Mercurial > repos > goeckslab > celesta
changeset 3:283636dbfba5 draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/celesta commit 36453551b1045adf20925d4eb6b5816c64475728
| author | goeckslab |
|---|---|
| date | Thu, 19 Sep 2024 17:17:51 +0000 |
| parents | 41aaffbb9473 |
| children | |
| files | celesta.xml celesta_plot_cells.R macros.xml |
| diffstat | 3 files changed, 7 insertions(+), 14 deletions(-) [+] |
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--- a/celesta.xml Mon Sep 16 18:51:31 2024 +0000 +++ b/celesta.xml Thu Sep 19 17:17:51 2024 +0000 @@ -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}'
--- a/celesta_plot_cells.R Mon Sep 16 18:51:31 2024 +0000 +++ b/celesta_plot_cells.R Thu Sep 19 17:17:51 2024 +0000 @@ -17,8 +17,6 @@ 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", @@ -37,26 +35,23 @@ CelestaObj <- readRDS(opt$rds) cell_types_to_plot <- strsplit(opt$celltypes, ",")[[1]] -# read prior marker info -prior <- read.csv(opt$prior, row.names = 1) +# get indices of cell types to plot from the prior marker table +cell_type_indices <- which(CelestaObj@prior_info[, 1] %in% cell_types_to_plot) -# get indices of cell types to plot from the prior marker table -cell_type_indices <- which(row.names(prior) %in% cell_types_to_plot) - +print("Cell types selected for plotting:") print(cell_types_to_plot) +print("Indices of cell types selected for plotting:") print(cell_type_indices) -print(row.names(prior)) - # create output directory if it doesn"t already exist dir.create("cell_assign_plots") # create the cell type plot g <- PlotCellsAnyCombination(cell_type_assignment_to_plot = CelestaObj@final_cell_type_assignment[, (CelestaObj@total_rounds + 1)], coords = CelestaObj@coords, - prior_info = prior_marker_info, + prior_info = CelestaObj@prior_info, cell_number_to_use = cell_type_indices, - test_size = 1, + test_size = opt$size, save_plot = FALSE) # create a unique output name for the plot based on the input cell types @@ -64,7 +59,6 @@ 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,
--- a/macros.xml Mon Sep 16 18:51:31 2024 +0000 +++ b/macros.xml Thu Sep 19 17:17:51 2024 +0000 @@ -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">