Mercurial > repos > gaelcge > r_signac_galaxy
view signac-dimplot.R @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author | gaelcge |
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date | Tue, 02 Aug 2022 19:11:27 +0000 |
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#!/usr/bin/env Rscript # Load optparse we need to check inputs suppressPackageStartupMessages(require(optparse)) # Load common functions suppressPackageStartupMessages(require(workflowscriptscommon)) # parse options option_list = list( make_option( c("--signac-object"), action = "store", default = NA, type = 'character', help = "" ), make_option( c("--dims"), action = "store", type = 'character', help = "Dimension for x-axis (default 1)" ), make_option( c("-p", "--pt-size"), action = "store", default = 1, type = 'integer', help = "Adjust point size for plotting" ), make_option( c("-l", "--label-size"), action = "store", default = 4, type = 'integer', help = "Sets size of labels." ), make_option( c("-d", "--do-label"), action = "store", default = FALSE, type = 'logical', help = "Whether to label the clusters." ), make_option( c("--group-by"), action = "store", default = 'ident', type = 'character', help = "Group (color) cells in different ways (for example, orig.ident)." ), make_option( c("--png-width"), action = "store", default = 1000, type = 'integer', help = "Width of png (px)." ), make_option( c("--png-height"), action = "store", default = 1000, type = 'integer', help = "Height of png file (px)." ), make_option( c("--output_image_file"), action = "store", default = NA, type = 'character', help = "File name in which to store serialized R matrix object." ) ) opt <- wsc_parse_args(option_list) suppressPackageStartupMessages(require(Seurat)) suppressPackageStartupMessages(require(Signac)) set.seed(1234) dims_use <- opt$dims if ( ! is.null(dims_use)){ dims_parsed <- wsc_parse_numeric(opt, 'dims') dims_use <- seq(from = dims_parsed[1], to = dims_parsed[2]) } # extract gene annotations from EnsDb signac_object <- readRDS(file = opt$signac_object) png(filename = opt$output_image_file, width = opt$png_width, height = opt$png_height) DimPlot(object = signac_object, dims = dims_use, pt.size = opt$pt_size, label.size = opt$label_size, group.by = opt$group_by) + NoLegend() dev.off()