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annotate Seurat.R @ 15:fab6ff46e019 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
author iuc
date Fri, 07 Jul 2023 01:43:02 +0000
parents c4db6ec33fec
children
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7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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1 #' ---
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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2 #' title: "Seurat Analysis"
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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3 #' author: "Performed using Galaxy"
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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4 #' params:
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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5 #' counts: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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6 #' min_cells: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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7 #' min_genes: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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8 #' low_thresholds: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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9 #' high_thresholds: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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10 #' numPCs: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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11 #' resolution: ""
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12 #' perplexity: ""
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13 #' min_pct: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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14 #' logfc_threshold: ""
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fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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15 #' end_step: ""
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16 #' showcode: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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17 #' warn: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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18 #' varstate: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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19 #' vlnfeat: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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20 #' featplot: ""
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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21 #' PCplots: ""
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fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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22 #' nmds: ""
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23 #' heatmaps: ""
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fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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24 #' norm_out: ""
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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25 #' variable_out: ""
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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26 #' pca_out : ""
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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27 #' clusters_out: ""
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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28 #' markers_out: ""
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29 #' ---
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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30
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31 # nolint start
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32 #+ echo=F, warning = F, message=F
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33 options(show.error.messages = F, error = function() {
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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34 cat(geterrmessage(), file = stderr()); q("no", 1, F)
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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35 })
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36 showcode <- as.logical(params$showcode)
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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37 warn <- as.logical(params$warn)
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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38 varstate <- as.logical(params$varstate)
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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39 vlnfeat <- as.logical(params$vlnfeat)
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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40 featplot <- as.logical(params$featplot)
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41 pc_plots <- as.logical(params$PCplots)
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42 nmds <- as.logical(params$nmds)
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43 heatmaps <- as.logical(params$heatmaps)
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44 end_step <- as.integer(params$end_step)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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45 norm_out <- as.logical(params$norm_out)
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321bdd834266 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 3cf715ec11e2c9944f46572e324e5b2db5aa151f"
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46 # we need that to not crash Galaxy with an UTF-8 error on German LC settings.
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47 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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48
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49 #+ echo = F, warning = `warn`, include =`varstate`
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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50 min_cells <- as.integer(params$min_cells)
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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51 min_genes <- as.integer(params$min_genes)
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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52 print(paste0("Minimum cells: ", min_cells))
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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53 print(paste0("Minimum features: ", min_genes))
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54 low_thresholds <- as.integer(params$low_thresholds)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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55 high_thresholds <- as.integer(params$high_thresholds)
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56 print(paste0("Umi low threshold: ", low_thresholds))
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
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57 print(paste0("Umi high threshold: ", high_thresholds))
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58
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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59 if (end_step >= 2) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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60 variable_out <- as.logical(params$variable_out)
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61 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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62
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63
15
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64 if (end_step >= 3) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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65 num_pcs <- as.integer(params$numPCs)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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66 print(paste0("Number of principal components: ", num_pcs))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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67 pca_out <- as.logical(params$pca_out)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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68 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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69 if (end_step >= 4) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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70 if (params$perplexity == "") {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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71 perplexity <- -1
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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72 print(paste0("Perplexity: ", perplexity))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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73 } else {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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74 perplexity <- as.integer(params$perplexity)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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75 print(paste0("Perplexity: ", perplexity))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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76 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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77 resolution <- as.double(params$resolution)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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78 print(paste0("Resolution: ", resolution))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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79 clusters_out <- as.logical(params$clusters_out)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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80 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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81 if (end_step >= 5) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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82 min_pct <- as.double(params$min_pct)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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83 logfc_threshold <- as.double(params$logfc_thresh)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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84 print(paste0("Minimum percent of cells", min_pct))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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85 print(paste0("Logfold change threshold", logfc_threshold))
