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comparison scater-plot-tsne.R @ 2:7a365ec81b52 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
author iuc
date Thu, 09 Sep 2021 12:24:17 +0000
parents b7ea9f09c02f
children
comparison
equal deleted inserted replaced
1:b7ea9f09c02f 2:7a365ec81b52
10 library(scater) 10 library(scater)
11 library(Rtsne) 11 library(Rtsne)
12 12
13 # parse options 13 # parse options
14 14
15 option_list = list( 15 option_list <- list(
16 make_option( 16 make_option(
17 c("-i", "--input-loom"), 17 c("-i", "--input-loom"),
18 action = "store", 18 action = "store",
19 default = NA, 19 default = NA,
20 type = 'character', 20 type = "character",
21 help = "A SingleCellExperiment object file in Loom format." 21 help = "A SingleCellExperiment object file in Loom format."
22 ), 22 ),
23 make_option( 23 make_option(
24 c("-c", "--colour-by"), 24 c("-c", "--colour-by"),
25 action = "store", 25 action = "store",
26 default = NULL, 26 default = NULL,
27 type = 'character', 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" 28 help = "Feature (from annotation file) to colour t-SNE plot points by. The values represented in this options should be categorical"
29 ), 29 ),
30 make_option( 30 make_option(
31 c("-s", "--size-by"), 31 c("-s", "--size-by"),
32 action = "store", 32 action = "store",
33 default = NULL, 33 default = NULL,
34 type = 'character', 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" 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 ), 36 ),
37 make_option( 37 make_option(
38 c("-p", "--shape-by"), 38 c("-p", "--shape-by"),
39 action = "store", 39 action = "store",
40 default = NULL, 40 default = NULL,
41 type = 'character', 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" 42 help = "Feature (from annotation file) to shape t-SNE plot points by. The values represented in this options should be categorical"
43 ), 43 ),
44 make_option( 44 make_option(
45 c("-o", "--output-plot-file"), 45 c("-o", "--output-plot-file"),
46 action = "store", 46 action = "store",
47 default = NA, 47 default = NA,
48 type = 'character', 48 type = "character",
49 help = "Path of the PDF output file to save plot to." 49 help = "Path of the PDF output file to save plot to."
50 ) 50 )
51 ) 51 )
52 52
53 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_plot_file')) 53 opt <- wsc_parse_args(option_list, mandatory = c("input_loom", "output_plot_file"))
54
54 # Check parameter values 55 # Check parameter values
55 56
56 if ( ! file.exists(opt$input_loom)){ 57 if (! file.exists(opt$input_loom)) {
57 stop((paste('File', opt$input_loom, 'does not exist'))) 58 stop((paste("File", opt$input_loom, "does not exist")))
58 } 59 }
59 60
61 # Filter out unexpressed features
60 62
61 # Input from Loom format 63 sce <- import(opt$input_loom, format = "loom", type = "SingleCellLoomExperiment")
64 sce <- logNormCounts(sce)
65 sce <- runTSNE(sce, perplexity = 10)
66 plot <- plotTSNE(sce, colour_by = opt$colour_by, size_by = opt$size_by, shape_by = opt$shape_by)
62 67
63 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment') 68 ggsave(opt$output_plot_file, plot, device = "pdf")
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")