Mercurial > repos > testtool > anno_peak_figure

changeset 1:6278004aa9b2 draft

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Uploaded
author testtool
date Tue, 28 Feb 2017 05:42:05 -0500
parents 88964c4b12a0
children a23d604eb17b
files annoPeakFigure/.RData annoPeakFigure/.Rhistory annoPeakFigure/._annoPeakFigure.png annoPeakFigure/annoPeakFigure.R annoPeakFigure/annoPeakFigure.png annoPeakFigure/annoPeakFigure.xml annoPeakFigure/test-data/annoPeakAnnoBar.png annoPeakFigure/test-data/annoPeakUpset.png
diffstat 8 files changed, 284 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
Binary file annoPeakFigure/.RData has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annoPeakFigure/.Rhistory	Tue Feb 28 05:42:05 2017 -0500
@@ -0,0 +1,265 @@
+TAB <- read.csv("input.csv")
+mysamples <- lapply(TAB$ID,function(x)getGEO(x))
+input <- function(TAB) { if(is(TAB, "csv")){
+TAB <- read.csv("input.csv")}
+else{
+print("error in data file")
+}}
+input()
+TAB <- read.csv("input.csv")}
+TAB <- read.csv("input.csv")
+test_func <- function(
+clusterSize=2,
+cutoff=0.2,
+platform_id='HM450',
+genome_id='hg19')
+{
+args = commandArgs(trailingOnly=TRUE)
+methyl_file = args[1]
+ChiPseq_file = args[2]
+output_file = args[3]
+options(warn=-1)
+TAB=read.csv(methyl_file)
+ChiPseq=import(ChiPseq_file)
+if(is.null(TAB)){
+stop("Must specify input files")
+}else{
+mysamples <- lapply(TAB$ID,function(x) getGEO(x))
+}
+wrappedFunction <- function(test_func)
+s0 <- lapply(mysamples,Table)
+id_ref<-lapply(s0,function(x)x$ID_REF)
+if(length(unique(id_ref)) != 1) {
+stop("Error different ID_REF for samples")
+} else if (is.null((unlist(unique(id_ref))))) {
+stop("NO GSM data avaliable")
+} else {
+values<-do.call("cbind",lapply(s0,function(x)x$VALUE))
+colnames(values)=TAB$ID
+rownames(values)=id_ref[[1]]
+cg <-  rownames(values)
+probe <- c(cg)
+hm450.hg19 <- getPlatform(platform=platform_id, genome=genome_id)
+probe.info <- hm450.hg19[probe]
+f <- data.table(probe=names(probe.info),CHR=as.data.frame(probe.info@seqnames)$value,
+BP=as.numeric(probe.info@elementMetadata$probeStart))
+designMatrix <- model.matrix(~ TAB$Phenotype)
+DMR <- bumphunter(values, design = designMatrix,
+pos=f$BP,cutoff=cutoff,chr=f$CHR)
+MAT <- DMR$table[which(DMR$table$L>=clusterSize),]
+METH <- GRanges(seqnames=MAT$chr,
+ranges=IRanges
+(start=MAT$start,
+end=MAT$end),
+value_pos=MAT$value)
+peaks<-findOverlapsOfPeaks(probe.info,ChiPseq,maxgap=5000)
+p <- peaks$peaklist$`probe.info///ChiPseq`
+peakAnno <- annotatePeak(p, file=peakAnno)
+output_file <- annotatePeak(p, file=output_file)
+}}
+test_func <- function(
+clusterSize=2,
+cutoff=0.2,
+platform_id='HM450',
+genome_id='hg19')
+{
+args = commandArgs(trailingOnly=TRUE)
+methyl_file = args[1]
+ChiPseq_file = args[2]
+output_file = args[3]
+options(warn=-1)
+TAB=read.csv(methyl_file)
+ChiPseq=import(ChiPseq_file)
+if(is.null(TAB)){
+stop("Must specify input files")
+}else{
+mysamples <- lapply(TAB$ID,function(x) getGEO(x))
+}
+wrappedFunction <- function(test_func)
+s0 <- lapply(mysamples,Table)
+id_ref<-lapply(s0,function(x)x$ID_REF)
+if(length(unique(id_ref)) != 1) {
+stop("Error different ID_REF for samples")
+} else if (is.null((unlist(unique(id_ref))))) {
+stop("NO GSM data avaliable")
+} else {
+values<-do.call("cbind",lapply(s0,function(x)x$VALUE))
+colnames(values)=TAB$ID
+rownames(values)=id_ref[[1]]
+cg <-  rownames(values)
+probe <- c(cg)
+hm450.hg19 <- getPlatform(platform=platform_id, genome=genome_id)
+probe.info <- hm450.hg19[probe]
+f <- data.table(probe=names(probe.info),CHR=as.data.frame(probe.info@seqnames)$value,
+BP=as.numeric(probe.info@elementMetadata$probeStart))
+designMatrix <- model.matrix(~ TAB$Phenotype)
+DMR <- bumphunter(values, design = designMatrix,
+pos=f$BP,cutoff=cutoff,chr=f$CHR)
+MAT <- DMR$table[which(DMR$table$L>=clusterSize),]
+METH <- GRanges(seqnames=MAT$chr,
+ranges=IRanges
+(start=MAT$start,
+end=MAT$end),
+value_pos=MAT$value)
+peaks<-findOverlapsOfPeaks(probe.info,ChiPseq,maxgap=5000)
+p <- peaks$peaklist$`probe.info///ChiPseq`
+peakAnno <- annotatePeak(p, file=peakAnno)
+output_file <- annotatePeak(p, file=output_file)
+}}
+)
+a<-c(3.2,3.7,3.6,3.9,3.7,3.5,3.8,4,3.5)
+a<-c(3.2,3.7,3.6,3.9,3.7,3.5,3.8,4,3.5)
+b<-c(2.9,2.7,2,6,2.7,2.5,2.5,3.2,3.1,3.3,2.8)
+a-b
+file<-read.csv("~/Documents/SS2.csv")
+head(file)
+e
+file
+t.test(file$WBT,file$WBA)
+t.test(file$WBT,file$WBA,paired=TRUE)
