diff celesta_plot_expression.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_expression.R	Wed Aug 28 12:46:48 2024 +0000
@@ -0,0 +1,108 @@
+# --------------------------------------------------------------------------------------------
+# Plot marker expression probabilities for cell assignment parameter optimization 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 arguments
+option_list <- list(
+  make_option(c("-i", "--imagingdata"), action = "store", default = NA, type = "character",
+              help = "Path to imaging data"),
+  make_option(c("-p", "--prior"), action = "store", default = NA, type = "character",
+              help = "Path to prior marker info file"),
+  make_option(c("-x", "--xcol"), action = "store", default = NA, type = "character",
+              help = "Name of column in adata.obs containing X coordinate"),
+  make_option(c("-y", "--ycol"), action = "store", default = NA, type = "character",
+              help = "Name of column in adata.obs containing Y coordinate"),
+  make_option(c("--filter"), action = "store_true", type = "logical", default = FALSE,
+              help = "Boolean to filter cells or not (default: no filtering)"),
+  make_option(c("--highfilter"), action = "store", default = 0.9, type = "double",
+              help = "High marker threshold if filtering cells (default: 0.9)"),
+  make_option(c("--lowfilter"), action = "store", default = 0.4, type = "double",
+              help = "Low marker threshold if filtering cells (default: 0.4)"),
+  make_option(c("-s", "--size"), action = "store", default = 1, type = "double",
+              help = "Point size for plotting"),
+  make_option(c("--width"), action = "store", default = 5, type = "integer",
+              help = "Width of plot (inches)"),
+  make_option(c("--height"), action = "store", default = 4, type = "integer",
+              help = "Height of plot (inches)")
+)
+
+### Functions
+anndata_to_celesta <- function(input_adata, x_col, y_col) {
+
+  #' Function to convert anndata object to dataframe readable by CELESTA
+  #' Coordinates columns in adata.obs are renamed to "X" and "Y", and placed at beginning of dataframe
+  #' Marker intensities are concatted columnwise to the X and Y coords. cols: X,Y,Marker_1,...Marker N
+
+  # initialize output as dataframe from adata.obs
+  celesta_input_dataframe <- data.frame(input_adata$obs)
+
+  # subset to X and Y coordinates from obs only
+  celesta_input_dataframe <- celesta_input_dataframe %>%
+    dplyr::select({{x_col}}, {{y_col}})
+
+  # rename X,Y column names to what CELESTA wants
+  colnames(celesta_input_dataframe) <- c("X", "Y")
+
+  # merge X,Y coords with marker intensities from adata.X
+  x_df <- data.frame(input_adata$X)
+  colnames(x_df) <- input_adata$var_names
+  celesta_input_dataframe <- cbind(celesta_input_dataframe, x_df)
+
+  return(celesta_input_dataframe)
+}
+
+### Main
+# parse args
+opt <- parse_args(OptionParser(option_list = option_list))
+
+# read anndata, convert to celesta format
+adata <- read_h5ad(opt$imagingdata)
+celesta_input_df <- anndata_to_celesta(adata, x_col = opt$xcol, y_col = opt$ycol)
+
+# read prior marker info
+prior <- read.csv(opt$prior, check.names = FALSE)
+
+# clean prior names, keeping a copy of originals for writing output
+prior_original_names <- colnames(prior)
+prior <- janitor::clean_names(prior, case = "all_caps")
+
+# clean input dataframe names
+celesta_input_df <- janitor::clean_names(celesta_input_df, case = "all_caps")
+
+# instantiate celesta object
+CelestaObj <- CreateCelestaObject(
+  project_title = "",
+  prior_marker_info = prior,
+  imaging_data_file = celesta_input_df
+)
+
+# if filtering is specified, filter out cells outside high and low thresholds
+if (opt$filter) {
+  print("filtering cells based on expression")
+  CelestaObj <- FilterCells(CelestaObj,
+                            high_marker_threshold = opt$highfilter,
+                            low_marker_threshold = opt$lowfilter)
+} else {
+  print("Proceeding to marker expression plotting without cell filtering")
+}
+
+# create output directory if it does not already exist
+dir.create("marker_exp_plots")
+
+# plot expression probability
+PlotExpProb(coords = CelestaObj@coords,
+            marker_exp_prob = CelestaObj@marker_exp_prob,
+            prior_marker_info = CelestaObj@prior_info,
+            save_plot = TRUE,
+            output_dir = "./marker_exp_plots")