Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac-runQC.R @ 0:6e0b320d8b6a draft default tip

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"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author gaelcge
date Tue, 02 Aug 2022 19:11:27 +0000
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1 #!/usr/bin/env Rscript
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2
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3 # Load optparse we need to check inputs
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4
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5 suppressPackageStartupMessages(require(optparse))
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6
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7 # Load common functions
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8
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9 suppressPackageStartupMessages(require(workflowscriptscommon))
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10
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11 # parse options
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12
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13 option_list = list(
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14 make_option(
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15 c("--signac-object"),
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16 action = "store",
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17 default = NA,
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18 type = 'character',
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19 help = ""
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20 ),
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21 make_option(
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22 c("--tss-threshold"),
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23 action = "store",
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24 default = NA,
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25 type = 'character',
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26 help = "TSS enrichment threshold for marking regions as high tss regions."
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27 ),
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28 make_option(
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29 c("--output-tss-plot"),
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30 action = "store",
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31 default = NA,
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32 type = 'character',
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33 help = "TSS output plot."
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34 ),
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35 make_option(
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36 c("--frag-history-plot"),
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37 action = "store",
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38 default = NA,
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39 type = 'character',
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40 help = "Fragment length periodicity plot."
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41 ),
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42 make_option(
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43 c("--fragment-file"),
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44 action = "store",
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45 default = NA,
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46 type = 'character',
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47 help = "Fragment file."
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48 ),
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49 make_option(
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50 c("-w", "--png-width"),
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51 action = "store",
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52 default = 1000,
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53 type = 'integer',
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54 help = "Width of png (px)."
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55 ),
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56 make_option(
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57 c("-j", "--png-height"),
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58 action = "store",
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59 default = 1000,
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60 type = 'integer',
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61 help = "Height of png file (px)."
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62 ),
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63 make_option(
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64 c("--output-object-file"),
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65 action = "store",
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66 default = NA,
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67 type = 'character',
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68 help = "File name in which to store serialized R matrix object."
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69 )
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70 )
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71
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72 opt <- wsc_parse_args(option_list)
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73
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74 suppressPackageStartupMessages(require(Seurat))
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75 suppressPackageStartupMessages(require(Signac))
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76 suppressPackageStartupMessages(require(GenomeInfoDb))
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77 suppressPackageStartupMessages(require(EnsDb.Hsapiens.v75))
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78 suppressPackageStartupMessages(require(EnsDb.Mmusculus.v79))
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79
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80 set.seed(1234)
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81
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82 # extract gene annotations from EnsDb
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83 signac_object <- readRDS(file = opt$signac_object)
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84
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85 ## Modify fragments file location
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86 # current_wd <- getwd()
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87 # new_framgent_file_loc <- paste(current_wd,"fragments.tsv.gz",sep = "/")
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88 # signac_object@assays$peaks@fragments[[1]]@path <- new_framgent_file_loc
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89 # signac_object@assays$peaks@fragments[[1]]@path <- opt$fragment_file
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90 #print(normalizePath(path = paste0(opt$fragment_file, '.tbi'), mustWork = TRUE))
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91 #system(paste0("mv ", paste0(opt$fragment_file, '.tbi'), ' ', normalizePath(path = paste0(opt$fragment_file, '.tbi'), mustWork = TRUE)))
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92 # The error was that the fragment file and fragment index file were not being imported into galaxy properly. They should be imported as tabluar.gz
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93 signac_object@assays$peaks@fragments[[1]] <- UpdatePath(signac_object@assays$peaks@fragments[[1]], opt$fragment_file)
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94
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95 # compute nucleosome signal score per cell
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96 signac_object <- NucleosomeSignal(object = signac_object)
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97
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98 # compute TSS enrichment score per cell
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99 signac_object <- TSSEnrichment(object = signac_object, fast = FALSE)
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100
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101 # add blacklist ratio and fraction of reads in peaks
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102 signac_object$pct_reads_in_peaks <- signac_object$peak_region_fragments / signac_object$passed_filters * 100
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103 signac_object$blacklist_ratio <- signac_object$blacklist_region_fragments / signac_object$peak_region_fragments
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104
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105 signac_object$high.tss <- ifelse(signac_object$TSS.enrichment > as.numeric(opt$tss_threshold), 'High', 'Low')
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106
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107 png(filename = opt$output_tss_plot, width = opt$png_width, height = opt$png_height)
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108 TSSPlot(signac_object, group.by = 'high.tss') + NoLegend()
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109 dev.off()
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110
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111 signac_object$nucleosome_group <- ifelse(signac_object$nucleosome_signal > 4, 'NS > 4', 'NS < 4')
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112
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113 png(filename = opt$frag_history_plot, width = opt$png_width, height = opt$png_height)
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114 FragmentHistogram(object = signac_object, group.by = 'nucleosome_group')
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115 dev.off()
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116
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117 print(summary(signac_object@meta.data))
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118
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119 # Output to a serialized R object
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120 saveRDS(signac_object, file = opt$output_object_file)