Mercurial > repos > vandelj > giant_gsea_format

annotate src/utils.R @ 1:d72f1bc5ce9e draft

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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
author vandelj
date Wed, 09 Sep 2020 10:36:26 +0000
parents 3022feec50fe
children 738ed1deed23
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3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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1 # Copyright (c) 2011-2013 Trevor L. Davis <trevor.l.davis@stanford.edu>
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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2 #
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3 # This file is free software: you may copy, redistribute and/or modify it
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4 # under the terms of the GNU General Public License as published by the
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5 # Free Software Foundation, either version 2 of the License, or (at your
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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6 # option) any later version.
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7 #
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8 # This file is distributed in the hope that it will be useful, but
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9 # WITHOUT ANY WARRANTY; without even the implied warranty of
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10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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11 # General Public License for more details.
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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12 #
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13 # You should have received a copy of the GNU General Public License
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14 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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17 #extendedDist function to correlation measure
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18 distExtended <- function(x,method) {
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19 if(method %in% c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"))return(dist(x,method = method))
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20 if(method %in% c("pearson", "spearman", "kendall"))return(as.dist(1-cor(t(x),method=method))/2)
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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21 if(method %in% c("absPearson", "absSpearman", "absKendall"))return(as.dist(1-abs(cor(t(x),method=method))))
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22 return(NULL)
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23 }
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25 ##comment function to display message and optionnaly add it to log file
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27 addComment <- function(text,addToFile=FALSE,fileName=NULL,append=TRUE,display=TRUE){
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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28 if(display)cat(paste(c(text,"\n"),collapse = " "))
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29 if(addToFile)write(paste(text,collapse = " "),fileName,append=append)
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30 }
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32 printSessionInfo <- function(fileName=NULL,append=TRUE){
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33 addComment("[INFO]R session info :",T,fileName,display=FALSE)
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34 tempInfo=sessionInfo()
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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35 write(paste(tempInfo$R.version$version.string),fileName,append=append)
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36 write(paste("Platform",tempInfo$platform,sep = " : "),fileName,append=append)
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37 write(paste("Running under",tempInfo$running,sep = " : "),fileName,append=append)
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38 write(paste("Local variables",tempInfo$locale,sep = " : "),fileName,append=append)
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39 write(paste("Attached base packages",paste(tempInfo$basePkgs,collapse = "; "),sep = " : "),fileName,append=append)
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40 if(length(tempInfo$otherPkgs)>0){
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41 lineToPrint=""
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42 for(iPack in tempInfo$otherPkgs){
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43 lineToPrint=paste(lineToPrint,iPack$Package," ",iPack$Version,"; ",sep = "")
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44 }
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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45 write(paste("Other attached packages",lineToPrint,sep = " : "),fileName,append=append)
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46 }
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47 if(length(tempInfo$loadedOnly)>0){
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48 lineToPrint=""
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49 for(iPack in tempInfo$loadedOnly){
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50 lineToPrint=paste(lineToPrint,iPack$Package," ",iPack$Version,"; ",sep = "")
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51 }
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52 write(paste("Loaded packages",lineToPrint,sep = " : "),fileName,append=append)
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53 }
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54 }
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55
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56 ##negative of a mathematical expression
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57 negativeExpression <- function(expression){
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58 expression=gsub("\\+","_toMinus_",expression)
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59 expression=gsub("\\-","+",expression)
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60 expression=gsub("_toMinus_","-",expression)
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61 if(substr(expression,1,1)!="-" && substr(expression,1,1)!="+"){
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62 expression=paste(c("-",expression),collapse="")
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63 }
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64
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65 return(expression)
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66 }
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67
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68 #' Returns file name of calling Rscript
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69 #'
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70 #' \code{get_Rscript_filename} returns the file name of calling Rscript
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71 #' @return A string with the filename of the calling script.
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72 #' If not found (i.e. you are in a interactive session) returns NA.
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73 #'
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74 #' @export
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75 get_Rscript_filename <- function() {
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76 prog <- sub("--file=", "", grep("--file=", commandArgs(), value=TRUE)[1])
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77 if( .Platform$OS.type == "windows") {
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78 prog <- gsub("\\\\", "\\\\\\\\", prog)
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79 }
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80 prog
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81 }
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82
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83 #' Recursively sorts a list
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84 #'
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85 #' \code{sort_list} returns a sorted list
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86 #' @param unsorted_list A list.
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87 #' @return A sorted list.
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88 #' @export
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89 sort_list <- function(unsorted_list) {
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90 for(ii in seq(along=unsorted_list)) {
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91 if(is.list(unsorted_list[[ii]])) {
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vandelj
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92 unsorted_list[[ii]] <- sort_list(unsorted_list[[ii]])
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vandelj
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93 }
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94 }
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vandelj
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95 unsorted_list[sort(names(unsorted_list))]
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96 }
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97
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98
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vandelj
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99 # Multiple plot function
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vandelj
parents:
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100 #
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vandelj
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101 # ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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102 # - cols: Number of columns in layout
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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103 # - layout: A matrix specifying the layout. If present, 'cols' is ignored.
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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104 #
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vandelj
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105 # If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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106 # then plot 1 will go in the upper left, 2 will go in the upper right, and
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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107 # 3 will go all the way across the bottom.
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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108 #
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vandelj
parents:
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109 multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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110 library(grid)
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vandelj
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111
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vandelj
parents:
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112 # Make a list from the ... arguments and plotlist
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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113 plots <- c(list(...), plotlist)
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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114
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vandelj
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115 numPlots = length(plots)
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116
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vandelj
parents:
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117 # If layout is NULL, then use 'cols' to determine layout
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vandelj
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118 if (is.null(layout)) {
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vandelj
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119 # Make the panel
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vandelj
parents:
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120 # ncol: Number of columns of plots
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vandelj
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121 # nrow: Number of rows needed, calculated from # of cols
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vandelj
parents:
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122 layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
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vandelj
parents:
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123 ncol = cols, nrow = ceiling(numPlots/cols))
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vandelj
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124 }
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125
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vandelj
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126 if (numPlots==1) {
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vandelj
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127 print(plots[[1]])
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128
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vandelj
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129 } else {
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vandelj
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130 # Set up the page
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vandelj
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131 grid.newpage()
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vandelj
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132 pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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133
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vandelj
parents:
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134 # Make each plot, in the correct location
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vandelj
parents:
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135 for (i in 1:numPlots) {
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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136 # Get the i,j matrix positions of the regions that contain this subplot
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vandelj
parents:
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137 matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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138
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vandelj
parents:
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139 print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
3022feec50fe "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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140 layout.pos.col = matchidx$col))
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vandelj
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141 }
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vandelj
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142 }
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vandelj
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143 }