_X4" |
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colnames(X) == "Z_Shift_L_X1" | colnames(X) == "Z_lm_L_X1" |
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colnames(X) == "Z_Shift_L_X2" | colnames(X) == "Z_lm_L_X2" |
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colnames(X) == "Z_Shift_L_X3" | colnames(X) == "Z_lm_L_X3" |
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colnames(X) == "Z_Shift_L_X4" | colnames(X) == "Z_lm_L_X4" ]
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#Reorder columns
|
||||
X_heatmap <- X_heatmap[,c(18,1,4,5,8,9,12,13,16,17,2,3,6,7,10,11,14,15)] #Four
|
||||
colnames(X_heatmap) <- gsub(pattern = "X1",replacement = Name1,colnames(X_heatmap))
|
||||
colnames(X_heatmap) <- gsub(pattern = "X2",replacement = Name2,colnames(X_heatmap))
|
||||
colnames(X_heatmap) <- gsub(pattern = "X3",replacement = Name3,colnames(X_heatmap))
|
||||
colnames(X_heatmap) <- gsub(pattern = "X4",replacement = Name4,colnames(X_heatmap))
|
||||
colnames(X_heatmap)[2] <- "Gene"
|
||||
}
|
||||
|
||||
|
||||
if (file.exists(inputFile[5])){
|
||||
X$ORF <- gsub("_1","",x=X$ORF)
|
||||
X$ORF <- gsub("_2","",x=X$ORF)
|
||||
X$ORF <- gsub("_3","",x=X$ORF)
|
||||
X$ORF <- gsub("_4","",x=X$ORF)
|
||||
|
||||
try(X[X$Gene_X1 == "",]$Gene_X1 <- X[X$Gene_X1 == "",]$OrfRep_X1)
|
||||
try(X[X$Gene_X2 == "",]$Gene_X2 <- X[X$Gene_X2 == "",]$OrfRep_X2)
|
||||
try(X[X$Gene_X3 == "",]$Gene_X3 <- X[X$Gene_X3 == "",]$OrfRep_X3)
|
||||
try(X[X$Gene_X4 == "",]$Gene_X4 <- X[X$Gene_X4 == "",]$OrfRep_X4)
|
||||
try(X[X$Gene_X5 == "",]$Gene_X5 <- X[X$Gene_X5 == "",]$OrfRep_X5)
|
||||
|
||||
X_heatmap <- X[colnames(X) == "ORF" | colnames(X) == "Gene_X1" |
|
||||
colnames(X) == "Z_Shift_K_X1" | colnames(X) == "Z_lm_K_X1" |
|
||||
colnames(X) == "Z_Shift_K_X2" | colnames(X) == "Z_lm_K_X2" |
|
||||
colnames(X) == "Z_Shift_K_X3" | colnames(X) == "Z_lm_K_X3" |
|
||||
colnames(X) == "Z_Shift_K_X4" | colnames(X) == "Z_lm_K_X4" |
|
||||
colnames(X) == "Z_Shift_K_X5" | colnames(X) == "Z_lm_K_X5" |
|
||||
colnames(X) == "Z_Shift_L_X1" | colnames(X) == "Z_lm_L_X1" |
|
||||
colnames(X) == "Z_Shift_L_X2" | colnames(X) == "Z_lm_L_X2" |
|
||||
colnames(X) == "Z_Shift_L_X3" | colnames(X) == "Z_lm_L_X3" |
|
||||
colnames(X) == "Z_Shift_L_X4" | colnames(X) == "Z_lm_L_X4" |
|
||||
colnames(X) == "Z_Shift_L_X5" | colnames(X) == "Z_lm_L_X5"]
|
||||
#Reorder columns
|
||||
X_heatmap <- X_heatmap[,c(22,1,4,5,8,9,12,13,16,17,20,21,2,3,6,7,10,11,14,15,18,19)]
|
||||
colnames(X_heatmap) <- gsub(pattern = "X1",replacement = Name1,colnames(X_heatmap))
|
||||
colnames(X_heatmap) <- gsub(pattern = "X2",replacement = Name2,colnames(X_heatmap))
|
||||
colnames(X_heatmap) <- gsub(pattern = "X3",replacement = Name3,colnames(X_heatmap))
|
||||
colnames(X_heatmap) <- gsub(pattern = "X4",replacement = Name4,colnames(X_heatmap))
|
||||
colnames(X_heatmap) <- gsub(pattern = "X5",replacement = Name5,colnames(X_heatmap))
|
||||
|
||||
colnames(X_heatmap)[2] <- "Gene"
|
||||
}
|
||||
|
||||
|
||||
#-----------------------------------------------------------------------------------------