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86 markers_out <- as.logical(params$markers_out)
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87 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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88
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
89
6
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 2
diff changeset
90 if (showcode == TRUE) print("Read in data, generate inital Seurat object")
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
91 #+ echo = `showcode`, warning = `warn`, message = F
2
321bdd834266 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 3cf715ec11e2c9944f46572e324e5b2db5aa151f"
iuc
parents: 1
diff changeset
92 counts <- read.delim(params$counts, row.names = 1)
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
93 seuset <- Seurat::CreateSeuratObject(counts = counts, min.cells = min_cells, min.features = min_genes)
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
94
6
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 2
diff changeset
95 if (showcode == TRUE && vlnfeat == TRUE) print("Raw data vizualization")
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 2
diff changeset
96 #+ echo = `showcode`, warning = `warn`, include=`vlnfeat`
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
97 if (vlnfeat == TRUE){
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
98 print(Seurat::VlnPlot(object = seuset, features = c("nFeature_RNA", "nCount_RNA")))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
99 print(Seurat::FeatureScatter(object = seuset, feature1 = "nCount_RNA", feature2 = "nFeature_RNA"))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
100 }
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
101
6
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 2
diff changeset
102 if (showcode == TRUE) print("Filter and normalize for UMI counts")
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
103 #+ echo = `showcode`, warning = `warn`
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
104 seuset <- subset(seuset, subset = `nCount_RNA` > low_thresholds & `nCount_RNA` < high_thresholds)
2
321bdd834266 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 3cf715ec11e2c9944f46572e324e5b2db5aa151f"
iuc
parents: 1
diff changeset
105 seuset <- Seurat::NormalizeData(seuset, normalization.method = "LogNormalize", scale.factor = 10000)
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
106 if (norm_out == TRUE) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
107 saveRDS(seuset, "norm_out.rds")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
108 }
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
109
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
110 if (end_step >= 2) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
111 #+ echo = FALSE
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
112 if (showcode == TRUE && featplot == TRUE) print("Variable Genes")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
113 #+ echo = `showcode`, warning = `warn`, include = `featplot`
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
114 seuset <- Seurat::FindVariableFeatures(object = seuset, selection.method = "mvp")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
115 if (featplot == TRUE) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
116 print(Seurat::VariableFeaturePlot(seuset, cols = c("black", "red"), selection.method = "disp"))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
117 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
118 seuset <- Seurat::ScaleData(object = seuset, vars.to.regress = "nCount_RNA")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
119 if (variable_out == TRUE) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
120 saveRDS(seuset, "var_out.rds")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
121 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
122 }
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
123
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
124 if (end_step >= 3) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
125 #+ echo = FALSE
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
126 if (showcode == TRUE && pc_plots == TRUE) print("PCA Visualization")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
127 #+ echo = `showcode`, warning = `warn`, include = `pc_plots`
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
128 seuset <- Seurat::RunPCA(seuset, npcs = num_pcs)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
129 seuset <- Seurat::JackStraw(seuset, dims = num_pcs, reduction = "pca", num.replicate = 100)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
130 seuset <- Seurat::ScoreJackStraw(seuset, dims = 1:num_pcs)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
131 if (pc_plots == TRUE) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
132 print(Seurat::VizDimLoadings(seuset, dims = 1:2))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
133 print(Seurat::DimPlot(seuset, dims = c(1, 2), reduction = "pca"))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
134 print(Seurat::DimHeatmap(seuset, dims = 1:num_pcs, nfeatures = 30, reduction = "pca"))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
135 print(Seurat::JackStrawPlot(seuset, dims = 1:num_pcs))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
136 print(Seurat::ElbowPlot(seuset, ndims = num_pcs, reduction = "pca"))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
137 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
138 if (pca_out == TRUE) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
139 saveRDS(seuset, "pca_out.rds")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
140 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
141 }
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
142
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
143 if (end_step >= 4) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
144 #+ echo = FALSE
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
145 if (showcode == TRUE && nmds == TRUE) print("tSNE and UMAP")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
146 #+ echo = `showcode`, warning = `warn`, include = `nmds`
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
147 seuset <- Seurat::FindNeighbors(object = seuset)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
148 seuset <- Seurat::FindClusters(object = seuset)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
149 if (perplexity == -1) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
150 seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution);
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
151 } else {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
152 seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution, perplexity = perplexity);
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
153 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
154 if (nmds == TRUE) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
155 print(Seurat::DimPlot(seuset, reduction = "tsne"))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
156 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
157 seuset <- Seurat::RunUMAP(seuset, dims = 1:num_pcs)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
158 if (nmds == TRUE) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
159 print(Seurat::DimPlot(seuset, reduction = "umap"))
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
160 }
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
161 if (clusters_out == TRUE) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
162 tsnedata <- Seurat::Embeddings(seuset, reduction="tsne")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
163 saveRDS(seuset, "tsne_out.rds")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
164 umapdata <- Seurat::Embeddings(seuset, reduction="umap")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
165 saveRDS(seuset, "umap_out.rds")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
166 }
6
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
iuc
parents: 2
diff changeset
167 }
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
168
1
7319f83ae734 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
iuc
parents:
diff changeset
169
15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
170 if (end_step == 5) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
171 #+ echo = FALSE
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
172 if (showcode == TRUE && heatmaps == TRUE) print("Marker Genes")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
parents: 9
diff changeset
173 #+ echo = `showcode`, warning = `warn`, include = `heatmaps`
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
iuc
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174 markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold)
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175 top10 <- dplyr::group_by(markers, cluster)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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176 top10 <- dplyr::top_n(top10, n = 10, wt = avg_log2FC)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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177 print(top10)
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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178 if (heatmaps == TRUE) {
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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179 print(Seurat::DoHeatmap(seuset, features = top10$gene))
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180 }
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181 if (markers_out == TRUE) {
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182 saveRDS(seuset, "markers_out.rds")
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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183 data.table::fwrite(x = markers, row.names=TRUE, sep="\t", file = "markers_out.tsv")
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184 }
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185 }
6
764f076e9d52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
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186 # nolint end