Mercurial > repos > iuc > raceid_inspectclusters

annotate scripts/cluster.R @ 10:c7ddb719554d 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 16:33:10 +0000
parents f3eb2291da05
children
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9fec5dd8fbb9 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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c7ddb719554d 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))
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8 stop("Please provide the config file")
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9 }
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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9fec5dd8fbb9 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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13 source(args[1])
9fec5dd8fbb9 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
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17 if (!is.null(filt.lbatch.regexes)) {
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18 lar <- filt.lbatch.regexes
9fec5dd8fbb9 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
c7ddb719554d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
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21 return(nn[grep(lar[[m]], nn)])
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22 })
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23 }
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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25 sc <- do.call(filterdata, c(sc, filt))
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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27 ## Get histogram metrics for library size and number of features
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28 raw_lib <- log10(colSums(as.matrix(sc@expdata)))
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29 raw_feat <- log10(colSums(as.matrix(sc@expdata) > 0))
41f34e925bd5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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30 filt_lib <- log10(colSums(as.matrix(getfdata(sc))))
41f34e925bd5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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31 filt_feat <- log10(colSums(as.matrix(getfdata(sc) > 0)))
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33 if (filt.geqone) {
41f34e925bd5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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34 filt_feat <- log10(colSums(as.matrix(getfdata(sc) >= 1))) # nolint
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35 }
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37 br <- 50
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38 par(mfrow = c(2, 2))
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39 print(hist(raw_lib, breaks = br, main = "RawData Log10 LibSize"))
41f34e925bd5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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40 print(hist(raw_feat, breaks = br, main = "RawData Log10 NumFeat"))
41f34e925bd5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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41 print(hist(filt_lib, breaks = br, main = "FiltData Log10 LibSize"))
41f34e925bd5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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42 tmp <- hist(filt_feat, breaks = br, main = "FiltData Log10 NumFeat")
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43 print(tmp)
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44 ## required, for extracting midpoint
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45 unq <- unique(filt_feat)
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46 if (length(unq) == 1) {
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47 abline(v = unq, col = "red", lw = 2)
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48 text(tmp$mids, table(filt_feat)[[1]] - 100,
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49 pos = 1,
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50 paste(10^unq, "\nFeatures\nin remaining\nCells",
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51 sep = ""
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52 ), cex = 0.8
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53 )
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54 }
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55
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56 if (filt.use.ccorrect) {
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57 par(mfrow = c(2, 2))
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58 sc <- do.call(CCcorrect, c(sc, filt.ccc))
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59 print(plotdimsat(sc, change = TRUE))
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60 print(plotdimsat(sc, change = FALSE))
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61 }
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62 return(sc)
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63 }
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64
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65 do.cluster <- function(sc) { # nolint
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66 sc <- do.call(compdist, c(sc, clust.compdist))
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67 sc <- do.call(clustexp, c(sc, clust.clustexp))
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68 if (clust.clustexp$sat) {
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69 print(plotsaturation(sc, disp = FALSE))
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70 print(plotsaturation(sc, disp = TRUE))
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71 }
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72 print(plotjaccard(sc))
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73 return(sc)
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74 }
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75
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76 do.outlier <- function(sc) { # nolint
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77 sc <- do.call(findoutliers, c(sc, outlier.findoutliers))
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78 if (outlier.use.randomforest) {
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79 sc <- do.call(rfcorrect, c(sc, outlier.rfcorrect))
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80 }
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81 print(plotbackground(sc))
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82 print(plotsensitivity(sc))
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83 print(plotoutlierprobs(sc))
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84 ## Heatmaps
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85 test1 <- list()
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86 test1$side <- 3
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87 test1$line <- 0 # 1 #3
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88
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89 x <- clustheatmap(sc, final = FALSE)
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90 print(do.call(mtext, c(paste("(Initial)"), test1)))
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91 x <- clustheatmap(sc, final = TRUE)
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92 print(do.call(mtext, c(paste("(Final)"), test1)))
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93 return(sc)
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94 }
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95
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96 do.clustmap <- function(sc) { # nolint
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97 sc <- do.call(comptsne, c(sc, cluster.comptsne))
