Mercurial > repos > iuc > scater_filter
diff scater-plot-tsne.R @ 2:7a365ec81b52 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 12:24:17 +0000 |
parents | b7ea9f09c02f |
children |
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--- a/scater-plot-tsne.R Tue Sep 03 14:27:39 2019 -0400 +++ b/scater-plot-tsne.R Thu Sep 09 12:24:17 2021 +0000 @@ -12,58 +12,57 @@ # parse options -option_list = list( +option_list <- list( make_option( c("-i", "--input-loom"), action = "store", default = NA, - type = 'character', + type = "character", help = "A SingleCellExperiment object file in Loom format." ), make_option( c("-c", "--colour-by"), action = "store", default = NULL, - type = 'character', + type = "character", help = "Feature (from annotation file) to colour t-SNE plot points by. The values represented in this options should be categorical" ), make_option( c("-s", "--size-by"), action = "store", default = NULL, - type = 'character', + type = "character", help = "Feature (from annotation file) to size t-SNE plot points by. The values represented in this options should be numerical and not categorical" ), make_option( c("-p", "--shape-by"), action = "store", default = NULL, - type = 'character', + type = "character", help = "Feature (from annotation file) to shape t-SNE plot points by. The values represented in this options should be categorical" ), make_option( c("-o", "--output-plot-file"), action = "store", default = NA, - type = 'character', + type = "character", help = "Path of the PDF output file to save plot to." ) ) -opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_plot_file')) +opt <- wsc_parse_args(option_list, mandatory = c("input_loom", "output_plot_file")) + # Check parameter values -if ( ! file.exists(opt$input_loom)){ - stop((paste('File', opt$input_loom, 'does not exist'))) +if (! file.exists(opt$input_loom)) { + stop((paste("File", opt$input_loom, "does not exist"))) } - -# Input from Loom format +# Filter out unexpressed features -scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment') -scle <- normalize(scle, exprs_values = 1) -scle <- runTSNE(scle, perplexity=10) -plot <- plotTSNE(scle, colour_by = opt$colour_by, size_by = opt$size_by, shape_by = opt$shape_by) +sce <- import(opt$input_loom, format = "loom", type = "SingleCellLoomExperiment") +sce <- logNormCounts(sce) +sce <- runTSNE(sce, perplexity = 10) +plot <- plotTSNE(sce, colour_by = opt$colour_by, size_by = opt$size_by, shape_by = opt$shape_by) - -ggsave(opt$output_plot_file, plot, device="pdf") +ggsave(opt$output_plot_file, plot, device = "pdf")