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annotate scripts/dropletutils.Rscript @ 3:f0de368eabca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
author iuc
date Tue, 15 Oct 2019 09:03:56 -0400
parents a8aa294401be
children cdf4443d5625
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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")
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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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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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"))
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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16 }
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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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 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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21
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f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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22 determineGeneIDs <- function(object){
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23 if (!is.null(rowData(object)$Symbol)){
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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24 return(rowData(object)$Symbol)
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25 }
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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26 return(rownames(object))
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27 }
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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29 getCounts <- function(object){
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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30 return(Matrix(counts(object), sparse=TRUE))
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31 }
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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33 writeOut <- function(object, fileout, typeout){
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34 if (typeout == "tsv"){
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35 writeTSV(fileout, getCounts(object))
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36 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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37 else if (typeout == "h5ad"){
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38 write10xCounts(fileout, getCounts(object),
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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39 type="HDF5",
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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40 gene.symbol=determineGeneIDs(object),
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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41 overwrite=TRUE)
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42 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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43 else if (typeout == "directory"){
3
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44 write10xCounts(fileout, getCounts(object),
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
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45 type="sparse",
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46 gene.symbol=determineGeneIDs(object),
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47 overwrite=TRUE)
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48 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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49 }
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51 read10xFiles <- function(filein, typein){
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52 sce <- NULL
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53 if (typein == "tsv"){
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54 ## Exploding memory problems occured here
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55 ## - 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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56 sce <- SingleCellExperiment(assays = list(counts = readSparseCounts(filein)))
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57 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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58 else if (typein == "h5ad"){
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59 sce <- read10xCounts(filein, col.names=T, type="HDF5") # use barcodes.tsv as column names
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60 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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61 else if (typein == "directory"){
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62 sce <- read10xCounts(filein, col.names=T, type="sparse")
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63 }
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64 counts(sce) <- setSparse(counts(sce))
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65 return(sce)
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66 }
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67
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68
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69 ## Methods
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72 doEmptyDrops <- function(files, eparams, in.type="directory", out.type="h5ad", fdr_threshold = 0.01){
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73 sce <- read10xFiles(files$infile, in.type)
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74
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75 eparams$... <- NULL ## hack
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76 eparams$m = Matrix(counts(sce), sparse=TRUE)
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77
0
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78 e.out <- do.call(emptyDrops, c(eparams))
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79
0
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80 bar.names <- colnames(sce)
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81 if (length(bar.names) != nrow(e.out)){
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82 stop("Length of barcodes and output metrics don't match.")
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83 }
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84 e.out <- cbind(bar.names, e.out)
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85 e.out$is.Cell <- e.out$FDR <= fdr_threshold
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86 e.out$is.CellAndLimited <- e.out$is.Cell & e.out$Limited
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87
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88 ## Write to Plot
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89 e.out$is.Cell[is.na(e.out$is.Cell)] <- FALSE
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90 xlim.dat <- e.out[complete.cases(e.out),]$Total
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91
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92 ## Write to table
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93 writeTSV(files$table, e.out[complete.cases(e.out),])
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94
0
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95 png(files$plot)
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96 plot(e.out$Total, -e.out$LogProb, col=ifelse(e.out$is.Cell, "red", "black"),
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97 xlab="Total UMI count", ylab="-Log Probability",
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98 xlim=c(min(xlim.dat),max(xlim.dat)))
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99 dev.off()
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100
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101 ## Filtered
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102 called <- NULL
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103 if (fdr_threshold != 0){
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104 called <- e.out$is.CellAndLimited
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105 } else {
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106 called <- e.out$is.Cell
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107 }
0
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108 called[is.na(called)] <- FALSE # replace NA's with FALSE
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109 sce.filtered <- sce[,called]
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110
3
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111 writeOut(sce.filtered, files$out, out.type)
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112
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113 message(paste("Cells:", sum(na.omit(e.out$is.Cell))))
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114 message(paste("Cells and Limited:", sum(na.omit(e.out$is.CellAndLimited))))
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115 }
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116
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117
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118 doDefaultDrops <- function(files, dparams, in.type="directory", out.type="h5ad"){
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119 sce <- read10xFiles(files$infile, in.type)
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120
1
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121 dparams$m = counts(sce)
0
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122 called <- do.call(defaultDrops, c(dparams))
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123
0
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124 # Filtered
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125 sce.filtered <- sce[,called]
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126
3
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127 writeOut(sce.filtered, files$out, out.type)
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128
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129 message(paste("Cells:", sum(called)))
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130 }
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131
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132
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133 doBarcodeRankings <- function(files, bparams, in.type="directory"){
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134 sce <- read10xFiles(files$infile, in.type)
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135
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136 bparams$... <- NULL ## hack
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137 bparams$m = counts(sce)
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138
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139 br.out <- do.call(barcodeRanks, c(bparams))
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140
0
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141 png(files$plot)
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142 plot(br.out$rank, br.out$total, log="xy", xlab="(log) Rank", ylab="(log) Total Number of Barcodes")
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143 o <- order(br.out$rank)
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144 lines(br.out$rank[o], br.out$fitted[o], col="red")
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145
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146 abline(h=br.out$knee, col="dodgerblue", lty=2)
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147 abline(h=br.out$inflection, col="forestgreen", lty=2)
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148 legend("bottomleft", lty=2, col=c("dodgerblue", "forestgreen"), legend=c("knee", "inflection"))
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149 dev.off()
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150
0
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151 print(paste("knee =", br.out$knee, ", inflection = ", br.out$inflection))
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152 }
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153
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154 ## Main
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155 set.seed(seed.val)
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156
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157 if (do.method == "barcodeRankings") {
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158 doBarcodeRankings(files, bparams, in.type)
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159
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160 } else if (do.method == "defaultDrops") {
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161 doDefaultDrops(files, dparams, in.type, out.type)
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162
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163 } else if (do.method == "emptyDrops") {
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164 doEmptyDrops(files, eparams, in.type, out.type, empty.fdr_threshold)
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165 }