|
||||
|
||||
#theme elements for plots
|
||||
theme_Publication <- function(base_size=14, base_family="sans") {
|
||||
(theme_foundation(base_size=base_size, base_family=base_family)
|
||||
+ theme(plot.title = element_text(face = "bold",
|
||||
size = rel(1.2), hjust = 0.5),
|
||||
text = element_text(),
|
||||
panel.background = element_rect(colour = NA),
|
||||
plot.background = element_rect(colour = NA),
|
||||
panel.border = element_rect(colour = NA),
|
||||
axis.title = element_text(face = "bold",size = rel(1)),
|
||||
axis.title.y = element_text(angle=90,vjust =2),
|
||||
axis.title.x = element_text(vjust = -0.2),
|
||||
axis.text = element_text(),
|
||||
axis.line = element_line(colour="black"),
|
||||
axis.ticks = element_line(),
|
||||
panel.grid.major = element_line(colour="#f0f0f0"),
|
||||
panel.grid.minor = element_blank(),
|
||||
legend.key = element_rect(colour = NA),
|
||||
legend.position = "bottom",
|
||||
legend.direction = "horizontal",
|
||||
legend.key.size= unit(0.2, "cm"),
|
||||
legend.spacing = unit(0, "cm"),
|
||||
legend.title = element_text(face="italic"),
|
||||
plot.margin=unit(c(10,5,5,5),"mm"),
|
||||
strip.background=element_rect(colour="#f0f0f0",fill="#f0f0f0"),
|
||||
strip.text = element_text(face="bold")
|
||||
))
|
||||
|
||||
}
|
||||
|
||||
scale_fill_Publication <- function(...){
|
||||
library(scales)
|
||||
discrete_scale("fill","Publication",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#ef3b2c","#662506","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)
|
||||
|
||||
}
|
||||
|
||||
scale_colour_Publication <- function(...){
|
||||
discrete_scale("colour","Publication",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#ef3b2c","#662506","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)
|
||||
|
||||
}
|
||||
|
||||
|
||||
theme_Publication_legend_right <- function(base_size=14, base_family="sans") {
|
||||
(theme_foundation(base_size=base_size, base_family=base_family)
|
||||
+ theme(plot.title = element_text(face = "bold",
|
||||
size = rel(1.2), hjust = 0.5),
|
||||
text = element_text(),
|
||||
panel.background = element_rect(colour = NA),
|
||||
plot.background = element_rect(colour = NA),
|
||||
panel.border = element_rect(colour = NA),
|
||||
axis.title = element_text(face = "bold",size = rel(1)),
|
||||
axis.title.y = element_text(angle=90,vjust =2),
|
||||
axis.title.x = element_text(vjust = -0.2),
|
||||
axis.text = element_text(),
|
||||
axis.line = element_line(colour="black"),
|
||||
axis.ticks = element_line(),
|
||||
panel.grid.major = element_line(colour="#f0f0f0"),
|
||||
panel.grid.minor = element_blank(),
|
||||
legend.key = element_rect(colour = NA),
|
||||
legend.position = "right",
|
||||
legend.direction = "vertical",
|
||||
legend.key.size= unit(0.5, "cm"),
|
||||
legend.spacing = unit(0, "cm"),
|
||||
legend.title = element_text(face="italic"),
|
||||
plot.margin=unit(c(10,5,5,5),"mm"),
|
||||
strip.background=element_rect(colour="#f0f0f0",fill="#f0f0f0"),
|
||||
strip.text = element_text(face="bold")
|
||||
))
|
||||
|
||||
}
|
||||
|
||||
