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annotate main.R @ 0:1fb6181c2c64 draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/naivestates commit 392f57d212a7499bf1d3e421112a32a56635bc67-dirty"
author perssond
date Fri, 12 Mar 2021 00:20:13 +0000
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1fb6181c2c64 "planemo upload for repository https://github.com/ohsu-comp-bio/naivestates commit 392f57d212a7499bf1d3e421112a32a56635bc67-dirty"
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1 #!/usr/bin/env Rscript
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2
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3 suppressMessages( library(tidyverse) )
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4 library( optparse )
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5 library( naivestates )
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6
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7 ## Identify directory of the script
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8 wd <- commandArgs( trailingOnly=FALSE ) %>%
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9 keep( ~grepl("--file=", .x) ) %>%
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10 str_replace( "--file=", "" ) %>% dirname()
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11 cat( "Running the script from", wd, "\n" )
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12
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13 ## Parse command-line arugments
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14 option_list <- list(
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15 make_option(c("-i", "--in"), type="character", help="Input file"),
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16 make_option(c("-o", "--out"), type="character", default="/data",
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17 help="Output directory"),
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18 make_option(c("-m", "--markers"), type="character", default="auto",
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19 help="Markers to model"),
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20 make_option(c("-p", "--plots"), type="character", default="off",
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21 help="Generate plots showing the fit"),
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22 make_option("--mct", type="character", default="",
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23 help="Marker -> cell type map in .csv format"),
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24 make_option("--id", type="character", default="CellID",
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25 help="Column containing cell IDs"),
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26 make_option("--log", type="character", default="auto",
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27 help="Whether to apply a log transform <yes|no|auto>"),
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28 make_option("--sfx", type="character", default="",
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29 help="Common suffix on marker columns (e.g., _cellMask)"),
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30 make_option("--umap", action="store_true", default=FALSE,
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31 help="Generate UMAP plots")
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32 )
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33 opt <- parse_args(OptionParser(option_list=option_list))
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34
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35 ## Argument verification
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36 if( !("in" %in% names(opt)) )
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37 stop( "Please provide an input file name with -i" )
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38 if( !(opt$log %in% c("yes","no","auto")) )
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39 stop( "--log must be one of <yes|no|auto>" )
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40 if( !(opt$plots %in% c("off", "pdf", "png")) )
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41 stop( "--plots must be one of <off|pdf|png>" )
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42
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43 ## Identify the sample name
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44 sn <- basename( opt$`in` ) %>% str_split( "\\." ) %>%
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45 pluck( 1, 1 )
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46 cat( "Inferred sample name:", sn, "\n" )
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47
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48 ## Read the data matrix
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49 X <- read_csv( opt$`in`, col_types=cols() )
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50 cat( "Read", nrow(X), "entries\n" )
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51
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52 ## Fix potential capitalization mismatch of --id
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53 if( !(opt$id %in% colnames(X)) )
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54 {
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55 ## Attempt to find a singular case-insensitive match
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56 i <- grep( tolower(opt$id), tolower(colnames(X)) )
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57 if( length(i) == 1 )
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58 {
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59 warning( " No such column ", opt$id,
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60 "; using ", colnames(X)[i], " instead" )
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61 opt$id <- colnames(X)[i]
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62 }
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63 else stop( "No such column ", opt$id,
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64 "; use --id to specify which column contains cell IDs" )
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65 }
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66
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67 ## Identify markers in the matrix
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68 mrkv <- findMarkers(setdiff(colnames(X), opt$id), opt$markers,
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69 opt$sfx, TRUE, TRUE)
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70
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71 ## Handle log transformation of the data
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72 if( opt$log == "yes" ||
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73 (opt$log == "auto" && max(X[mrkv], na.rm=TRUE) > 1000) )
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74 {
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75 cat( "Applying a log10 transform\n" )
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76 X <- X %>% mutate_at( unname(mrkv), ~log10(.x+1) )
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77 }
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78
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79 ## Fit Gaussian mixture models
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80 GMM <- GMMfit(X, opt$id, !!!mrkv)
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81 fnMdl <- file.path( opt$out, str_c(sn, "-models.csv") )
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82 cat( "Saving models to", fnMdl, "\n" )
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83 GMMmodels(GMM) %>% write_csv( fnMdl )
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84
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85 ## Reshape the matrix back to cells-by-marker format
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86 Y <- GMMreshape(GMM)
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87
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88 cat( "------\n" )
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89
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90 ## Find the default cell type map
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91 if( opt$mct != "" ) {
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92
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93 ## Load marker -> cell type associations
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94 cat( "Loading cell type map from", opt$mct, "\n" )
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95 mct <- read_csv( opt$mct, col_types=cols() ) %>%
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96 distinct() %>% filter(Marker %in% colnames(Y))
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97
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98 if( nrow(mct) == 0 ) {
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99 warning( "No usable marker -> cell type mappings detected" )
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100 Y <- findDominant(Y, opt$id)
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101 } else {
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102 cat( "Using the following marker -> cell type map:\n" )
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103 walk2( mct$Marker, mct$State, ~cat(.x, "->", .y, "\n") )
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104 Y <- callStates(Y, opt$id, mct)
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105 }
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106 } else {
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107 cat( "No marker -> cell type mapping provided\n" )
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108 Y <- findDominant(Y, opt$id)
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109 }
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110
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111 cat( "------\n" )
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112
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113 ## Identify the output location(s)
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114 fnOut <- file.path( opt$out, str_c(sn, "-states.csv") )
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115 cat( "Saving probabilities and calls to", fnOut, "\n")
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116 Y %>% write_csv( fnOut )
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117
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118 ## Generates plots as necessary
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119 if( opt$plots != "off" )
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120 {
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121 ## Create a separate directory for plots
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122 dirPlot <- file.path( opt$out, "plots", sn )
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123 dir.create(dirPlot, recursive=TRUE, showWarnings=FALSE)
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124
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125 ## Fit overview
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126 fn <- file.path( file.path(opt$out, "plots"), str_c(sn, "-allfits.", opt$plots) )
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127 ggf <- plotFitOverview(GMM)
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128 suppressMessages(ggsave( fn, ggf, width=12, height=8 ))
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129
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130 ## Compute a UMAP projection
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131 if( opt$umap ) {
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132 cat( "Computing a UMAP projection...\n" )
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133 U <- umap( Y, c(opt$id, "State", "Dominant") )
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134
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135 ## Generate and write a summary plot
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136 gg <- plotSummary( U )
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137 fn <- file.path( file.path(opt$out, "plots"), str_c(sn, "-summary.", opt$plots) )
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138 suppressMessages(ggsave( fn, gg, width=9, height=7 ))
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139 cat( "Plotted summary to", fn, "\n" )
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140
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141 ## Generate and write faceted probabilities plot
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142 gg <- plotProbs( U, c(opt$id, "State", "Dominant") )
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143 fn <- file.path( file.path(opt$out, "plots"), str_c(sn, "-probs.", opt$plots) )
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144 suppressMessages(ggsave( fn, gg, width=9, height=7 ))
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145 cat( "Plotted probabilities to", fn, "\n" )
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146 }
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147
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148 ## Generate and write out plots for individual marker fits
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149 for( i in names(mrkv) )
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150 {
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151 gg <- plotMarker(GMM, i)
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152 fn <- file.path( dirPlot, str_c(i,".",opt$plots) )
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153 suppressMessages(ggsave( fn, gg ))
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154 cat( "Wrote", fn, "\n" )
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155 }
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156 }