Mercurial > repos > gaelcge > r_signac_galaxy

comparison signac-dimplot.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("--signac-object"),
16 action = "store",
17 default = NA,
18 type = 'character',
19 help = ""
20 ),
21 make_option(
22 c("--dims"),
23 action = "store",
24 type = 'character',
25 help = "Dimension for x-axis (default 1)"
26 ),
27 make_option(
28 c("-p", "--pt-size"),
29 action = "store",
30 default = 1,
31 type = 'integer',
32 help = "Adjust point size for plotting"
33 ),
34 make_option(
35 c("-l", "--label-size"),
36 action = "store",
37 default = 4,
38 type = 'integer',
39 help = "Sets size of labels."
40 ),
41 make_option(
42 c("-d", "--do-label"),
43 action = "store",
44 default = FALSE,
45 type = 'logical',
46 help = "Whether to label the clusters."
47 ),
48 make_option(
49 c("--group-by"),
50 action = "store",
51 default = 'ident',
52 type = 'character',
53 help = "Group (color) cells in different ways (for example, orig.ident)."
54 ),
55 make_option(
56 c("--png-width"),
57 action = "store",
58 default = 1000,
59 type = 'integer',
60 help = "Width of png (px)."
61 ),
62 make_option(
63 c("--png-height"),
64 action = "store",
65 default = 1000,
66 type = 'integer',
67 help = "Height of png file (px)."
68 ),
69 make_option(
70 c("--output_image_file"),
71 action = "store",
72 default = NA,
73 type = 'character',
74 help = "File name in which to store serialized R matrix object."
75 )
76 )
77
78 opt <- wsc_parse_args(option_list)
79
80 suppressPackageStartupMessages(require(Seurat))
81 suppressPackageStartupMessages(require(Signac))
82
83 set.seed(1234)
84
85 dims_use <- opt$dims
86 if ( ! is.null(dims_use)){
87 dims_parsed <- wsc_parse_numeric(opt, 'dims')
88 dims_use <- seq(from = dims_parsed[1], to = dims_parsed[2])
89 }
90
91 # extract gene annotations from EnsDb
92 signac_object <- readRDS(file = opt$signac_object)
93
94 png(filename = opt$output_image_file, width = opt$png_width, height = opt$png_height)
95 DimPlot(object = signac_object, dims = dims_use, pt.size = opt$pt_size, label.size = opt$label_size, group.by = opt$group_by) + NoLegend()
96 dev.off()