+mysamples <- lapply(TAB$ID,function(x) TablegetGEO(x))
+require("GEOquery",quietly = TRUE)
+require("BiocGenerics",quietly = TRUE)
+args <- commandArgs(trailingOnly = TRUE)
+csv_file = args[1]
+#csv_file <- ("test-data/input.csv")
+TAB=read.csv(csv_file)
+if(is.null(TAB)){
+stop("Must specify input files")
+}else{
+mysamples <- lapply(TAB$ID,function(x) TablegetGEO(x))
+}
+csv_file <- ("test-data/input.csv")
+TAB=read.csv(csv_file)
+TAB
+csv_file<-("test-data/input.csv")
+TAB = read.csv(csv_file)
+TAB
+??bumphunter
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+options(warn = -1)
+#args <- commandArgs(trailingOnly = TRUE)
+#DMR = args[1]
+#annoPeakFigure = args[2]
+setwd('/Users/katarzynamurat/Desktop/galaxy/test-data')
+DMR <- ("DMR.bed")
+DMRInfo = read.table(
+DMR,
+header = FALSE,
+sep = "\t",
+stringsAsFactors = FALSE,
+quote = ""
+)
+DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
+ranges = IRanges
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
+annoPeakFigure <- ('annoPeakFigure.png')
+png(file = annoPeakFigure, width = 1500,height = 700, units = "px", bg = "white")
+genes= lapply(annotatePeak, function(i) as.data.frame(i)$geneId)
+vennplot(genes)
+dev.off()
+genes= lapply(as.list(annotatePeak), function(i) as.data.frame(i)$geneId)
+vennplot(genes)
+peakAnnoList <- lapply(DMRPeaks, annotatePeak)
+peakAnnoList
+annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
+peakAnnoList <- lapply(DMRPeaks, annotatePeak)
+peakAnnoList
+annoPeakFigure <- ('annoPeakFigure.png')
+png(file = annoPeakFigure, width = 1500,height = 700, units = "px", bg = "white")
+plotAnnoBar(peakAnno)
+dev.off()
+annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
+annoPeakFigure <- ('annoPeakFigure.png')
+png(file = annoPeakFigure, width = 1500,height = 700, units = "px", bg = "white")
+plotAnnoBar(annotatePeak)
+dev.off()
+png(file = annoPeakFigure, width = 800,height = 400, units = "px", bg = "white")
+plotAnnoBar(annotatePeak)
+dev.off()
+png(file = annoPeakFigure, width = 800,height = 400, units = "px", bg = "white", pointsize = 12)
+plotAnnoBar(annotatePeak)
+dev.off()
+annoPeakFigure <- ('annoPeakFigure.png')
+png(file = annoPeakFigure, width = 800,height = 400, units = "px", bg = "white", pointsize = 12)
+plotAnnoBar(annotatePeak)
+dev.off()
+options(warn = -1)
+args <- commandArgs(trailingOnly = TRUE)
+DMR = args[1]
+annoPeakFigure = args[2]
+DMR <- ("test-data/DMR.bed")
+DMRInfo = read.table(
+DMR,
+header = FALSE,
+sep = "\t",
+stringsAsFactors = FALSE,
+quote = ""
+)
+DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
+ranges = IRanges
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
+annoPeakFigure <- ('test-data/annoPeakFigure.png')
+png(file = annoPeakFigure,
+width = 1200,
+height = 600)
+plotAnnoBar(annotatePeak)
+upsetplot(annotatePeak, vennpie = TRUE)
+dev.off()
+annoPeakFigure1 <- ('test-data/annoPeakUpset.png')
+annoPeakFigure2 <- ('test-data/annoPeakAnnoBar.png')
+png(file = annoPeakFigure1,
+width = 1200,
+height = 600)
+plotAnnoBar(annotatePeak)
+dev.off()
+png(file = annoPeakFigure2,
+width = 1200,
+height = 600)
+upsetplot(annotatePeak, vennpie = TRUE)
+dev.off()
+getwd()
+setwd("/Users/katarzynamurat/Desktop/annoPeakFigure")
+annoPeakFigure1 <- ('test-data/annoPeakUpset.png')
+annoPeakFigure2 <- ('test-data/annoPeakAnnoBar.png')
+png(file = annoPeakFigure1,
+width = 1200,
+height = 600)
+plotAnnoBar(annotatePeak)
+dev.off()
+png(file = annoPeakFigure2,
+width = 1200,
+height = 600)
+upsetplot(annotatePeak, vennpie = TRUE)
+dev.off()
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+options(warn = -1)
+DMR <- ("test-data/DMR.bed")
+DMRInfo = read.table(
+DMR,
+header = FALSE,
+sep = "\t",
+stringsAsFactors = FALSE,
+quote = ""
+)
+DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
+ranges = IRanges
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
+annoPeakFigure1 <- ('test-data/annoPeakUpset.png')
+annoPeakFigure2 <- ('test-data/annoPeakAnnoBar.png')
+png(file = annoPeakFigure1,
+width = 1200,
+height = 600)
+plotAnnoBar(annotatePeak)
+dev.off()
+png(file = annoPeakFigure2,
+width = 1200,
+height = 600)
+upsetplot(annotatePeak, vennpie = TRUE)
+dev.off()
+getwd()
Binary file annoPeakFigure/._annoPeakFigure.png has changed
--- a/annoPeakFigure/annoPeakFigure.R	Mon Feb 06 10:58:35 2017 -0500
+++ b/annoPeakFigure/annoPeakFigure.R	Tue Feb 28 05:42:05 2017 -0500
@@ -5,7 +5,8 @@
 
