Mercurial > repos > gaelcge > r_signac_galaxy

comparison 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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-1:000000000000 0:6e0b320d8b6a
1 #!/usr/bin/env Rscript
2
3 # Load optparse we need to check inputs
4
5 suppressPackageStartupMessages(require(optparse))
6
7 # Load common functions
8
9 suppressPackageStartupMessages(require(workflowscriptscommon))
10
11 # parse options
12
13 option_list = list(
14 make_option(
15 c("--h5-file"),
16 action = "store",
17 default = NA,
18 type = 'character',
19 help = "Filtered peak BC matrix file in h5 format."
20 ),
21 make_option(
22 c("--metadata"),
23 action = "store",
24 default = NA,
25 type = 'character',
26 help = "Metadata file."
27 ),
28 make_option(
29 c("--genome"),
30 action = "store",
31 default = NA,
32 type = 'character',
33 help = "Genome version."
34 ),
35 make_option(
36 c("--output-object-file"),
37 action = "store",
38 default = NA,
39 type = 'character',
40 help = "File name in which to store serialized R matrix object."
41 ),
42 make_option(
43 c("--fragment-file"),
44 action = "store",
45 default = NA,
46 type = 'character',
47 help = "Fragment file from CellRanger-ATAC."
48 ),
49 make_option(
50 c("--min-cells"),
51 action = "store",
52 default = NA,
53 type = 'character',
54 help = "Lower number of cells identified per peak."
55 ),
56 make_option(
57 c("--min-features"),
58 action = "store",
59 default = NA,
60 type = 'character',
61 help = "Minimum number of features per cell to be retained."
62 )
63 )
64
65 opt <- wsc_parse_args(option_list)
66
67 suppressPackageStartupMessages(require(Seurat))
68 suppressPackageStartupMessages(require(Signac))
69
70 atac_h5_matrix <- Read10X_h5(filename = opt$h5_file)
71 print(paste("counts:",dim(atac_h5_matrix)))
72
73 metadata <- read.csv(
74 file = opt$metadata,
75 header = TRUE,
76 row.names = 1
77 )
78 print(paste("metadata:",dim(metadata)))
79
80 chrom_assay <- CreateChromatinAssay(
81 counts = atac_h5_matrix,
82 sep = c(":", "-"),
83 genome = opt$genome,
84 fragments = opt$fragment_file,
85 min.cells = as.numeric(opt$min_cells),
86 min.features = as.numeric(opt$min_features)
87 )
88 print(chrom_assay)
89
90 #metadata <- subset(metadata,rownames(metadata) %in% colnames(chrom_assay))
91
92 signac_object <- CreateSeuratObject(
93 counts = chrom_assay,
94 assay = "peaks",
95 meta.data = metadata
96 )
97 print(signac_object)
98 print(signac_object[['peaks']])
99 print(granges(signac_object))
100 # cat(c(
101 # '# Object summary',
102 # capture.output(print(signac_object)),
103 # '\n# Metadata sample',
104 # capture.output(head(signac_object@meta.data))
105 # ),
106 # sep = '\n')
107
108 # Output to a serialized R object
109
110 saveRDS(signac_object, file = opt$output_object_file)