--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signac-dimplot.R	Tue Aug 02 19:11:27 2022 +0000
@@ -0,0 +1,96 @@
+#!/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()