scale_fill_Publication <- function(...){
|
||||
discrete_scale("fill","Publication",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#ef3b2c","#662506","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)
|
||||
|
||||
}
|
||||
|
||||
scale_colour_Publication <- function(...){
|
||||
discrete_scale("colour","Publication",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#ef3b2c","#662506","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
#www.geneontology.org/ontology/gene_ontology_edit.obo file
|
||||
Ontology <- get_ontology(file=ontology_obo_input,propagate_relationships = "is_a",extract_tags = "minimal")
|
||||
print(Ontology)
|
||||
#all ORFs associated with GO term
|
||||
GO2ALLORFs <- as.list(org.Sc.sgdGO2ALLORFS)
|
||||
print('429')
|
||||
|
||||
|
||||
#Gene_Association is the gene association to GO term file
|
||||
#Gene_Association <- read.delim("Documents/Hartman_Lab/SGD_Downloads/gene_association.sgd",skip=8,header=FALSE,quote="",col.names = c("Database","Database_Object_ID","Database_Object_Symbol","NOT","GO_ID","Database_Reference","Evidence","With_or_From","Aspect","Database_Object_Name","Database_Object_Synonym","Database_Object_Type","taxon","Date","Assigned_By","OtherInfo","Empty"))
|
||||
#Gene_Association$ORF <- str_split_fixed(as.character(Gene_Association$Database_Object_Synonym),"\\|",2)[,1]
|
||||
#Gene_Association$GO_ID_Numeric <- as.integer(str_split_fixed(as.character(Gene_Association$GO_ID),"\\:",2)[,2])
|
||||
|
||||
|
||||
#Terms is the GO term list jwr moved up to TAABLES
|
||||
Terms <- read.delim(file=GOtermstab_file,header=FALSE,quote = "",col.names = c("GO_ID","GO_Term","GO_Aspect","GO_Term_Definition"))
|
||||
|
||||
#-----------------------------------------------------------------------
|
||||
|
||||
#-----------------------------------------------------------------------------------------------------
|
||||
#BIG LOOP BIG LOOP ------------------------------------------------------
|
||||
colormapbreaks <- c(-12,-10,-8,-6,-4,-2,2,4,6,8,10,12)
|
||||
for(s in 1:dim(XX3)[1]){
|
||||
#Ontology <- get_ontology(file="Documents/Hartman_Lab/SGD_Downloads/gene_ontology_edit.obo",propagate_relationships = "is_a",extract_tags = "minimal")
|
||||
#Ontology_Everything <- get_ontology(file="Documents/Hartman_Lab/SGD_Downloads/gene_ontology_edit.obo",propagate_relationships = "is_a",extract_tags = "everything")
|
||||
#GO_ID_Arg <- "GO:0006325"
|
||||
GO_ID_Arg_loop <- as.character(XX3[s,1])
|
||||
GOTerm_parent <- get_descendants(Ontology,roots = GO_ID_Arg_loop)
|
||||
#GOTerm_parent <- get_descendants(Ontology,roots = "GO:0006325")
|
||||
#only make plots if parent term has fewer than 500 children
|
||||
|
||||
print('for(s in 1:dim(XX3)[1]){ -454')
|
||||
|
||||
Parent_Size <- length(as.vector(GO2ALLORFs[GO_ID_Arg_loop][[1]]))
|
||||
|
||||
if(length(GOTerm_parent) > 100){
|
||||
#print(length(GOTerm_parent))
|
||||
next()
|
||||
}
|
||||
|
||||
|
||||
Parent_Size <- length(as.vector(GO2ALLORFs[GO_ID_Arg_loop][[1]]))
|
||||
if(Parent_Size < 2){
|
||||
next()
|
||||
}
|
||||
if(Parent_Size > 2000){
|
||||
