diff celesta_plot_cells.R @ 0:8001319743c0 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/celesta commit 0ec46718dfd00f37ccae4e2fa133fa8393fe6d92

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/celesta_plot_cells.R	Wed Aug 28 12:46:48 2024 +0000
@@ -0,0 +1,76 @@
+# ---------------------------------------------------------------------------------
+# Plot assigned cell type combinations with CELESTA
+# ---------------------------------------------------------------------------------
+
+suppressWarnings(suppressMessages(library(janitor)))
+suppressWarnings(suppressMessages(library(optparse)))
+suppressWarnings(suppressMessages(library(dplyr)))
+suppressWarnings(suppressMessages(library(anndataR)))
+suppressWarnings(suppressMessages(library(Rmixmod)))
+suppressWarnings(suppressMessages(library(spdep)))
+suppressWarnings(suppressMessages(library(ggplot2)))
+suppressWarnings(suppressMessages(library(reshape2)))
+suppressWarnings(suppressMessages(library(zeallot)))
+suppressWarnings(suppressMessages(library(CELESTA)))
+
+# define command line args
+option_list <- list(
+  make_option(c("-r", "--rds"), action = "store", default = "celestaobj.rds", type = "character",
+              help = "Path to CelestaObj RDS"),
+  make_option(c("-p", "--prior"), action = "store", default = NA, type = "character",
+              help = "Path to prior marker info file"),
+  make_option(c("-c", "--celltypes"), action = "store", default = NA, type = "character",
+              help = "Comma-separated list of cell types to plot"),
+  make_option(c("-s", "--size"), action = "store", default = 1, type = "double",
+              help = "Point size for plotting"),
+  make_option(c("--width"), action = "store", default = 12, type = "integer",
+              help = "Width of plot (inches)"),
+  make_option(c("--height"), action = "store", default = 12, type = "integer",
+              help = "Height of plot (inches)"),
+  make_option(c("--dpi"), action = "store", default = 300, type = "integer",
+              help = "DPI (dots per inch) of plot")
+)
+
+# parse args
+opt <- parse_args(OptionParser(option_list = option_list))
+
+CelestaObj <- readRDS(opt$rds)
+cell_types_to_plot <- strsplit(opt$celltypes, ",")[[1]]
+
+# read prior marker info
+prior <- read.csv(opt$prior, row.names = 1)
+
+# get indices of cell types to plot from the prior marker table
+cell_type_indices <- which(row.names(prior) %in% cell_types_to_plot)
+
+print(cell_types_to_plot)
+print(cell_type_indices)
+
+print(row.names(prior))
+
+# create output directory if it doesn"t already exist
+dir.create("cell_assign_plots")
+
+# create the cell type plot
+g <- PlotCellsAnyCombination(cell_type_assignment_to_plot = CelestaObj@final_cell_type_assignment[, (CelestaObj@total_rounds + 1)],
+                             coords = CelestaObj@coords,
+                             prior_info = prior_marker_info,
+                             cell_number_to_use = cell_type_indices,
+                             test_size = 1,
+                             save_plot = FALSE)
+
+# create a unique output name for the plot based on the input cell types
+cell_types_cleaned <- paste(make_clean_names(cell_types_to_plot), collapse = "")
+output_name <- paste(c("plot_cells_", cell_types_cleaned, ".png"), collapse = "")
+
+# save to subdir
+# FIXME: may want to expose plotting params to galaxy
+ggsave(
+  path = "cell_assign_plots",
+  filename = output_name,
+  plot = g,
+  width = opt$width,
+  height = opt$height,
+  units = "in",
+  dpi = opt$dpi
+)