Mercurial > repos > iuc > scater_normalize

annotate scater-pca-filter.R @ 1:b32ae8dfa72b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author iuc
date Tue, 03 Sep 2019 14:23:23 -0400
parents 0cb9a5f830fc
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0cb9a5f830fc 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
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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2 #Filters a SingleCellExperiment object, using PCA on the following metrics:
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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3 # "pct_counts_top_100_features"
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4 # "total_features"
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5 # "pct_counts_feature_control"
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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6 # "total_features_feature_control"
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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7 # "log10_total_counts_endogenous"
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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8 # "log10_total_counts_feature_control"
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9
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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10 # Load optparse we need to check inputs
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11 library(optparse)
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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12 library(workflowscriptscommon)
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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13 library(LoomExperiment)
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14 library(scater)
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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15 library(mvoutlier)
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16
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17 # parse options
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18 option_list = list(
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19 make_option(
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20 c("-i", "--input-loom"),
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21 action = "store",
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22 default = NA,
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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23 type = 'character',
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24 help = "A SingleCellExperiment object file in Loom format."
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25 ),
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26 make_option(
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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27 c("-o", "--output-loom"),
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28 action = "store",
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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29 default = NA,
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30 type = 'character',
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31 help = "File name in which to store the SingleCellExperiment object in Loom format."
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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32 )
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33 )
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34
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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35 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_loom'))
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36
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37 # Check parameter values
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38
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39 if ( ! file.exists(opt$input_loom)){
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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40 stop((paste('File', opt$input_loom, 'does not exist')))
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41 }
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42
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43 # Input from Loom format
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44
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45 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment')
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46 print(paste("Starting with", ncol(scle), "cells and", nrow(scle), "features."))
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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47
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48 # Run PCA on data and detect outliers
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49 scle <- runPCA(scle, use_coldata = TRUE, detect_outliers = TRUE)
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50
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51 # Filter out outliers
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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52 scle <- scle[, !scle$outlier]
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53
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54 print(paste("Ending with", ncol(scle), "cells and", nrow(scle), "features."))
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55
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56 # Output to a Loom file
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57 if (file.exists(opt$output_loom)) {
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58 file.remove(opt$output_loom)
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59 }
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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60 export(scle, opt$output_loom, format='loom')