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98 sc <- do.call(compfr, c(sc, cluster.compfr))
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99 sc <- do.call(compumap, c(sc, cluster.compumap))
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100 return(sc)
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101 }
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102
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103
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104 mkgenelist <- function(sc) {
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105 ## Layout
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106 test <- list()
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107 test$side <- 4
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108 test$line <- -2
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109 test$cex <- 0.8
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110
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111 df <- c()
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112 options(cex = 1)
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113 plot.new()
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114 lapply(unique(sc@cpart), function(n) {
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115 dg <- clustdiffgenes(sc, cl = n, pvalue = genelist.pvalue)$dg
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116
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117 dg_goi <- dg[dg$fc > genelist.foldchange, ]
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118 dg_goi_table <- head(dg_goi, genelist.tablelim)
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119 df <<- rbind(df, cbind(n, dg_goi_table))
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120
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121 goi <- head(rownames(dg_goi_table), genelist.plotlim)
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122
0
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123 print(plotmarkergenes(sc, goi))
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124 buffer <- paste(rep("", 36), collapse = " ")
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125 print(do.call(mtext, c(paste(buffer, "Cluster ", n), test)))
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126 test$line <- -1
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127 print(do.call(mtext, c(paste(buffer, "Sig. Genes"), test)))
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128 test$line <- 0
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129 print(do.call(mtext, c(paste(
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130 buffer, "(fc > ",
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131 genelist.foldchange, ")"
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132 ), test)))
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133 })
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134 write.table(df, file = out.genelist, sep = "\t", quote = FALSE)
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135 }
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136
4
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137
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138 writecellassignments <- function(sc) {
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139 dat <- sc@cluster$kpart
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140 tab <- data.frame(
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141 row.names = NULL,
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142 cells = names(dat),
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143 cluster.initial = dat,
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144 cluster.final = sc@cpart,
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145 is.outlier = names(dat) %in% sc@out$out
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146 )
4
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147
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148 write.table(tab,
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149 file = out.assignments, sep = "\t",
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150 quote = FALSE, row.names = FALSE
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151 )
4
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152 }
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153
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154
0
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155 pdf(out.pdf)
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156
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157 if (use.filtnormconf) {
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158 sc <- do.filter(sc)
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159 message(paste(
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160 " - Source:: genes:", nrow(sc@expdata),
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161 ", cells:", ncol(sc@expdata)
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162 ))
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163 message(paste(
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164 " - Filter:: genes:", nrow(as.matrix(getfdata(sc))),
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165 ", cells:", ncol(as.matrix(getfdata(sc)))
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166 ))
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167 message(paste(
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168 " :: ",
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169 sprintf("%.1f", 100 * nrow(as.matrix(
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170 getfdata(sc)
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171 )) / nrow(sc@expdata)),
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172 "% of genes remain,",
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173 sprintf("%.1f", 100 * ncol(as.matrix(
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174 getfdata(sc)
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175 )) / ncol(sc@expdata)),
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176 "% of cells remain"
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177 ))
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178 write.table(as.matrix(sc@ndata),
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179 file = out.table, col.names = NA,
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180 row.names = TRUE, sep = "\t", quote = FALSE
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181 )
0
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182 }
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183
6
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184 if (use.cluster) {
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185 par(mfrow = c(2, 2))
0
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186 sc <- do.cluster(sc)
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187
6
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188 par(mfrow = c(2, 2))
0
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189 sc <- do.outlier(sc)
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190
6
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191 par(mfrow = c(2, 2), mar = c(1, 1, 6, 1))
0
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192 sc <- do.clustmap(sc)
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193
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194 mkgenelist(sc)
4
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195 writecellassignments(sc)
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196 }
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197
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198 dev.off()
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199
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200 saveRDS(sc, out.rdat)