--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signac-LSI.R	Tue Aug 02 19:11:27 2022 +0000
@@ -0,0 +1,78 @@
+#!/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("--min-cutoff"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = ""
+  ),
+  make_option(
+    c("--output-depthcor"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "TSS output plot."
+  ),
+  make_option(
+    c("-w", "--png-width"),
+    action = "store",
+    default = 1000,
+    type = 'integer',
+    help = "Width of png (px)."
+  ),
+  make_option(
+    c("-j", "--png-height"),
+    action = "store",
+    default = 1000,
+    type = 'integer',
+    help = "Height of png file (px)."
+  ),
+  make_option(
+    c("--output-object-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(Signac))
+
+set.seed(1234)
+
+# extract gene annotations from EnsDb
+signac_object <- readRDS(file = opt$signac_object)
+
+
+signac_object <- RunTFIDF(signac_object)
+signac_object <- FindTopFeatures(signac_object, min.cutoff = opt$min_cutoff)
+signac_object <- RunSVD(signac_object)
+
+## Plot the Depth correlation plot
+png(filename = opt$output_depthcor, width = opt$png_width, height = opt$png_height)
+DepthCor(signac_object)
+dev.off()
+
+# Output to a serialized R object
+saveRDS(signac_object, file = opt$output_object_file)