Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac-createObject.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("--h5-file"),
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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 = "Filtered peak BC matrix file in h5 format."
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20 ),
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21 make_option(
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22 c("--metadata"),
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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 = "Metadata file."
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27 ),
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28 make_option(
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29 c("--genome"),
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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 = "Genome version."
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34 ),
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35 make_option(
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36 c("--output-object-file"),
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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 = "File name in which to store serialized R matrix object."
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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 from CellRanger-ATAC."
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48 ),
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49 make_option(
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50 c("--min-cells"),
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51 action = "store",
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52 default = NA,
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53 type = 'character',
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54 help = "Lower number of cells identified per peak."
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55 ),
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56 make_option(
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57 c("--min-features"),
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58 action = "store",
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59 default = NA,
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60 type = 'character',
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61 help = "Minimum number of features per cell to be retained."
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62 )
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63 )
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64
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65 opt <- wsc_parse_args(option_list)
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66
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67 suppressPackageStartupMessages(require(Seurat))
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68 suppressPackageStartupMessages(require(Signac))
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69
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70 atac_h5_matrix <- Read10X_h5(filename = opt$h5_file)
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71 print(paste("counts:",dim(atac_h5_matrix)))
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72
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73 metadata <- read.csv(
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74 file = opt$metadata,
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75 header = TRUE,
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76 row.names = 1
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77 )
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78 print(paste("metadata:",dim(metadata)))
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79
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80 chrom_assay <- CreateChromatinAssay(
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81 counts = atac_h5_matrix,
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82 sep = c(":", "-"),
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83 genome = opt$genome,
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84 fragments = opt$fragment_file,
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85 min.cells = as.numeric(opt$min_cells),
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86 min.features = as.numeric(opt$min_features)
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87 )
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88 print(chrom_assay)
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89
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90 #metadata <- subset(metadata,rownames(metadata) %in% colnames(chrom_assay))
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91
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92 signac_object <- CreateSeuratObject(
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93 counts = chrom_assay,
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94 assay = "peaks",
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95 meta.data = metadata
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96 )
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97 print(signac_object)
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98 print(signac_object[['peaks']])
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99 print(granges(signac_object))
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100 # cat(c(
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101 # '# Object summary',
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102 # capture.output(print(signac_object)),
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103 # '\n# Metadata sample',
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104 # capture.output(head(signac_object@meta.data))
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105 # ),
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106 # sep = '\n')
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107
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108 # Output to a serialized R object
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109
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110 saveRDS(signac_object, file = opt$output_object_file)