plot_marker_express_List: Plot a nested list of genes as a multi-page pdf

In lahuuki/DeconvoBuddies: Helper Functions for LIBD Deconvolution

Plot a nested list of genes as a multi-page pdf

Description

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.

Usage

plot_marker_express_List(
  sce,
  gene_list,
  pdf_fn = NULL,
  cellType_col = "cellType",
  gene_name_col = "gene_name",
  color_pal = NULL,
  plot_points = FALSE
)

Arguments

sce	SummarizedExperiment-class object
gene_list	A named list containing the names of genes to plot
pdf_fn	A character() of the pdf filename to plot to, if NULL returns all plots
cellType_col	The character() name of colData column containing cell type for sce data
gene_name_col	The character() name of rowData matching the gene name from gene_list
color_pal	A named character(1) vector that contains a color pallet matching the values in cellType_col.
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

Value

A pdf with violin plots for the expression of top marker genes for all cell types

See Also

Other expression plotting functions: plot_gene_express(), plot_marker_express(), plot_marker_express_ALL()

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)

lahuuki/DeconvoBuddies documentation built on Aug. 12, 2024, 8:38 p.m.