Mercurial > repos > iuc > scater_create_qcmetric_ready_sce

comparison scater-plot-tsne.R @ 1:fd808de478b1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author iuc
date Tue, 03 Sep 2019 14:26:31 -0400
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children b834074a9aff
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0:2d455a7e8a3d 1:fd808de478b1
1 #!/usr/bin/env Rscript
2
3 # Creates a t-SNE plot of a normalised SingleCellExperiment object.
4
5 # Load optparse we need to check inputs
6
7 library(optparse)
8 library(workflowscriptscommon)
9 library(LoomExperiment)
10 library(scater)
11 library(Rtsne)
12
13 # parse options
14
15 option_list = list(
16 make_option(
17 c("-i", "--input-loom"),
18 action = "store",
19 default = NA,
20 type = 'character',
21 help = "A SingleCellExperiment object file in Loom format."
22 ),
23 make_option(
24 c("-c", "--colour-by"),
25 action = "store",
26 default = NULL,
27 type = 'character',
28 help = "Feature (from annotation file) to colour t-SNE plot points by. The values represented in this options should be categorical"
29 ),
30 make_option(
31 c("-s", "--size-by"),
32 action = "store",
33 default = NULL,
34 type = 'character',
35 help = "Feature (from annotation file) to size t-SNE plot points by. The values represented in this options should be numerical and not categorical"
36 ),
37 make_option(
38 c("-p", "--shape-by"),
39 action = "store",
40 default = NULL,
41 type = 'character',
42 help = "Feature (from annotation file) to shape t-SNE plot points by. The values represented in this options should be categorical"
43 ),
44 make_option(
45 c("-o", "--output-plot-file"),
46 action = "store",
47 default = NA,
48 type = 'character',
49 help = "Path of the PDF output file to save plot to."
50 )
51 )
52
53 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_plot_file'))
54 # Check parameter values
55
56 if ( ! file.exists(opt$input_loom)){
57 stop((paste('File', opt$input_loom, 'does not exist')))
58 }
59
60
61 # Input from Loom format
62
63 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment')
64 scle <- normalize(scle, exprs_values = 1)
65 scle <- runTSNE(scle, perplexity=10)
66 plot <- plotTSNE(scle, colour_by = opt$colour_by, size_by = opt$size_by, shape_by = opt$shape_by)
67
68
69 ggsave(opt$output_plot_file, plot, device="pdf")