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annotate scripts/dropletutils.Rscript @ 2:a8aa294401be draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
author iuc
date Fri, 06 Sep 2019 10:56:16 -0400
parents cfe1e6c28d95
children f0de368eabca
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4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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1 ## Load in data
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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2 args = commandArgs(trailingOnly = T)
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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3 if (length(args) != 1){
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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4 stop("Please provide the config file")
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5 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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7 suppressWarnings(suppressPackageStartupMessages(require(DropletUtils)))
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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8 suppressWarnings(suppressPackageStartupMessages(require(Matrix)))
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cfe1e6c28d95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 40d4a92c62d75fe931baba8657cde006a26d84cf"
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9 suppressWarnings(suppressPackageStartupMessages(require(scater)))
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4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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11 source(args[1])
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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13 ## Helper functions
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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14 setSparse <- function(obj){
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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15 return(as(obj, "dgCMatrix"))
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16 }
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18 writeTSV <- function(fileout, obj){
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19 write.table(as.matrix(obj), file=fileout, col.names=NA, sep='\t', quote=FALSE)
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20 }
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22 writeOut <- function(counts, fileout, typeout){
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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23 if (typeout == "tsv"){
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24 writeTSV(fileout, counts)
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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25 }
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26 else if (typeout == "h5ad"){
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27 write10xCounts(fileout, counts, type="HDF5", overwrite=TRUE)
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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28 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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29 else if (typeout == "directory"){
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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30 write10xCounts(fileout, counts, type="sparse", overwrite=TRUE)
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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31 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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32 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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35 read10xFiles <- function(filein, typein){
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36 sce <- NULL
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37 if (typein == "tsv"){
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38 ## Exploding memory problems occured here
cfe1e6c28d95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 40d4a92c62d75fe931baba8657cde006a26d84cf"
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39 ## - solution is to use the readSparseCounts function from scater
cfe1e6c28d95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 40d4a92c62d75fe931baba8657cde006a26d84cf"
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40 sce <- SingleCellExperiment(assays = list(counts = readSparseCounts(filein)))
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41 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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42 else if (typein == "h5ad"){
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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43 sce <- read10xCounts(filein, col.names=T, type="HDF5") # use barcodes.tsv as column names
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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44 }
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45 else if (typein == "directory"){
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46 sce <- read10xCounts(filein, col.names=T, type="sparse")
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47 }
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48 counts(sce) <- setSparse(counts(sce))
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49 return(sce)
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50 }
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53 ## Methods
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56 doEmptyDrops <- function(files, eparams, in.type="directory", out.type="h5ad", fdr_threshold = 0.01){
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57 sce <- read10xFiles(files$infile, in.type)
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59 eparams$... <- NULL ## hack
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60 eparams$m = Matrix(counts(sce), sparse=TRUE)
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61
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62 e.out <- do.call(emptyDrops, c(eparams))
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64 bar.names <- colnames(sce)
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65 if (length(bar.names) != nrow(e.out)){
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66 stop("Length of barcodes and output metrics don't match.")
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67 }
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68 e.out <- cbind(bar.names, e.out)
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69 e.out$is.Cell <- e.out$FDR <= fdr_threshold
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70 e.out$is.CellAndLimited <- e.out$is.Cell & e.out$Limited
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71
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72 ## Write to Plot
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73 e.out$is.Cell[is.na(e.out$is.Cell)] <- FALSE
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74 xlim.dat <- e.out[complete.cases(e.out),]$Total
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75
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76 ## Write to table
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77 writeTSV(files$table, e.out[complete.cases(e.out),])
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78
0
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79 png(files$plot)
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80 plot(e.out$Total, -e.out$LogProb, col=ifelse(e.out$is.Cell, "red", "black"),
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81 xlab="Total UMI count", ylab="-Log Probability",
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82 xlim=c(min(xlim.dat),max(xlim.dat)))
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83 dev.off()
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84
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85 ## Filtered
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86 called <- NULL
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87 if (fdr_threshold != 0){
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88 called <- e.out$is.CellAndLimited
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89 } else {
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90 called <- e.out$is.Cell
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91 }
0
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92 called[is.na(called)] <- FALSE # replace NA's with FALSE
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93 sce.filtered <- sce[,called]
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94
0
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95 writeOut(counts(sce.filtered), files$out, out.type)
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96
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97 message(paste("Cells:", sum(na.omit(e.out$is.Cell))))
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98 message(paste("Cells and Limited:", sum(na.omit(e.out$is.CellAndLimited))))
0
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99 }
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100
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101
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102 doDefaultDrops <- function(files, dparams, in.type="directory", out.type="h5ad"){
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103 sce <- read10xFiles(files$infile, in.type)
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104
1
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105 dparams$m = counts(sce)
0
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106 called <- do.call(defaultDrops, c(dparams))
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107
0
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108 # Filtered
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109 sce.filtered <- sce[,called]
2
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110
0
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111 writeOut(Matrix(counts(sce.filtered),sparse=TRUE), files$out, out.type)
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112
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113 message(paste("Cells:", sum(called)))
0
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114 }
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115
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116
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117 doBarcodeRankings <- function(files, bparams, in.type="directory"){
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118 sce <- read10xFiles(files$infile, in.type)
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119
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120 bparams$... <- NULL ## hack
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121 bparams$m = counts(sce)
0
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122
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123 br.out <- do.call(barcodeRanks, c(bparams))
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124
0
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125 png(files$plot)
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126 plot(br.out$rank, br.out$total, log="xy", xlab="(log) Rank", ylab="(log) Total Number of Barcodes")
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127 o <- order(br.out$rank)
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128 lines(br.out$rank[o], br.out$fitted[o], col="red")
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129
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130 abline(h=br.out$knee, col="dodgerblue", lty=2)
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131 abline(h=br.out$inflection, col="forestgreen", lty=2)
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132 legend("bottomleft", lty=2, col=c("dodgerblue", "forestgreen"), legend=c("knee", "inflection"))
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133 dev.off()
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134
0
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135 print(paste("knee =", br.out$knee, ", inflection = ", br.out$inflection))
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136 }
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137
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138 ## Main
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139 set.seed(seed.val)
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140
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141 if (do.method == "barcodeRankings") {
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142 doBarcodeRankings(files, bparams, in.type)
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143
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144 } else if (do.method == "defaultDrops") {
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145 doDefaultDrops(files, dparams, in.type, out.type)
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146
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147 } else if (do.method == "emptyDrops") {
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148 doEmptyDrops(files, eparams, in.type, out.type, empty.fdr_threshold)
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149 }