Mercurial > repos > iuc > raceid_clustering

annotate scripts/clusterinspect.R @ 4:ee0bbc160cb1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author iuc
date Mon, 12 Aug 2019 13:00:12 -0400
parents 4ea021bd7513
children a4b734cd253b
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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
4
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2 VERSION = "0.5"
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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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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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4 args = commandArgs(trailingOnly = T)
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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6 if (length(args) != 1){
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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7 message(paste("VERSION:", VERSION))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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8 stop("Please provide the config file")
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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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()
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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16 test$side = 3
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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17 test$line = 3
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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19 do.plotting <- function(sc){
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21 sc.tmp <- sc
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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23 ## If it's a subset, we need to get clever and subset specific parts
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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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])
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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27 ## Subselect partitions for initial and final clusters
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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28 sc.tmp@cpart <- sc.tmp@cpart[cellstokeep]
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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29 sc.tmp@cluster$kpart <- sc.tmp@cluster$kpart[cellstokeep]
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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31 ## Subselect tSNE and FR data
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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32 ## - Note: no names in tsne, so we assume it follows the ndata naming
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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33 sc.tmp@tsne <- sc.tmp@tsne[colnames(sc.tmp@ndata) %in% cellstokeep,]
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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34 sc.tmp@fr <- sc.tmp@fr[cellstokeep,]
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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35 }
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37 print(plotmap(sc.tmp, final = FALSE, 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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38 print(do.call(mtext, c("Initial Clustering tSNE", test)))
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ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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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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ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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41 print(plotmap(sc.tmp, final = FALSE, fr = TRUE))
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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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42 print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test)))
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ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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43 print(plotmap(sc.tmp, final = TRUE, fr = TRUE))
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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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44 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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45 }
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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48 do.inspect.symbolmap <- function(sc){
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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49 if (!is.null(plotsym.use.typeremoveregex)){
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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50 plotsym$types = sub(plotsym.use.typeremoveregex, "", colnames(sc@ndata))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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51
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52 if (!is.null(plotsym.use.typeremoveregex.subselect)){
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53 plotsym$subset = plotsym$types[grep(plotsym.use.typeremoveregex.subselect, plotsym$types)]
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54 }
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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55 }
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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56 plotsym$fr = FALSE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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57 print(do.call(plotsymbolsmap, c(sc, plotsym)))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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58 print(do.call(mtext, c("Symbols tSNE", test)))
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59 plotsym$fr = TRUE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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60 print(do.call(plotsymbolsmap, c(sc, plotsym)))
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61 print(do.call(mtext, c("Symbols FR", test)))
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62 }
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63
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64 do.inspect.diffgene <- function(sc){
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65
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66 getSubNames <- function(lob, sc){
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67 use.names <- NULL
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68 if (!is.null(lob$manual)){
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69 use.names <- lob$manual
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70 }
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71 else if (!is.null(lob$regex)){
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72 nm <- colnames(sc@ndata)
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73 use.names <- nm[grep(lob$regex, nm)]
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74 }
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75 else if (!is.null(lob$cln)){
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76 use.names <- names(sc@cpart)[sc@cpart %in% lob$cln]
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77 }
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78 if (is.null(use.names)){
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79 stop("A or B names not given!")
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80 }
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81 return(use.names)
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82 }
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83
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84 A <- getSubNames(gfdat.A.use, sc)
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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85 B <- getSubNames(gfdat.B.use, sc)
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86
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87 fdat <- getfdata(sc, n=c(A,B))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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88 dexp <- diffexpnb(fdat, A=A, B=B)
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89 ## options for diffexpnb are mostly about DESeq, ignore
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90 plotdiffg$x = dexp
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91 print(do.call(plotdiffgenesnb, c(plotdiffg)))
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92 print(do.call(mtext, c("Diff Genes", test)))
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93 }
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94
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95
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96 do.inspect.genesofinterest <- function(sc){
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97 if (is.null(plotexp$n)){ ## No title, and one gene? Use gene name
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98 if (length(plotexp$g) == 1){
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99 plotexp$n <- plotexp$g
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100 } else {
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101 plotexp$n <- paste(plotexp$g, collapse=", ")
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102 }
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103 }
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104
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105 title <- paste(":", plotexp$n)
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106 plotexp$n <- ""
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107
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108 plotexp$logsc=FALSE; plotexp$fr = FALSE
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109 print(do.call(plotexpmap, c(sc, plotexp)))
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110 print(do.call(mtext, c(paste("tSNE", title), test)))
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111
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112 plotexp$logsc=TRUE; plotexp$fr = FALSE
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113 print(do.call(plotexpmap, c(sc, plotexp)))
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114 print(do.call(mtext, c(paste("tSNE (Log)", title), test)))
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115
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116 plotexp$logsc=FALSE; plotexp$fr = TRUE
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117 print(do.call(plotexpmap, c(sc, plotexp)))
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118 print(do.call(mtext, c(paste("FR", title), test)))
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119
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120 plotexp$logsc=TRUE; plotexp$fr = TRUE
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121 print(do.call(plotexpmap, c(sc, plotexp)))
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122 print(do.call(mtext, c(paste("FR (Log)", title), test)))
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123
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124 if (!is.null(plotmarkg$samples)){
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125 reg <- plotmarkg$samples
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126 plotmarkg$samples <- sub("(\\_\\d+)$","", colnames(sc@ndata))
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127 }
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128 print(do.call(plotmarkergenes, c(sc, plotmarkg)))
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129 }
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130
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131 sc <- in.rdat
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132
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133 pdf(out.pdf)
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134 if (perform.plotting) do.plotting(sc)
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135 if (perform.symbolmap) do.inspect.symbolmap(sc)
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136 if (perform.genesofinterest) do.inspect.genesofinterest(sc)
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137 if (perform.diffgene) do.inspect.diffgene(sc)
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138 dev.off()