 args <- commandArgs(trailingOnly = TRUE)
 DMR = args[1]
-annoPeakFigure = args[2]
+annoPeakFigure1 = args[2]
+annoPeakFigure2 = args[3]
 
 #DMR <- ("test-data/DMR.bed")
 DMRInfo = read.table(
@@ -22,12 +23,22 @@
 
 annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
 
-#annoPeakFigure <- ('test-data/annoPeakFigure.png')
+#annoPeakFigure1 <- ('test-data/annoPeakUpset.png')
+#annoPeakFigure2 <- ('test-data/annoPeakAnnoBar.png')
 
-png(file = annoPeakFigure,
+png(file = annoPeakFigure1,
+    width = 1200,
+    height = 600)
+
+plotAnnoBar(annotatePeak)
+
+dev.off()
+
+png(file = annoPeakFigure2,
     width = 1200,
     height = 600)
 
 upsetplot(annotatePeak, vennpie = TRUE)
 
 dev.off()
+
Binary file annoPeakFigure/annoPeakFigure.png has changed
--- a/annoPeakFigure/annoPeakFigure.xml	Mon Feb 06 10:58:35 2017 -0500
+++ b/annoPeakFigure/annoPeakFigure.xml	Tue Feb 28 05:42:05 2017 -0500
@@ -5,14 +5,15 @@
 <stdio>
    <exit_code range="1:" />
 </stdio>
-  <command> Rscript $__tool_directory__/annoPeakFigure.R "$DMR" "$annoPeakFigure"</command>
+  <command> Rscript $__tool_directory__/annoPeakFigure.R "$DMR" "$annoPeakFigure1" "$annoPeakFigure2"</command>
   <inputs>
     <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file">
       <validator type="empty_field" message="This field is required."/>
     </param>
   </inputs>
   <outputs>
-    <data format="png" name="annoPeakFigure" label="annoPeakFigure.png"/>
+    <data format="png" name="annoPeakFigure1" label="annoPeakUpset.png"/>
+    <data format="png" name="annoPeakFigure2" label="annoPeakAnnoBar.png"/>
   </outputs>
   <tests>
     <test>
@@ -23,7 +24,8 @@
           </collection>
         </element>
         </param>
-        <output format="png" name="annoPeakFigure" label="test-data/annoPeakFigure.png"/>
+        <output format="png" name="annoPeakFigure" label="test-data/annoPeakUpset.png"/>
+        <output format="png" name="annoPeakFigure" label="test-data/annoPeakAnnoBar.png"/>
         </test>
     </tests>
   <help>
Binary file annoPeakFigure/test-data/annoPeakAnnoBar.png has changed
Binary file annoPeakFigure/test-data/annoPeakUpset.png has changed