Mercurial > repos > iuc > raceid_clustering

annotate scripts/clusterinspect.R @ 10:49776718ae90 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
author iuc
date Tue, 05 Nov 2024 16:33:40 +0000
parents 0bff0ee0683a
children
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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1 #!/usr/bin/env R
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2 VERSION <- "0.5" # nolint
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4 args <- commandArgs(trailingOnly = TRUE)
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6 if (length(args) != 1) {
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49776718ae90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
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7 message(paste("VERSION:", VERSION))
49776718ae90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
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8 stop("Please provide the config file")
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9 }
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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11 suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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12 source(args[1])
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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14 ## layout
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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15 test <- list()
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16 test$side <- 3
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17 test$line <- 3
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19 do.plotting <- function(sc) { # nolint
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21 sc_tmp <- sc
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23 ## If it's a subset, we need to get clever and subset specific parts
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24 if (!(is.null(plotting.cln) || is.na(plotting.cln))) {
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25 cellstokeep <- names(sc_tmp@cpart[sc_tmp@cpart %in% plotting.cln])
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27 ## Subselect partitions for initial and final clusters
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28 sc_tmp@cpart <- sc_tmp@cpart[cellstokeep]
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29 sc_tmp@cluster$kpart <- sc_tmp@cluster$kpart[cellstokeep]
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31 ## Subselect tSNE and FR data
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32 sc_tmp@tsne <- sc_tmp@tsne[colnames(sc_tmp@ndata) %in% cellstokeep, ]
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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33 sc_tmp@umap <- sc_tmp@umap[colnames(sc_tmp@ndata) %in% cellstokeep, ]
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34 sc_tmp@fr <- sc_tmp@fr[cellstokeep, ]
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35 }
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37 print(plotmap(sc_tmp, final = FALSE, fr = FALSE))
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38 print(do.call(mtext, c("Initial Clustering tSNE", test)))
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39 print(plotmap(sc_tmp, final = TRUE, fr = FALSE))
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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40 print(do.call(mtext, c("Final Clustering tSNE", test)))
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41 print(plotmap(sc_tmp, final = FALSE, um = TRUE))
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42 print(do.call(mtext, c("Initial Clustering UMAP", test)))
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43 print(plotmap(sc_tmp, final = TRUE, um = TRUE))
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44 print(do.call(mtext, c("Final Clustering UMAP", test)))
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45 print(plotmap(sc_tmp, final = FALSE, fr = TRUE))
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46 print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test)))
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47 print(plotmap(sc_tmp, final = TRUE, fr = TRUE))
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48 print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test)))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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49 }
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52 do.inspect.symbolmap <- function(sc) { # nolint
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53 if (!is.null(plotsym.use.typeremoveregex)) {
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54 plotsym$types <- sub(
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55 plotsym.use.typeremoveregex, "",
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56 colnames(sc@ndata)
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57 )
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59 if (!is.null(plotsym.use.typeremoveregex.subselect)) {
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60 plotsym$subset <- plotsym$types[grep(
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61 plotsym.use.typeremoveregex.subselect,
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62 plotsym$types
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63 )]
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64 }
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65 }
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66 plotsym$fr <- FALSE
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67 print(do.call(plotsymbolsmap, c(sc, plotsym)))
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68 print(do.call(mtext, c("Symbols tSNE", test)))
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69 plotsym$fr <- TRUE
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70 print(do.call(plotsymbolsmap, c(sc, plotsym)))
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71 print(do.call(mtext, c("Symbols FR", test)))
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72 }
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74 do.inspect.diffgene <- function(sc) { # nolint
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76 getSubNames <- function(lob, sc) { # nolint
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77 use_names <- NULL
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78 if (!is.null(lob$manual)) {
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79 use_names <- lob$manual
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80 } else if (!is.null(lob$regex)) {
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81 nm <- colnames(sc@ndata)
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82 use_names <- nm[grep(lob$regex, nm)]
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83 } else if (!is.null(lob$cln)) {
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84 use_names <- names(sc@cpart)[sc@cpart %in% lob$cln]
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85 }
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86 if (is.null(use_names)) {
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87 stop("A or B names not given!")
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88 }
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89 return(use_names)
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90 }
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91
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92 A <- getSubNames(gfdat.A.use, sc) # nolint
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93 B <- getSubNames(gfdat.B.use, sc) # nolint
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94
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95 fdat <- getfdata(sc, n = c(A, B))
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96 dexp <- diffexpnb(fdat, A = A, B = B)
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97 ## options for diffexpnb are mostly about DESeq, ignore
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98 plotdiffg$x <- dexp
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99 print(do.call(plotdiffgenesnb, c(plotdiffg)))
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100 print(do.call(mtext, c("Diff Genes", test)))
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101 }
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102
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103
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104 do.inspect.genesofinterest <- function(sc) { # nolint
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105 if (is.null(plotexp$n)) { ## No title, and one gene? Use gene name
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106 if (length(plotexp$g) == 1) {
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107 plotexp$n <- plotexp$g
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108 } else {
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109 plotexp$n <- paste(plotexp$g, collapse = ", ")
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110 }
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111 }
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112
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113 title <- paste(":", plotexp$n)
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114 plotexp$n <- ""
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115
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116 plotexp$logsc <- FALSE
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117 plotexp$fr <- FALSE
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118 print(do.call(plotexpmap, c(sc, plotexp)))
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119 print(do.call(mtext, c(paste("tSNE", title), test)))
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120
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121 plotexp$logsc <- TRUE
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122 plotexp$fr <- FALSE
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123 print(do.call(plotexpmap, c(sc, plotexp)))
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124 print(do.call(mtext, c(paste("tSNE (Log)", title), test)))
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125
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126 plotexp$logsc <- FALSE
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127 plotexp$fr <- TRUE
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128 print(do.call(plotexpmap, c(sc, plotexp)))
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129 print(do.call(mtext, c(paste("FR", title), test)))
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130
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131 plotexp$logsc <- TRUE
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132 plotexp$fr <- TRUE
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133 print(do.call(plotexpmap, c(sc, plotexp)))
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134 print(do.call(mtext, c(paste("FR (Log)", title), test)))
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135
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136 if (!is.null(plotmarkg$samples)) {
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137 reg <- plotmarkg$samples
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138 plotmarkg$samples <- sub("(\\_\\d+)$", "", colnames(sc@ndata))
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139 }
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140 print(do.call(plotmarkergenes, c(sc, plotmarkg)))
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141 }
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142
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143 sc <- in.rdat
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144
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145 pdf(out.pdf)
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146 if (perform.plotting) do.plotting(sc)
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147 if (perform.symbolmap) do.inspect.symbolmap(sc)
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148 if (perform.genesofinterest) do.inspect.genesofinterest(sc)
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149 if (perform.diffgene) do.inspect.diffgene(sc)
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150 dev.off()