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 45, onefile = TRUE)
|
||||
print('pdf2000 469')
|
||||
for(i in 1:length(GOTerm_parent)){
|
||||
GO_Term <- GOTerm_parent[i]
|
||||
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
|
||||
GO_Term_Name <- as.character(Terms[Terms$GO_ID == GO_Term_Num,]$GO_Term)
|
||||
#Genes_Annotated_to_Term <- Gene_Association[Gene_Association$GO_ID == GO_Term,]
|
||||
All_Genes_Annotated_to_Term <- as.vector(GO2ALLORFs[GO_Term][[1]])
|
||||
Genes_Annotated_to_Term <- X_heatmap[X_heatmap$ORF %in% All_Genes_Annotated_to_Term,]
|
||||
X0 <- as.matrix(Genes_Annotated_to_Term[,3:dim(Genes_Annotated_to_Term)[2]])
|
||||
if(dim(Genes_Annotated_to_Term)[1] > 2){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "row", cexCol = 0.7, cexRow = 0.5, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
}
|
||||
dev.off()
|
||||
}
|
||||
|
||||
if(Parent_Size >= 1000 && Parent_Size <= 2000){
|
||||
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 35, onefile = TRUE)
|
||||
for(i in 1:length(GOTerm_parent)){
|
||||
GO_Term <- GOTerm_parent[i]
|
||||
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
|
||||
GO_Term_Name <- as.character(Terms[Terms$GO_ID == GO_Term_Num,]$GO_Term)
|
||||
#Genes_Annotated_to_Term <- Gene_Association[Gene_Association$GO_ID == GO_Term,]
|
||||
All_Genes_Annotated_to_Term <- as.vector(GO2ALLORFs[GO_Term][[1]])
|
||||
Genes_Annotated_to_Term <- X_heatmap[X_heatmap$ORF %in% All_Genes_Annotated_to_Term,]
|
||||
X0 <- as.matrix(Genes_Annotated_to_Term[,3:dim(Genes_Annotated_to_Term)[2]])
|
||||
if(dim(Genes_Annotated_to_Term)[1] > 2){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "row", cexCol = 0.7, cexRow = 0.6, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
}
|
||||
dev.off()
|
||||
}
|
||||
if(Parent_Size >= 500 && Parent_Size <= 1000){
|
||||
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 30, onefile = TRUE)
|
||||
for(i in 1:length(GOTerm_parent)){
|
||||
GO_Term <- GOTerm_parent[i]
|
||||
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
|
||||
GO_Term_Name <- as.character(Terms[Terms$GO_ID == GO_Term_Num,]$GO_Term)
|
||||
#Genes_Annotated_to_Term <- Gene_Association[Gene_Association$GO_ID == GO_Term,]
|
||||
All_Genes_Annotated_to_Term <- as.vector(GO2ALLORFs[GO_Term][[1]])
|
||||
Genes_Annotated_to_Term <- X_heatmap[X_heatmap$ORF %in% All_Genes_Annotated_to_Term,]
|
||||
X0 <- as.matrix(Genes_Annotated_to_Term[,3:dim(Genes_Annotated_to_Term)[2]])
|
||||
if(dim(Genes_Annotated_to_Term)[1] > 2){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "row", cexCol = 0.7, cexRow = 0.6, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
}
|
||||
dev.off()
|
||||
}
|
||||
if(Parent_Size >= 200 && Parent_Size <= 500){
|
||||
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 25, onefile = TRUE)
|
||||
for(i in 1:length(GOTerm_parent)){
|
||||
GO_Term <- GOTerm_parent[i]
|
||||
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
|
||||
GO_Term_Name <- as.character(Terms[Terms$GO_ID == GO_Term_Num,]$GO_Term)
|
||||
#Genes_Annotated_to_Term <- Gene_Association[Gene_Association$GO_ID == GO_Term,]
