Mercurial > repos > iuc > scater_plot_dist_scatter

annotate scater-manual-filter.R @ 2:81e5bdff4853 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
author iuc
date Thu, 09 Sep 2021 12:23:33 +0000
parents 2e41b35b5bdd
children
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1 #!/usr/bin/env Rscript
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2 # Manually filter SingleCellExperiment with user-defined parameters
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3
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4 # Load optparse we need to check inputs
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5 library(optparse)
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6 library(workflowscriptscommon)
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7 library(LoomExperiment)
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8 library(scater)
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9
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10 # parse options
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11 option_list <- list(
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12 make_option(
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13 c("-i", "--input-loom"),
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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 SingleCellExperiment object file in Loom format"
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18 ),
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19 make_option(
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20 c("-l", "--library-size"),
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21 action = "store",
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22 default = 0,
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23 type = "numeric",
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24 help = "Minimum library size (mapped reads) to filter cells on"
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25 ),
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26 make_option(
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27 c("-m", "--percent-counts-MT"),
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28 action = "store",
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29 default = 100,
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30 type = "numeric",
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31 help = "Maximum % of mitochondrial genes expressed per cell. Cells that exceed this value will be filtered out"
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32 ),
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33 make_option(
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34 c("-f", "--expressed-features"),
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35 action = "store",
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36 default = 100,
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37 type = "numeric",
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38 help = "Remove cells that have less than the given number of expressed features"
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39 ),
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40 make_option(
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41 c("-d", "--detection-limit"),
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42 action = "store",
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43 default = 0,
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44 type = "numeric",
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45 help = "Number of reads mapped to a feature above which it to be deemed as expressed"
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46 ),
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47 make_option(
2
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48 c("-e", "--min-cells-expressed"),
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49 action = "store",
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50 default = 0,
2
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51 type = "numeric",
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52 help = "Remove features that occur in less than the given number of cells"
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53 ),
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54 make_option(
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55 c("-o", "--output-loom"),
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56 action = "store",
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57 default = NA,
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58 type = "character",
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59 help = "File name in which to store the SingleCellExperiment object in Loom format"
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60 )
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61 )
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62
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63 opt <- wsc_parse_args(option_list, mandatory = c("input_loom", "output_loom"))
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64
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65 # Check parameter values
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66
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67 if (! file.exists(opt$input_loom)) {
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68 stop((paste("File", opt$input_loom, "does not exist")))
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69 }
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70
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71 # Filter out unexpressed features
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72
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73 sce <- import(opt$input_loom, format = "loom", type = "SingleCellLoomExperiment")
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74 print(paste("Starting with", ncol(sce), "cells and", nrow(sce), "features."))
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75
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76 # Filter out low quality cells
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77
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78 # Filter low library sizes
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79 passing_total <- sce$total > opt$library_size
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80 sce <- sce[, passing_total]
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81 print(paste("After filtering out low library counts: ", ncol(sce), "cells and", nrow(sce), "features."))
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82
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83 # Filter out high MT counts
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84 passing_mt_counts <- sce$subsets_Mito_percent < opt$percent_counts_MT
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85 sce <- sce[, passing_mt_counts]
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86 print(paste("After filtering out high MT gene counts: ", ncol(sce), "cells and", nrow(sce), "features."))
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87
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88 expr_features <- sce$detected > opt$expressed_features
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89 sce <- sce[, expr_features]
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90 print(paste("After filtering out cells with low feature counts: ", ncol(sce), "cells and", nrow(sce), "features."))
81e5bdff4853 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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91
81e5bdff4853 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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92 # Create a logical vector of features that are expressed (above detection_limit)
81e5bdff4853 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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93 feature_expressed <- nexprs(sce, detection_limit = opt$detection_limit, byrow = TRUE) > opt$min_cells_expressed
81e5bdff4853 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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94 sce <- sce[feature_expressed, ]
81e5bdff4853 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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95 print(paste("After filtering out rare features: ", ncol(sce), "cells and", nrow(sce), "features."))
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4887c4c69847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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96
4887c4c69847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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97 # Output to a Loom file
4887c4c69847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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98 if (file.exists(opt$output_loom)) {
4887c4c69847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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99 file.remove(opt$output_loom)
4887c4c69847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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100 }
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81e5bdff4853 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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101 export(sce, opt$output_loom, format = "loom")