Mercurial > repos > iuc > raceid_clustering

annotate scripts/cluster.R @ 6:a4b734cd253b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
author iuc
date Thu, 15 Apr 2021 18:58:21 +0000
parents ee0bbc160cb1
children 0bff0ee0683a
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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 = T)
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6 if (length(args) != 1) {
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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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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)))
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12 ## suppressWarnings(suppressPackageStartupMessages(require(scran))) # nolint
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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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13 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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16 do.filter <- function(sc) { # nolint
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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17 if (!is.null(filt.lbatch.regexes)) {
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18 lar <- filt.lbatch.regexes
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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19 nn <- colnames(sc@expdata)
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20 filt$LBatch <- lapply(1:length(lar), function(m) { # nolint
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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21 return(nn[grep(lar[[m]], nn)])})
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22 }
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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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24 sc <- do.call(filterdata, c(sc, filt))
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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26 ## Get histogram metrics for library size and number of features
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27 raw_lib <- log10(colSums(as.matrix(sc@expdata)))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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28 raw_feat <- log10(colSums(as.matrix(sc@expdata) > 0))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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29 filt_lib <- log10(colSums(as.matrix(getfdata(sc))))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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30 filt_feat <- log10(colSums(as.matrix(getfdata(sc) > 0)))
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32 if (filt.geqone) {
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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33 filt_feat <- log10(colSums(as.matrix(getfdata(sc) >= 1))) # nolint
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34 }
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36 br <- 50
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37 par(mfrow = c(2, 2))
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38 print(hist(raw_lib, breaks = br, main = "RawData Log10 LibSize"))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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39 print(hist(raw_feat, breaks = br, main = "RawData Log10 NumFeat"))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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40 print(hist(filt_lib, breaks = br, main = "FiltData Log10 LibSize"))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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41 tmp <- hist(filt_feat, breaks = br, main = "FiltData Log10 NumFeat")
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42 print(tmp)
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43 ## required, for extracting midpoint
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44 unq <- unique(filt_feat)
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45 if (length(unq) == 1) {
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46 abline(v = unq, col = "red", lw = 2)
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47 text(tmp$mids, table(filt_feat)[[1]] - 100, pos = 1,
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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48 paste(10^unq, "\nFeatures\nin remaining\nCells",
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49 sep = ""), cex = 0.8)
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50 }
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52 if (filt.use.ccorrect) {
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53 par(mfrow = c(2, 2))
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54 sc <- do.call(CCcorrect, c(sc, filt.ccc))
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55 print(plotdimsat(sc, change = T))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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56 print(plotdimsat(sc, change = F))
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57 }
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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58 return(sc)
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59 }
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61 do.cluster <- function(sc) { # nolint
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62 sc <- do.call(compdist, c(sc, clust.compdist))
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63 sc <- do.call(clustexp, c(sc, clust.clustexp))
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64 if (clust.clustexp$sat) {
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65 print(plotsaturation(sc, disp = F))
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66 print(plotsaturation(sc, disp = T))
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67 }
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68 print(plotjaccard(sc))
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69 return(sc)
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70 }
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72 do.outlier <- function(sc) { # nolint
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73 sc <- do.call(findoutliers, c(sc, outlier.findoutliers))
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74 if (outlier.use.randomforest) {
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75 sc <- do.call(rfcorrect, c(sc, outlier.rfcorrect))
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76 }
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77 print(plotbackground(sc))
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78 print(plotsensitivity(sc))
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79 print(plotoutlierprobs(sc))
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80 ## Heatmaps
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81 test1 <- list()
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82 test1$side <- 3
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83 test1$line <- 0 #1 #3
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84
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85 x <- clustheatmap(sc, final = FALSE)
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86 print(do.call(mtext, c(paste("(Initial)"), test1)))
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87 x <- clustheatmap(sc, final = TRUE)
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88 print(do.call(mtext, c(paste("(Final)"), test1)))
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89 return(sc)
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90 }
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91
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92 do.clustmap <- function(sc) { # nolint
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93 sc <- do.call(comptsne, c(sc, cluster.comptsne))
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94 sc <- do.call(compfr, c(sc, cluster.compfr))
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95 sc <- do.call(compumap, c(sc, cluster.compumap))
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96 return(sc)
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97 }
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98
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99
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100 mkgenelist <- function(sc) {
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101 ## Layout
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102 test <- list()
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103 test$side <- 4
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104 test$line <- -2
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105 test$cex <- 0.8
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106
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107 df <- c()
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108 options(cex = 1)
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109 plot.new()
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110 lapply(unique(sc@cpart), function(n) {
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111 dg <- clustdiffgenes(sc, cl = n, pvalue = genelist.pvalue)$dg
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112
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113 dg_goi <- dg[dg$fc > genelist.foldchange, ]
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114 dg_goi_table <- head(dg_goi, genelist.tablelim)
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115 df <<- rbind(df, cbind(n, dg_goi_table))
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116
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117 goi <- head(rownames(dg_goi_table), genelist.plotlim)
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118
0
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119 print(plotmarkergenes(sc, goi))
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120 buffer <- paste(rep("", 36), collapse = " ")
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121 print(do.call(mtext, c(paste(buffer, "Cluster ", n), test)))
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122 test$line <- -1
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123 print(do.call(mtext, c(paste(buffer, "Sig. Genes"), test)))
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124 test$line <- 0
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125 print(do.call(mtext, c(paste(buffer, "(fc > ",
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126 genelist.foldchange, ")"), test)))
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127 })
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128 write.table(df, file = out.genelist, sep = "\t", quote = F)
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129 }
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130
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131
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132 writecellassignments <- function(sc) {
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133 dat <- sc@cluster$kpart
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134 tab <- data.frame(row.names = NULL,
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135 cells = names(dat),
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136 cluster.initial = dat,
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137 cluster.final = sc@cpart,
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138 is.outlier = names(dat) %in% sc@out$out)
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139
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140 write.table(tab, file = out.assignments, sep = "\t",
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141 quote = F, row.names = F)
4
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142 }
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143
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144
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145 pdf(out.pdf)
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146
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147 if (use.filtnormconf) {
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148 sc <- do.filter(sc)
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149 message(paste(" - Source:: genes:", nrow(sc@expdata),
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150 ", cells:", ncol(sc@expdata)))
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151 message(paste(" - Filter:: genes:", nrow(as.matrix(getfdata(sc))),
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152 ", cells:", ncol(as.matrix(getfdata(sc)))))
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153 message(paste(" :: ",
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154 sprintf("%.1f", 100 * nrow(as.matrix(
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155 getfdata(sc))) / nrow(sc@expdata)),
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156 "% of genes remain,",
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157 sprintf("%.1f", 100 * ncol(as.matrix(
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158 getfdata(sc))) / ncol(sc@expdata)),
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159 "% of cells remain"))
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160 write.table(as.matrix(sc@ndata), file = out.table, col.names = NA,
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161 row.names = T, sep = "\t", quote = F)
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162 }
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163
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164 if (use.cluster) {
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165 par(mfrow = c(2, 2))
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166 sc <- do.cluster(sc)
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167
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168 par(mfrow = c(2, 2))
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169 sc <- do.outlier(sc)
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170
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171 par(mfrow = c(2, 2), mar = c(1, 1, 6, 1))
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172 sc <- do.clustmap(sc)
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173
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174 mkgenelist(sc)
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175 writecellassignments(sc)
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176 }
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177
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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178 dev.off()
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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180 saveRDS(sc, out.rdat)