Mercurial > repos > gaelcge > r_signac_galaxy
annotate signac-dimplot.R @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author | gaelcge |
---|---|
date | Tue, 02 Aug 2022 19:11:27 +0000 |
parents | |
children |
rev | line source |
---|---|
0
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
1 #!/usr/bin/env Rscript |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
2 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
3 # Load optparse we need to check inputs |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
4 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
5 suppressPackageStartupMessages(require(optparse)) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
6 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
7 # Load common functions |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
8 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
9 suppressPackageStartupMessages(require(workflowscriptscommon)) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
10 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
11 # parse options |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
12 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
13 option_list = list( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
14 make_option( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
15 c("--signac-object"), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
16 action = "store", |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
17 default = NA, |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
18 type = 'character', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
19 help = "" |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
20 ), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
21 make_option( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
22 c("--dims"), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
23 action = "store", |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
24 type = 'character', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
25 help = "Dimension for x-axis (default 1)" |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
26 ), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
27 make_option( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
28 c("-p", "--pt-size"), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
29 action = "store", |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
30 default = 1, |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
31 type = 'integer', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
32 help = "Adjust point size for plotting" |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
33 ), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
34 make_option( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
35 c("-l", "--label-size"), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
36 action = "store", |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
37 default = 4, |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
38 type = 'integer', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
39 help = "Sets size of labels." |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
40 ), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
41 make_option( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
42 c("-d", "--do-label"), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
43 action = "store", |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
44 default = FALSE, |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
45 type = 'logical', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
46 help = "Whether to label the clusters." |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
47 ), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
48 make_option( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
49 c("--group-by"), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
50 action = "store", |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
51 default = 'ident', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
52 type = 'character', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
53 help = "Group (color) cells in different ways (for example, orig.ident)." |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
54 ), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
55 make_option( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
56 c("--png-width"), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
57 action = "store", |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
58 default = 1000, |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
59 type = 'integer', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
60 help = "Width of png (px)." |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
61 ), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
62 make_option( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
63 c("--png-height"), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
64 action = "store", |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
65 default = 1000, |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
66 type = 'integer', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
67 help = "Height of png file (px)." |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
68 ), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
69 make_option( |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
70 c("--output_image_file"), |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
71 action = "store", |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
72 default = NA, |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
73 type = 'character', |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
74 help = "File name in which to store serialized R matrix object." |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
75 ) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
76 ) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
77 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
78 opt <- wsc_parse_args(option_list) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
79 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
80 suppressPackageStartupMessages(require(Seurat)) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
81 suppressPackageStartupMessages(require(Signac)) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
82 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
83 set.seed(1234) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
84 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
85 dims_use <- opt$dims |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
86 if ( ! is.null(dims_use)){ |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
87 dims_parsed <- wsc_parse_numeric(opt, 'dims') |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
88 dims_use <- seq(from = dims_parsed[1], to = dims_parsed[2]) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
89 } |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
90 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
91 # extract gene annotations from EnsDb |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
92 signac_object <- readRDS(file = opt$signac_object) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
93 |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
94 png(filename = opt$output_image_file, width = opt$png_width, height = opt$png_height) |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
95 DimPlot(object = signac_object, dims = dims_use, pt.size = opt$pt_size, label.size = opt$label_size, group.by = opt$group_by) + NoLegend() |
6e0b320d8b6a
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
gaelcge
parents:
diff
changeset
|
96 dev.off() |