|
||||
All_Genes_Annotated_to_Term <- as.vector(GO2ALLORFs[GO_Term][[1]])
|
||||
Genes_Annotated_to_Term <- X_heatmap[X_heatmap$ORF %in% All_Genes_Annotated_to_Term,]
|
||||
X0 <- as.matrix(Genes_Annotated_to_Term[,3:dim(Genes_Annotated_to_Term)[2]])
|
||||
if(dim(Genes_Annotated_to_Term)[1] > 2){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "row", cexCol = 0.7, cexRow = 0.7, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
}
|
||||
dev.off()
|
||||
}
|
||||
if(Parent_Size >= 100 && Parent_Size <= 200){
|
||||
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 20, onefile = TRUE)
|
||||
for(i in 1:length(GOTerm_parent)){
|
||||
GO_Term <- GOTerm_parent[i]
|
||||
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
|
||||
GO_Term_Name <- as.character(Terms[Terms$GO_ID == GO_Term_Num,]$GO_Term)
|
||||
#Genes_Annotated_to_Term <- Gene_Association[Gene_Association$GO_ID == GO_Term,]
|
||||
All_Genes_Annotated_to_Term <- as.vector(GO2ALLORFs[GO_Term][[1]])
|
||||
Genes_Annotated_to_Term <- X_heatmap[X_heatmap$ORF %in% All_Genes_Annotated_to_Term,]
|
||||
X0 <- as.matrix(Genes_Annotated_to_Term[,3:dim(Genes_Annotated_to_Term)[2]])
|
||||
if(dim(Genes_Annotated_to_Term)[1] > 2){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "row", cexCol = 0.7, cexRow = 0.7, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
}
|
||||
dev.off()
|
||||
}
|
||||
if(Parent_Size >= 60 && Parent_Size <= 100){
|
||||
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 15, onefile = TRUE)
|
||||
for(i in 1:length(GOTerm_parent)){
|
||||
GO_Term <- GOTerm_parent[i]
|
||||
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
|
||||
GO_Term_Name <- as.character(Terms[Terms$GO_ID == GO_Term_Num,]$GO_Term)
|
||||
#Genes_Annotated_to_Term <- Gene_Association[Gene_Association$GO_ID == GO_Term,]
|
||||
All_Genes_Annotated_to_Term <- as.vector(GO2ALLORFs[GO_Term][[1]])
|
||||
Genes_Annotated_to_Term <- X_heatmap[X_heatmap$ORF %in% All_Genes_Annotated_to_Term,]
|
||||
X0 <- as.matrix(Genes_Annotated_to_Term[,3:dim(Genes_Annotated_to_Term)[2]])
|
||||
if(dim(Genes_Annotated_to_Term)[1] > 2){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "row", cexCol = 0.7, cexRow = 0.7, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
}
|
||||
dev.off()
|
||||
}
|
||||
if(Parent_Size >= 30 && Parent_Size <= 60){
|
||||
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 10, onefile = TRUE)
|
||||
for(i in 1:length(GOTerm_parent)){
|
||||
GO_Term <- GOTerm_parent[i]
|
||||
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
|
||||
GO_Term_Name <- as.character(Terms[Terms$GO_ID == GO_Term_Num,]$GO_Term)
|
||||
#Genes_Annotated_to_Term <- Gene_Association[Gene_Association$GO_ID == GO_Term,]
|
||||
All_Genes_Annotated_to_Term <- as.vector(GO2ALLORFs[GO_Term][[1]])
|
||||
Genes_Annotated_to_Term <- X_heatmap[X_heatmap$ORF %in% All_Genes_Annotated_to_Term,]
|
||||
X0 <- as.matrix(Genes_Annotated_to_Term[,3:dim(Genes_Annotated_to_Term)[2]])
|
||||
if(dim(Genes_Annotated_to_Term)[1] > 2){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "row", cexCol = 0.7, cexRow = 0.7, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
