Mapscape plots

library(mapscape)
library(htmlwidgets)

library(ithi.utils)
load_base_libs()
library(ithi.meta)
library(ithi.ihc)
library(ithi.figures)

Parameters

db_path <- snakemake@params$db

mapscape_input_directories = snakemake@input$mapscape_inputs
ihc_table_path <- snakemake@input$ihc_table
tils_for_cluster <- snakemake@params$tiltypes
molecular_subtype_file <- snakemake@input$molsubtypes
nclusts <- snakemake@params$nclusts

reformat_andrew_table <- function(dat, db_path, patient_id) {
    dat$patient_id <- patient_id
    dat <- subset(dat, !sample_id %in% c("Pv2", "Rec2", "Rec3"))
    dat <- dat %>% plyr::rename(c(sample_id = "plot_id", long_sample_id = "sample_id"))
    dat_remapped <- ithi.meta::remap_sample_ids(dat, db_path)
    dat_remapped$abbrev_id <- stringr::str_extract(dat_remapped$condensed_id, 
        "[A-Za-z0-9]+$")
    dat_remapped <- dat_remapped %>% plyr::rename(c(sample_id = "old_sample_id", 
        sample_key = "long_sample_id", plot_id = "old_plot_id", abbrev_id = "sample_id"))
    if ("location_id" %in% colnames(dat_remapped)) {
        dat_remapped$location_id <- dat_remapped$sample_id
    }
    return(dat_remapped)
}

annotation_colours <- ithi.figures::get_annotation_colours()
cluster_colours <- annotation_colours$til_cluster_colours
ihc_table <- fread(ihc_table_path)
tiltypes <- unlist(tils_for_cluster)
molsubtypes <- fread(molecular_subtype_file)

tilheat <- ithi.figures::plot_til_density_heatmap(ihc_table, tiltypes, nclusts, 
    molsubtypes, annotation_colours)

tilclust <- as.hclust(ComplexHeatmap::column_dend(tilheat))
clusters <- cutree(tilclust, nclusts) %>% as.data.frame %>% setNames(c("cluster")) %>% 
    tibble::rownames_to_column(var = "condensed_id")

plot_mapscape <- function(input_dir) {
    patient_id <- stringr::str_extract(input_dir, "[0-9]+$")
    
    clonal_prev = read.table(file.path(input_dir, "clonal_prevalence_table.tsv"), 
        sep = "\t", header = T)
    tree_edges = read.table(file.path(input_dir, "tree_edges.tsv"), sep = "\t", 
        header = T)
    sample_locations = read.table(file.path(input_dir, "sample_locations.tsv"), 
        sep = "\t", header = T)
    sample_locations$long_sample_id <- df_as_map(clonal_prev, sample_locations$sample_id, 
        from = "sample_id", to = "long_sample_id")
    img_ref = "/shahlab/alzhang/projects/ITH_Immune/paper/miscellaneous/FF4D00-0.8.png"
    # img_ref =
    # '~/shahlab/projects/ITH_Immune/paper/miscellaneous/FF4D00-0.8.png'
    
    clonal_prev <- reformat_andrew_table(clonal_prev, db_path, patient_id)
    
    
    sample_locations <- reformat_andrew_table(sample_locations, db_path, patient_id)
    sample_locations <- subset(sample_locations, select = c(sample_id, location_id, 
        x, y))
    
    sample_colours <- unique(subset(clonal_prev, select = c(sample_id, condensed_id)))
    sample_colours$colour <- ithi.meta::df_as_map(clusters, sample_colours$condensed_id, 
        from = "condensed_id", to = "cluster") %>% plyr::mapvalues(from = c(1, 
        2, 3), to = c("N-TIL", "S-TIL", "ES-TIL")) %>% plyr::mapvalues(from = names(cluster_colours), 
        to = unname(cluster_colours)) %>% stringr::str_extract("#[0-9A-Z]{6}")
    sample_colours$colour[is.na(sample_colours$colour)] <- "#000000"
    
    til_cluster_colours <- data.frame(cluster = names(cluster_colours), colour = stringr::str_extract(unname(cluster_colours), 
        "\\#[0-9A-Z]{6}"))
    
    clonal_prev <- subset(clonal_prev, select = c(clone_idx, long_sample_id, 
        clonal_prev, sample_id, clone_id))
    
    plot_title <- paste0("Patient ", patient_id)
    
    mapscape(clonal_prev = clonal_prev, tree_edges = tree_edges, sample_locations = sample_locations, 
        img_ref = img_ref, show_warnings = FALSE, sample_colours = sample_colours, 
        til_cluster_colours = til_cluster_colours, plot_title = plot_title)
}

Plots

htmltools::tagList(lapply(mapscape_input_directories, function(dir) {
    patient_id <- stringr::str_extract(dir, "[0-9]+$")
    print(patient_id)
    plot_mapscape(dir)
}))

[1] "1"
[1] "2"
[1] "3"
[1] "4"
[1] "7"
[1] "9"
[1] "10"
[1] "11"
[1] "12"
[1] "13"
[1] "14"
[1] "15"
[1] "16"
[1] "17"