Mercurial > repos > iuc > scater_plot_tsne
annotate scater-manual-filter.R @ 0:a30f4bfe8f01 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author | iuc |
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date | Tue, 03 Sep 2019 14:30:21 -0400 |
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children | 2b09ca1c5e41 |
rev | line source |
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0
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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1 #!/usr/bin/env Rscript |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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2 # Manually filter SingleCellExperiment with user-defined parameters |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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3 |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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4 # Load optparse we need to check inputs |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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5 library(optparse) |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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6 library(workflowscriptscommon) |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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7 library(LoomExperiment) |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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8 library(scater) |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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9 |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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10 # parse options |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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11 option_list = list( |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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12 make_option( |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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13 c("-i", "--input-loom"), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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14 action = "store", |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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15 default = NA, |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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16 type = 'character', |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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17 help = "A SingleCellExperiment object file in Loom format." |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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18 ), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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19 make_option( |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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20 c("-d", "--detection-limit"), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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21 action = "store", |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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22 default = 0, |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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23 type = 'numeric', |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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24 help = "Numeric scalar providing the value above which observations are deemed to be expressed" |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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25 ), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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26 make_option( |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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27 c("-l", "--library-size"), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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28 action = "store", |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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29 default = 0, |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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30 type = 'numeric', |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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31 help = "Minimum library size (mapped reads) to filter cells on" |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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32 ), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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33 make_option( |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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34 c("-e", "--expressed-genes"), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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35 action = "store", |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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36 default = 0, |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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37 type = 'numeric', |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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38 help = "Minimum number of expressed genes to filter cells on" |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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39 ), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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40 make_option( |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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41 c("-m", "--percent-counts-MT"), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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42 action = "store", |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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43 default = 100, |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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44 type = 'numeric', |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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45 help = "Maximum % of mitochondrial genes expressed per cell. Cells that exceed this value will be filtered out." |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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46 ), |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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47 make_option( |
a30f4bfe8f01
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48 c("-o", "--output-loom"), |
a30f4bfe8f01
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49 action = "store", |
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50 default = NA, |
a30f4bfe8f01
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51 type = 'character', |
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52 help = "File name in which to store the SingleCellExperiment object in Loom format." |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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53 ) |
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54 ) |
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55 |
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56 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_loom')) |
a30f4bfe8f01
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57 |
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58 # Check parameter values |
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59 |
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60 if ( ! file.exists(opt$input_loom)){ |
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61 stop((paste('File', opt$input_loom, 'does not exist'))) |
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62 } |
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63 |
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64 # Filter out unexpressed features |
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65 |
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66 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment') |
a30f4bfe8f01
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67 print(paste("Starting with", ncol(scle), "cells and", nrow(scle), "features.")) |
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68 |
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69 # Create a logical vector of features that are expressed (above detection_limit) |
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70 feature_expressed <- nexprs(scle, detection_limit = opt$detection_limit, exprs_values = 1, byrow=TRUE) > 0 |
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71 scle <- scle[feature_expressed, ] |
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72 |
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73 print(paste("After filtering out unexpressed features: ", ncol(scle), "cells and", nrow(scle), "features.")) |
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74 |
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75 # Filter low library sizes |
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76 to_keep <- scle$total_counts > opt$library_size |
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77 scle <- scle[, to_keep] |
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78 |
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79 print(paste("After filtering out low library counts: ", ncol(scle), "cells and", nrow(scle), "features.")) |
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80 |
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81 |
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82 # Filter low expressed genes |
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83 to_keep <- scle$total_features_by_counts > opt$expressed_genes |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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84 scle <- scle[, to_keep] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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85 |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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86 print(paste("After filtering out low expressed: ", ncol(scle), "cells and", nrow(scle), "features.")) |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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87 |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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88 |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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89 # Filter out high MT counts |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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90 to_keep <- scle$pct_counts_MT < opt$percent_counts_MT |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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91 scle <- scle[, to_keep] |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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92 |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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93 print(paste("After filtering out high MT gene counts: ", ncol(scle), "cells and", nrow(scle), "features.")) |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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94 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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95 # Output to a Loom file |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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96 if (file.exists(opt$output_loom)) { |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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97 file.remove(opt$output_loom) |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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98 } |
a30f4bfe8f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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99 export(scle, opt$output_loom, format='loom') |