diff batchcorrection-57edfd3943ab/easyrlibrary-lib/miniTools.R @ 4:23314e1192d4 draft default tip

Uploaded

--- a/batchcorrection-57edfd3943ab/easyrlibrary-lib/miniTools.R	Tue May 02 09:47:22 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,133 +0,0 @@
-#####################################################
-# Mini tools for Galaxy scripting
-# Coded by: M.Petera, 
-# - -
-# R functions to use in R scripts and wrappers
-# to make things easier (lightening code, reducing verbose...)
-# - -
-# V0: script structure + first functions
-# V1: addition of functions to handle special characters in identifiers
-#####################################################
-
-
-# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
-# Function to call packages without printing all the verbose
-# (only getting the essentials, like warning messages for example)
-
-shyLib <- function(...){
-	for(i in 1:length(list(...))){
-		suppressPackageStartupMessages(library(list(...)[[i]],character.only=TRUE))
-	}
-}
-
-#example: shyLib("xcms","pcaMethods")
-
-
-
-# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
-# Fonction pour sourcer les scripts R requis
-# /!\ ATTENTION : actuellement la fonction n'est pas chargee au lancement du script,
-# il faut donc la copier-coller dans le wrapper R pour pouvoir l'utiliser. 
-
-if(FALSE){
-source_local <- function(...){
-	argv <- commandArgs(trailingOnly = FALSE)
-	base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
-	for(i in 1:length(list(...))){
-		source(paste(base_dir, list(...)[[i]], sep="/"))
-	}
-}
-}
-
-#example: source_local("filter_script.R","RcheckLibrary.R")
-
-
-
-# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
-# Functions to stock identifiers before applying make.names() and
-# to reinject it into final matrices
-# Note: it reproduces the original order of datasets' identifiers
-# - - -
-# stockID: stocks original identifiers and original order
-# -> needs checked data regarding table match
-# reproduceID: reinjects original identifiers and original order into final tables
-# -> function to be used at the very end, when exporting tables
-
-stockID <- function(dataMatrix, Metadata, Mtype){
-  # dataMatrix = data.frame containing dataMatrix
-  # Metadata = data.frame containing sampleMetadata or variableMetadata
-  # Mtype = "sample" or "variable" depending on Metadata content
-  cname <- colnames(dataMatrix)[1]
-      # dataMatrix temporary-stock + transfo - - - -
-  if(Mtype=="sample"){
-    id.ori <- colnames(dataMatrix)[-1] 
-    colnames(dataMatrix) <- make.names(colnames(dataMatrix)) 
-  }
-  if(Mtype=="variable"){
-    id.ori <- dataMatrix[,1] 
-    dataMatrix[,1] <- make.names(dataMatrix[,1]) 
-  }
-      # global stock - - - - - - - - - - - - - - - -
-  id.new <- data.frame(order.ori=c(1:length(Metadata[,1])),Metadata[,1],
-					   id.new=make.names(Metadata[,1]),id.ori,
-					   id.new.DM=make.names(id.ori),stringsAsFactors=FALSE)
-  colnames(id.new)[c(2,4)] <- c(colnames(Metadata)[1],cname)
-      # Metadata transfo + returning data - - - - - 
-  Metadata[,1] <- make.names(Metadata[,1]) 
-  return(list(id.match=id.new, dataMatrix=dataMatrix, Metadata=Metadata))
-}
-#example: A<-stockID(myDM,mysM,"sample") ; myDM<-A$dataMatrix ; mysM<-A$Metadata ; A<-A$id.match
-
-reproduceID <- function(dataMatrix, Metadata, Mtype, id.match){
-  # dataMatrix = data.frame containing dataMatrix
-  # Metadata = data.frame containing sampleMetadata or variableMetadata
-  # Mtype = "sample" or "variable" depending on Metadata content
-  # id.match = 'id.match' element produced by stockID
-      #Metadada - - - - - - - - - - - - - - 
-  temp.table <- id.match[,c(1,2,3)]
-  ## Removing deleted rows
-  for(i in 1:(dim(id.match)[1])){
-	if(!(temp.table[i,3]%in%Metadata[,1])){temp.table[i,1] <- 0}
-  }
-  if(length(which(temp.table[,1]==0))!=0){
-	temp.table <- temp.table[-c(which(temp.table[,1]==0)),]
-  }
-  ## Restoring original identifiers and order
-  temp.table <- merge(x=temp.table,y=Metadata,by.x=3,by.y=1)
-  temp.table <- temp.table[order(temp.table$order.ori),]
-  Metadata <- temp.table[,-c(1,2)]
-  rownames(Metadata) <- NULL
-      #dataMatrix - - - - - - - - - - - - - 
-  rownames(dataMatrix)<-dataMatrix[,1]
-  if(Mtype=="sample"){
-    dataMatrix <- t(dataMatrix[,-1])
-  }
-  temp.table <- id.match[,c(1,4,5)]
-  ## Removing deleted rows
-  for(i in 1:(dim(id.match)[1])){
-	if(!(temp.table[i,3]%in%rownames(dataMatrix))){temp.table[i,1] <- 0}
-  }
-  if(length(which(temp.table[,1]==0))!=0){
-	temp.table <- temp.table[-c(which(temp.table[,1]==0)),]
-  }
-  ## Restoring original identifiers and order
-  temp.table <- merge(x=temp.table,y=dataMatrix,by.x=3,by.y=0)
-  temp.table <- temp.table[order(temp.table$order.ori),]
-  if(Mtype=="variable"){
-	dataMatrix <- temp.table[,-c(1,2,4)]
-	colnames(dataMatrix)[1] <- colnames(id.match)[4]
-  } else {
-	rownames(temp.table) <- temp.table[,3]
-	temp.table <- t(temp.table[,-c(1,2,3)])
-	dataMatrix <- data.frame(rownames(temp.table),temp.table)
-	colnames(dataMatrix)[1] <- colnames(id.match)[4]
-  }
-  rownames(dataMatrix) <- NULL
-      # return datasets - - - - - - - - - - - 
-  return(list(dataMatrix=dataMatrix, Metadata=Metadata))
-}
-#example: B<-reproduceID(myDM,mysM,"sample",A) ; myDM<-B$dataMatrix ; mysM<-B$Metadata
-
-
-
-# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -