#' Plot a nested list of genes as a multi-page pdf
#'
#' This function plots a nested list of genes as a multi-page PDF, one for each sub list.
#' A use case is plotting known marker genes for multiple cell types over cell type
#' clusters with unknown identities.
#'
#' @param sce [SummarizedExperiment-class][SummarizedExperiment::SummarizedExperiment-class] object
#' @param pdf_fn A `character()` of the pdf filename to plot to, if `NULL` returns all plots
#' @param gene_list A named list containing the names of genes to plot
#' @param cellType_col The `character()` name of `colData` column containing cell type for `sce` data
#' @param gene_name_col The `character()` name of `rowData` matching the gene name from `gene_list`
#' @param color_pal A named `character(1)` vector that contains a color pallet matching the values in `cellType_col`.
#' @param plot_points A logical indicating whether to plot points over the violin,
#' defaults to `FALSE` as these often become over plotted and quite large (especially when saved as PDF)
#' #' @inheritParams plot_marker_express_ALL
#'
#' @return A pdf with violin plots for the expression of top marker genes for all cell types
#'
#' @export
#'
#' @examples
#' ## Fetch sce example data
#' if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
#'
#' ## Create list-of-lists of genes to plot, names of sub-list become title of page
#' my_gene_list <- list(Inhib = c("GAD2", "SAMD5"), Astro = c("RGS20", "PRDM16"))
#'
#' # Return a list of plots
#' plots <- plot_marker_express_List(
#' sce_DLPFC_example,
#' gene_list = my_gene_list,
#' cellType_col = "cellType_broad_hc"
#' )
#'
#' print(plots[[1]])
#'
#' # Plot marker gene expression to PDF, one page per cell type in stats
#' pdf_file <- tempfile("test_marker_expression_List", fileext = ".pdf")
#'
#' plot_marker_express_List(
#' sce_DLPFC_example,
#' gene_list = my_gene_list,
#' pdf_fn = pdf_file,
#' cellType_col = "cellType_broad_hc"
#' )
#'
#' if (interactive()) browseURL(pdf_file)
#'
#' @family expression plotting functions
#' @importFrom ggplot2 ggplot geom_violin geom_text facet_wrap stat_summary
#' @importFrom SummarizedExperiment colData
plot_marker_express_List <- function(
sce,
gene_list,
pdf_fn = NULL,
cellType_col = "cellType",
gene_name_col = "gene_name",
color_pal = NULL,
plot_points = FALSE) {
stopifnot(cellType_col %in% colnames(colData(sce)))
if (!identical(rownames(sce), SummarizedExperiment::rowData(sce)[[gene_name_col]])) {
message("Using ", gene_name_col, " as gene names")
rownames(sce) <- SummarizedExperiment::rowData(sce)[[gene_name_col]]
}
marker_plots <- purrr::map2(
gene_list, names(gene_list),
~ plot_gene_express(
sce = sce,
genes = .x,
cat = cellType_col,
color_pal = color_pal,
plot_points = plot_points,
title = .y
)
)
if (is.null(pdf_fn)) {
return(marker_plots)
} else {
grDevices::pdf(pdf_fn)
print(marker_plots)
grDevices::dev.off()
}
}
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