Mercurial > repos > iuc > scater_plot_tsne
comparison scater-plot-pca.R @ 1:2b09ca1c5e41 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
author | iuc |
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date | Thu, 09 Sep 2021 12:24:39 +0000 |
parents | a30f4bfe8f01 |
children |
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0:a30f4bfe8f01 | 1:2b09ca1c5e41 |
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9 library(LoomExperiment) | 9 library(LoomExperiment) |
10 library(scater) | 10 library(scater) |
11 | 11 |
12 # parse options | 12 # parse options |
13 | 13 |
14 option_list = list( | 14 option_list <- list( |
15 make_option( | 15 make_option( |
16 c("-i", "--input-loom"), | 16 c("-i", "--input-loom"), |
17 action = "store", | 17 action = "store", |
18 default = NA, | 18 default = NA, |
19 type = 'character', | 19 type = "character", |
20 help = "A SingleCellExperiment object file in Loom format." | 20 help = "A SingleCellExperiment object file in Loom format." |
21 ), | 21 ), |
22 make_option( | 22 make_option( |
23 c("-c", "--colour-by"), | 23 c("-c", "--colour-by"), |
24 action = "store", | 24 action = "store", |
25 default = NULL, | 25 default = NULL, |
26 type = 'character', | 26 type = "character", |
27 help = "Feature (from annotation file) to colour PCA plot points by. The values represented in this options should be categorical" | 27 help = "Feature (from annotation file) to colour PCA plot points by. The values represented in this options should be categorical" |
28 ), | 28 ), |
29 make_option( | 29 make_option( |
30 c("-s", "--size-by"), | 30 c("-s", "--size-by"), |
31 action = "store", | 31 action = "store", |
32 default = NULL, | 32 default = NULL, |
33 type = 'character', | 33 type = "character", |
34 help = "Feature (from annotation file) to size PCA plot points by. The values represented in this options should be numerical and not categorical" | 34 help = "Feature (from annotation file) to size PCA plot points by. The values represented in this options should be numerical and not categorical" |
35 ), | 35 ), |
36 make_option( | 36 make_option( |
37 c("-p", "--shape-by"), | 37 c("-p", "--shape-by"), |
38 action = "store", | 38 action = "store", |
39 default = NULL, | 39 default = NULL, |
40 type = 'character', | 40 type = "character", |
41 help = "Feature (from annotation file) to shape PCA plot points by. The values represented in this options should be categorical" | 41 help = "Feature (from annotation file) to shape PCA plot points by. The values represented in this options should be categorical" |
42 ), | 42 ), |
43 make_option( | 43 make_option( |
44 c("-o", "--output-plot-file"), | 44 c("-o", "--output-plot-file"), |
45 action = "store", | 45 action = "store", |
46 default = NA, | 46 default = NA, |
47 type = 'character', | 47 type = "character", |
48 help = "Path of the PDF output file to save plot to." | 48 help = "Path of the PDF output file to save plot to." |
49 ) | 49 ) |
50 ) | 50 ) |
51 | 51 |
52 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_plot_file')) | 52 opt <- wsc_parse_args(option_list, mandatory = c("input_loom", "output_plot_file")) |
53 | |
53 # Check parameter values | 54 # Check parameter values |
54 | 55 |
55 if ( ! file.exists(opt$input_loom)){ | 56 if (! file.exists(opt$input_loom)) { |
56 stop((paste('File', opt$input_loom, 'does not exist'))) | 57 stop((paste("File", opt$input_loom, "does not exist"))) |
57 } | 58 } |
58 | 59 |
60 # Filter out unexpressed features | |
59 | 61 |
60 # Input from Loom format | 62 sce <- import(opt$input_loom, format = "loom", type = "SingleCellLoomExperiment") |
63 sce <- logNormCounts(sce) | |
64 sce <- runPCA(sce) | |
61 | 65 |
62 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment') | 66 plot <- plotReducedDim(sce, dimred = "PCA", colour_by = opt$colour_by, size_by = opt$size_by, shape_by = opt$shape_by) |
63 scle <- normalize(scle, exprs_values = 1) | |
64 scle <- runPCA(scle) | |
65 plot <- plotReducedDim(scle, "PCA", colour_by = opt$colour_by, size_by = opt$size_by, shape_by = opt$shape_by) | |
66 #do the scatter plot of reads vs genes | |
67 | 67 |
68 ggsave(opt$output_plot_file, plot, device="pdf") | 68 ggsave(opt$output_plot_file, plot, device = "pdf") |