Merge pull request #90 from goeckslab/celesta-prior-bugfix

Fix celesta plot_cells indexing bug
goeckslab · Sep 19, 2024 · 3645355 · 3645355
2 parents ace0722 + 4fec4b2
commit 3645355
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Showing 3 changed files with 6 additions and 13 deletions.
diff --git a/tools/celesta/celesta.xml b/tools/celesta/celesta.xml
@@ -43,7 +43,6 @@
             #end if  
             #for $p in $runmode.plot_cells:
                 && Rscript '$__tool_directory__/celesta_plot_cells.R'
-                    --prior '$prior_info'
                     --celltypes '${p.cell_types}'
                     --size '${p.test_size}' 
                     --height '${p.height}' 

diff --git a/tools/celesta/celesta_plot_cells.R b/tools/celesta/celesta_plot_cells.R
@@ -17,8 +17,6 @@ suppressWarnings(suppressMessages(library(CELESTA)))
 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",
@@ -37,34 +35,30 @@ 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)
+cell_type_indices <- which(CelestaObj@prior_info[, 1] %in% cell_types_to_plot)
 
+print("Cell types selected for plotting:")
 print(cell_types_to_plot)
+print("Indices of cell types selected for plotting:")
 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,
+                             prior_info = CelestaObj@prior_info,
                              cell_number_to_use = cell_type_indices,
-                             test_size = 1,
+                             test_size = opt$size,
                              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,

diff --git a/tools/celesta/macros.xml b/tools/celesta/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.0.0.9</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.01</token>
 
     <xml name="celesta_requirements">