Mercurial > repos > goeckslab > celesta

comparison celesta_plot_cells.R @ 3:283636dbfba5 draft default tip

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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 8001319743c0
children
comparison
equal deleted inserted replaced
2:41aaffbb9473 3:283636dbfba5
15 15
16 # define command line args 16 # define command line args
17 option_list <- list( 17 option_list <- list(
18 make_option(c("-r", "--rds"), action = "store", default = "celestaobj.rds", type = "character", 18 make_option(c("-r", "--rds"), action = "store", default = "celestaobj.rds", type = "character",
19 help = "Path to CelestaObj RDS"), 19 help = "Path to CelestaObj RDS"),
20 make_option(c("-p", "--prior"), action = "store", default = NA, type = "character",
21 help = "Path to prior marker info file"),
22 make_option(c("-c", "--celltypes"), action = "store", default = NA, type = "character", 20 make_option(c("-c", "--celltypes"), action = "store", default = NA, type = "character",
23 help = "Comma-separated list of cell types to plot"), 21 help = "Comma-separated list of cell types to plot"),
24 make_option(c("-s", "--size"), action = "store", default = 1, type = "double", 22 make_option(c("-s", "--size"), action = "store", default = 1, type = "double",
25 help = "Point size for plotting"), 23 help = "Point size for plotting"),
26 make_option(c("--width"), action = "store", default = 12, type = "integer", 24 make_option(c("--width"), action = "store", default = 12, type = "integer",
35 opt <- parse_args(OptionParser(option_list = option_list)) 33 opt <- parse_args(OptionParser(option_list = option_list))
36 34
37 CelestaObj <- readRDS(opt$rds) 35 CelestaObj <- readRDS(opt$rds)
38 cell_types_to_plot <- strsplit(opt$celltypes, ",")[[1]] 36 cell_types_to_plot <- strsplit(opt$celltypes, ",")[[1]]
39 37
40 # read prior marker info 38 # get indices of cell types to plot from the prior marker table
41 prior <- read.csv(opt$prior, row.names = 1) 39 cell_type_indices <- which(CelestaObj@prior_info[, 1] %in% cell_types_to_plot)
42 40
43 # get indices of cell types to plot from the prior marker table 41 print("Cell types selected for plotting:")
44 cell_type_indices <- which(row.names(prior) %in% cell_types_to_plot)
45
46 print(cell_types_to_plot) 42 print(cell_types_to_plot)
43 print("Indices of cell types selected for plotting:")
47 print(cell_type_indices) 44 print(cell_type_indices)
48
49 print(row.names(prior))
50 45
51 # create output directory if it doesn"t already exist 46 # create output directory if it doesn"t already exist
52 dir.create("cell_assign_plots") 47 dir.create("cell_assign_plots")
53 48
54 # create the cell type plot 49 # create the cell type plot
55 g <- PlotCellsAnyCombination(cell_type_assignment_to_plot = CelestaObj@final_cell_type_assignment[, (CelestaObj@total_rounds + 1)], 50 g <- PlotCellsAnyCombination(cell_type_assignment_to_plot = CelestaObj@final_cell_type_assignment[, (CelestaObj@total_rounds + 1)],
56 coords = CelestaObj@coords, 51 coords = CelestaObj@coords,
57 prior_info = prior_marker_info, 52 prior_info = CelestaObj@prior_info,
58 cell_number_to_use = cell_type_indices, 53 cell_number_to_use = cell_type_indices,
59 test_size = 1, 54 test_size = opt$size,
60 save_plot = FALSE) 55 save_plot = FALSE)
61 56
62 # create a unique output name for the plot based on the input cell types 57 # create a unique output name for the plot based on the input cell types
63 cell_types_cleaned <- paste(make_clean_names(cell_types_to_plot), collapse = "") 58 cell_types_cleaned <- paste(make_clean_names(cell_types_to_plot), collapse = "")
64 output_name <- paste(c("plot_cells_", cell_types_cleaned, ".png"), collapse = "") 59 output_name <- paste(c("plot_cells_", cell_types_cleaned, ".png"), collapse = "")
65 60
66 # save to subdir 61 # save to subdir
67 # FIXME: may want to expose plotting params to galaxy
68 ggsave( 62 ggsave(
69 path = "cell_assign_plots", 63 path = "cell_assign_plots",
70 filename = output_name, 64 filename = output_name,
71 plot = g, 65 plot = g,
72 width = opt$width, 66 width = opt$width,