if(dim(Genes_Annotated_to_Term)[1] <= 2 && dim(Genes_Annotated_to_Term)[1] > 0){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "none", cexCol = 0.7, cexRow = 0.7, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
}
|
||||
|
||||
dev.off()
|
||||
}
|
||||
if(Parent_Size >= 3 && Parent_Size <= 30){
|
||||
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 7, onefile = TRUE)
|
||||
for(i in 1:length(GOTerm_parent)){
|
||||
GO_Term <- GOTerm_parent[i]
|
||||
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
|
||||
GO_Term_Name <- as.character(Terms[Terms$GO_ID == GO_Term_Num,]$GO_Term)
|
||||
#Genes_Annotated_to_Term <- Gene_Association[Gene_Association$GO_ID == GO_Term,]
|
||||
All_Genes_Annotated_to_Term <- as.vector(GO2ALLORFs[GO_Term][[1]])
|
||||
Genes_Annotated_to_Term <- X_heatmap[X_heatmap$ORF %in% All_Genes_Annotated_to_Term,]
|
||||
X0 <- as.matrix(Genes_Annotated_to_Term[,3:dim(Genes_Annotated_to_Term)[2]])
|
||||
if(dim(Genes_Annotated_to_Term)[1] > 2){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "row", cexCol = 0.7, cexRow = 0.7, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
if(dim(Genes_Annotated_to_Term)[1] <= 2 && dim(Genes_Annotated_to_Term)[1] > 0){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "none", cexCol = 0.7, cexRow = 0.7, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
}
|
||||
dev.off()
|
||||
}
|
||||
if(Parent_Size == 2){
|
||||
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 7, onefile = TRUE)
|
||||
for(i in 1:length(GOTerm_parent)){
|
||||
GO_Term <- GOTerm_parent[i]
|
||||
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
|
||||
GO_Term_Name <- as.character(Terms[Terms$GO_ID == GO_Term_Num,]$GO_Term)
|
||||
#Genes_Annotated_to_Term <- Gene_Association[Gene_Association$GO_ID == GO_Term,]
|
||||
All_Genes_Annotated_to_Term <- as.vector(GO2ALLORFs[GO_Term][[1]])
|
||||
Genes_Annotated_to_Term <- X_heatmap[X_heatmap$ORF %in% All_Genes_Annotated_to_Term,]
|
||||
X0 <- as.matrix(Genes_Annotated_to_Term[,3:dim(Genes_Annotated_to_Term)[2]])
|
||||
if(dim(Genes_Annotated_to_Term)[1] > 2){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "row", cexCol = 0.7, cexRow = 0.7, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
if(dim(Genes_Annotated_to_Term)[1] <= 2 && dim(Genes_Annotated_to_Term)[1] > 0){
|
||||
try(heatmap.2(x=X0,
|
||||
Rowv=TRUE, Colv=NA, distfun = dist, hclustfun = hclust,
|
||||
dendrogram = "none", cexCol = 0.7, cexRow = 0.7, scale = "none",
|
||||
breaks=colormapbreaks, symbreaks=FALSE, colsep = c(2,4,6), sepcolor= "white", offsetCol = 0.1,
|
||||
ylab = "Gene",
|
||||
cellnote = round(X0,digits=0), notecex = 0.5, key=TRUE,
|
||||
keysize=0.5, trace="none", density.info=c("none"), margins=c(10,8),
|
||||
na.color="red", col=brewer.pal(11,"PuOr"),
|
||||
main=GO_Term_Name,
|
||||
#ColSideColors=ev_repeat,
|
||||
labRow=as.character(Genes_Annotated_to_Term$Gene)))
|
||||
}
|
||||
print('740')
|
||||
}
|
||||
dev.off()
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user