diff galaxy/stat_anova/abims_anova.r @ 2:b6298c38e53f draft

planemo upload commit b931b0c4ca182ea28a9ed1365bece9b2326fd64c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy/stat_anova/abims_anova.r	Mon Mar 28 15:49:04 2016 -0400
@@ -0,0 +1,132 @@
+#!/usr/local/public/bin/Rscript
+# version="1.1"
+
+# date: 06-06-2012
+# update: 18-02-2014
+# **Authors** Gildas Le Corguille  ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr 
+
+# abims_anova.r version 20140218
+
+library(batch)
+
+
+# function avova
+anova = function (file, sampleinfo, mode="column", condition=1, interaction=F, method="BH", threshold=0.01, selection_method="intersection", sep=";", dec=".", outputdatapvalue="anova.data.output", outputdatafiltered="anova.datafiltered.output") {
+	
+ 
+	if (sep=="tabulation") sep="\t"
+    	if (sep=="semicolon") sep=";"
+    	if (sep=="comma") sep=","
+
+	anova_formula_operator = "+"
+	if (interaction) anova_formula_operator = "*"
+  
+  	# -- import --
+	data=read.table(file, header = TRUE, row.names=1, sep = sep, quote="\"", dec = dec, fill = TRUE, comment.char="",na.strings = "NA")
+	
+  	if (mode == "row") data=t(data)
+	
+	sampleinfoTab=read.table(sampleinfo, header = TRUE, row.names=1, sep = sep, quote="\"")
+	rownames(sampleinfoTab) = make.names(rownames(sampleinfoTab))
+
+	
+	# -- group --
+	match_data_sampleinfoTab = match(rownames(data),rownames(sampleinfoTab))
+	if (sum(is.na(match_data_sampleinfoTab)) > 0) {
+	  write("ERROR: There is a problem during to match sample names from the data matrix and from the sample info (presence of NA).", stderr())
+	  write("You may need to use change the mode (column/row)", stderr())
+	  write("10 first sample names in the data matrix:", stderr())
+	  write(head(colnames(data)), stderr())
+	  write("10 first sample names in the sample info:", stderr())
+	  write(head(rownames(sampleinfoTab)), stderr())
+	  quit("no",status=10)
+	}
+  
+	
+	# -- anova --
+  
+  	# formula
+	grps=list()
+	anova_formula_s = "data ~ "
+	cat("\ncontrasts:\n")
+	for (i in 1:length(condition)) {
+	  grps[[i]] = factor(sampleinfoTab[,condition[i]][match_data_sampleinfoTab])
+	  anova_formula_s = paste(anova_formula_s, "grps[[",i,"]]",anova_formula_operator, sep="")
+	  cat(condition[i],"\t",levels(grps[[i]]),"\n")
+	# write("Current groups: ", stderr())
+	# write(grp[[i]], stderr())
+	}
+	anova_formula_s = substr(anova_formula_s, 1, nchar(anova_formula_s)-1)
+	anova_formula = as.formula(anova_formula_s)
+
+
+	
+	# anova
+	manovaObjectList = manova(anova_formula)
+	manovaList = summary.aov(manovaObjectList)
+	
+  	# condition renaming
+	manovaRownames = gsub(" ","",rownames(manovaList[[1]]))
+	manovaNbrPvalue = length(manovaRownames)-1
+	manovaRownames = manovaRownames[-(manovaNbrPvalue+1)]
+	
+	for (i in 1:length(condition)) {
+	  manovaRownames = sub(paste("grps\\[\\[",i,"\\]\\]",sep=""),condition[i],manovaRownames)
+  	  anova_formula_s = sub(paste("grps\\[\\[",i,"\\]\\]",sep=""),condition[i],anova_formula_s)
+	}
+
+  	# log
+  	cat("\nanova_formula",anova_formula_s,"\n")
+	
+	# p-value
+	aovPValue = sapply(manovaList,function(x){x[-(manovaNbrPvalue+1),5]})
+	if(length(condition) == 1) aovPValue = t(aovPValue)
+	rownames(aovPValue) = paste("pvalue_",manovaRownames,sep="")
+  
+	# p-value adjusted
+	if(length(condition) == 1) {
+		aovAdjPValue = t(p.adjust(aovPValue,method=method))
+	} else {
+		aovAdjPValue = apply(aovPValue,2,p.adjust, method=method)
+	}
+	rownames(aovAdjPValue) = paste("pvalueadjusted.",method,".",manovaRownames,sep="")
+	
+	# selection
+	colSumThreshold = colSums(aovAdjPValue <= threshold)
+	if (selection_method == "intersection") {
+		datafiltered = data[,colSumThreshold == nrow(aovAdjPValue )]
+	} else {
+		datafiltered = data[,colSumThreshold != 0]
+	}
+	
+	#data=rbind(data, aovPValue, aovAdjPValue)
+	data=rbind(data, aovAdjPValue)
+
+	
+	if (mode == "row") {
+	  data=t(data)
+	  datafiltered=t(datafiltered)
+	}
+	
+	# -- output / return --
+	write.table(data, outputdatapvalue, sep=sep, quote=F, col.names = NA)
+	write.table(datafiltered, outputdatafiltered, sep=sep, quote=F, col.names = NA)
+	
+	# log 
+	cat("\nthreshold:",threshold,"\n")
+	cat("result:",nrow(datafiltered),"/",nrow(data),"\n")
+  
+	quit("no",status=0)
+}
+
+# log
+cat("ANOVA\n\n")
+cat("Arguments\n")
+args <- commandArgs(trailingOnly = TRUE)
+print(args)
+
+listArguments = parseCommandArgs(evaluate=FALSE)
+do.call(anova, listArguments)
+
+
+