Mercurial > repos > iuc > scater_normalize

annotate scater-create-qcmetric-ready-sce.R @ 0:87757f7b9974 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author iuc
date Thu, 18 Jul 2019 11:13:05 -0400
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87757f7b9974 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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1 #!/usr/bin/env Rscript
87757f7b9974 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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2 #Creates a SingleCellExperiment object, which scater's calculateQCMetrics already applied
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3
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4 library(optparse)
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5 library(workflowscriptscommon)
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6 library(scater)
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7 library(LoomExperiment)
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8
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9 # parse options
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10 #SCE-specific options
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11 option_list = list(
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12 make_option(
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13 c("-a", "--counts"),
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14 action = "store",
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15 default = NA,
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16 type = 'character',
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17 help = "A tab-delimited expression matrix. The first column of all files is assumed to be feature names and the first row is assumed to be sample names."
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18 ),
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19 make_option(
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20 c("-r", "--row-data"),
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21 action = "store",
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22 default = NULL,
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23 type = 'character',
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24 help = "Path to TSV (tab-delimited) format file describing the features. Row names from the expression matrix (-a), if present, become the row names of the SingleCellExperiment."
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25 ),
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26 make_option(
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27 c("-c", "--col-data"),
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28 action = "store",
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29 default = NULL,
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30 type = 'character',
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31 help = "Path to TSV format file describing the samples (annotation). The number of rows (samples) must equal the number of columns in the expression matrix."
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32 ),
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33 #The scater-specific options
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34 make_option(
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35 c("--assay-name"),
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36 action = "store",
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37 default = 'counts',
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38 type = 'character',
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39 help= "String specifying the name of the 'assay' of the 'object' that should be used to define expression."
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40 ),
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41 make_option(
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42 c("-f", "--mt-controls"),
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43 action = "store",
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44 default = NULL,
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45 type = 'character',
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46 help = "Path to file containing a list of the mitochondrial control genes"
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47 ),
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48 make_option(
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49 c("-p", "--ercc-controls"),
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50 action = "store",
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51 default = NULL,
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52 type = 'character',
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53 help = "Path to file containing a list of the ERCC controls"
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54 ),
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55 make_option(
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56 c("-l", "--cell-controls"),
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57 action = "store",
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58 default = NULL,
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59 type = 'character',
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60 help = "Path to file (one cell per line) to be used to derive a vector of cell (sample) names used to identify cell controls (for example, blank wells or bulk controls)."
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61 ),
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62 make_option(
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63 c("-o", "--output-loom"),
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64 action = "store",
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65 default = NA,
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66 type = 'character',
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67 help = "File name in which to store the SingleCellExperiment object in Loom format."
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68 )
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69 )
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70
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71 opt <- wsc_parse_args(option_list, mandatory = c('counts', 'output_loom'))
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72
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73 # Read the expression matrix
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74
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75 counts <- wsc_split_string(opt$counts)
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76 reads <- read.table(counts)
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77
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78 # Read row and column annotations
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79
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80 rowdata <- opt$row_data
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81
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82 if ( ! is.null(opt$row_data) ){
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83 rowdata <- read.delim(opt$row_data)
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84 }
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85
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86 coldata <- opt$col_data
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87
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88 if ( ! is.null(opt$col_data) ){
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89 coldata <- read.delim(opt$col_data)
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90 }
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91
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92 # Now build the object
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93 assays <- list(as.matrix(reads))
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94 names(assays) <- c(opt$assay_name)
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95 scle <- SingleCellLoomExperiment(assays = assays, colData = coldata, rowData = rowdata)
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96 # Define spikes (if supplied)
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97
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98
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99 #Scater options
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100
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101 # Check feature_controls (only mitochondrial and ERCC used for now)
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102 feature_controls_list = list()
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103 if (! is.null(opt$mt_controls) && opt$mt_controls != 'NULL'){
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104 if (! file.exists(opt$mt_controls)){
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105 stop((paste('Supplied feature_controls file', opt$mt_controls, 'does not exist')))
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106 } else {
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107 mt_controls <- readLines(opt$mt_controls)
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108 feature_controls_list[["MT"]] <- mt_controls
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109 }
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110 }
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111
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112 if (! is.null(opt$ercc_controls) && opt$ercc_controls != 'NULL'){
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113 if (! file.exists(opt$ercc_controls)){
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114 stop((paste('Supplied feature_controls file', opt$ercc_controls, 'does not exist')))
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115 } else {
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116 ercc_controls <- readLines(opt$ercc_controls)
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117 feature_controls_list[["ERCC"]] <- ercc_controls
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118 }
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119 } else {
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120 ercc_controls <- character()
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121 }
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122
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123 # Check cell_controls
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124 cell_controls_list <- list()
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125 if (! is.null(opt$cell_controls) && opt$cell_controls != 'NULL'){
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126 if (! file.exists(opt$cell_controls)){
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127 stop((paste('Supplied feature_controls file', opt$cell_controls, 'does not exist')))
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128 } else {
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129 cell_controls <- readLines(opt$cell_controls)
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130 cell_controls_list[["empty"]] <- cell_controls
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131 }
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132 }
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133
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134
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135 # calculate QCMs
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136 scle <- calculateQCMetrics(scle, exprs_values = opt$assay_name, feature_controls = feature_controls_list, cell_controls = cell_controls_list)
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137
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138 # Output to a Loom file
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139 if (file.exists(opt$output_loom)) {
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140 file.remove(opt$output_loom)
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141 }
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142 export(scle, opt$output_loom, format='loom')