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comparison GalFilter/miniTools.R @ 0:2c9afaf849ad draft

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author melpetera
date Thu, 23 Feb 2017 04:39:36 -0500
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-1:000000000000 0:2c9afaf849ad
1 #####################################################
2 # Mini tools for Galaxy scripting
3 # Coded by: M.Petera,
4 # - -
5 # R functions to use in R scripts and wrappers
6 # to make things easier (lightening code, reducing verbose...)
7 # - -
8 # V0: script structure + first functions
9 # V1: addition of functions to handle special characters in identifiers
10 #####################################################
11
12
13 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
14 # Function to call packages without printing all the verbose
15 # (only getting the essentials, like warning messages for example)
16
17 shyLib <- function(...){
18 for(i in 1:length(list(...))){
19 suppressPackageStartupMessages(library(list(...)[[i]],character.only=TRUE))
20 }
21 }
22
23 #example: shyLib("xcms","pcaMethods")
24
25
26
27 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
28 # Fonction pour sourcer les scripts R requis
29 # /!\ ATTENTION : actuellement la fonction n'est pas chargee au lancement du script,
30 # il faut donc la copier-coller dans le wrapper R pour pouvoir l'utiliser.
31
32 if(FALSE){
33 source_local <- function(...){
34 argv <- commandArgs(trailingOnly = FALSE)
35 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
36 for(i in 1:length(list(...))){
37 source(paste(base_dir, list(...)[[i]], sep="/"))
38 }
39 }
40 }
41
42 #example: source_local("filter_script.R","RcheckLibrary.R")
43
44
45
46 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
47 # Functions to stock identifiers before applying make.names() and
48 # to reinject it into final matrices
49 # Note: it reproduces the original order of datasets' identifiers
50 # - - -
51 # stockID: stocks original identifiers and original order
52 # -> needs checked data regarding table match
53 # reproduceID: reinjects original identifiers and original order into final tables
54 # -> function to be used at the very end, when exporting tables
55
56 stockID <- function(dataMatrix, Metadata, Mtype){
57 # dataMatrix = data.frame containing dataMatrix
58 # Metadata = data.frame containing sampleMetadata or variableMetadata
59 # Mtype = "sample" or "variable" depending on Metadata content
60 cname <- colnames(dataMatrix)[1]
61 # dataMatrix temporary-stock + transfo - - - -
62 if(Mtype=="sample"){
63 id.ori <- colnames(dataMatrix)[-1]
64 colnames(dataMatrix) <- make.names(colnames(dataMatrix))
65 }
66 if(Mtype=="variable"){
67 id.ori <- dataMatrix[,1]
68 dataMatrix[,1] <- make.names(dataMatrix[,1])
69 }
70 # global stock - - - - - - - - - - - - - - - -
71 id.new <- data.frame(order.ori=c(1:length(Metadata[,1])),Metadata[,1],
72 id.new=make.names(Metadata[,1]),id.ori,
73 id.new.DM=make.names(id.ori),stringsAsFactors=FALSE)
74 colnames(id.new)[c(2,4)] <- c(colnames(Metadata)[1],cname)
75 # Metadata transfo + returning data - - - - -
76 Metadata[,1] <- make.names(Metadata[,1])
77 return(list(id.match=id.new, dataMatrix=dataMatrix, Metadata=Metadata))
78 }
79 #example: A<-stockID(myDM,mysM,"sample") ; myDM<-A$dataMatrix ; mysM<-A$Metadata ; A<-A$id.match
80
81 reproduceID <- function(dataMatrix, Metadata, Mtype, id.match){
82 # dataMatrix = data.frame containing dataMatrix
83 # Metadata = data.frame containing sampleMetadata or variableMetadata
84 # Mtype = "sample" or "variable" depending on Metadata content
85 # id.match = 'id.match' element produced by stockID
86 #Metadada - - - - - - - - - - - - - -
87 temp.table <- id.match[,c(1,2,3)]
88 ## Removing deleted rows
89 for(i in 1:(dim(id.match)[1])){
90 if(!(temp.table[i,3]%in%Metadata[,1])){temp.table[i,1] <- 0}
91 }
92 if(length(which(temp.table[,1]==0))!=0){
93 temp.table <- temp.table[-c(which(temp.table[,1]==0)),]
94 }
95 ## Restoring original identifiers and order
96 temp.table <- merge(x=temp.table,y=Metadata,by.x=3,by.y=1)
97 temp.table <- temp.table[order(temp.table$order.ori),]
98 Metadata <- temp.table[,-c(1,2)]
99 rownames(Metadata) <- NULL
100 #dataMatrix - - - - - - - - - - - - -
101 rownames(dataMatrix)<-dataMatrix[,1]
102 if(Mtype=="sample"){
103 dataMatrix <- t(dataMatrix[,-1])
104 }
105 temp.table <- id.match[,c(1,4,5)]
106 ## Removing deleted rows
107 for(i in 1:(dim(id.match)[1])){
108 if(!(temp.table[i,3]%in%rownames(dataMatrix))){temp.table[i,1] <- 0}
109 }
110 if(length(which(temp.table[,1]==0))!=0){
111 temp.table <- temp.table[-c(which(temp.table[,1]==0)),]
112 }
113 ## Restoring original identifiers and order
114 temp.table <- merge(x=temp.table,y=dataMatrix,by.x=3,by.y=0)
115 temp.table <- temp.table[order(temp.table$order.ori),]
116 if(Mtype=="variable"){
117 dataMatrix <- temp.table[,-c(1,2,4)]
118 colnames(dataMatrix)[1] <- colnames(id.match)[4]
119 } else {
120 rownames(temp.table) <- temp.table[,3]
121 temp.table <- t(temp.table[,-c(1,2,3)])
122 dataMatrix <- data.frame(rownames(temp.table),temp.table)
123 colnames(dataMatrix)[1] <- colnames(id.match)[4]
124 }
125 rownames(dataMatrix) <- NULL
126 # return datasets - - - - - - - - - - -
127 return(list(dataMatrix=dataMatrix, Metadata=Metadata))
128 }
129 #example: B<-reproduceID(myDM,mysM,"sample",A) ; myDM<-B$dataMatrix ; mysM<-B$Metadata
130
131
132
133 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -