plot_marker_express_List: Plot a nested list of genes as a multi-page pdf
In LieberInstitute/DeconvoBuddies: Helper Functions for LIBD Deconvolution

View source: R/plot_marker_express_List.R

plot_marker_express_List

R Documentation

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()` of `character()` vectors 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(1)` name of `colData()` column containing cell type for `sce` data. It should match `cellType.target` in `stats`.
`gene_name_col`	The `character(1)` name of `rowData()` matching the gene name from `gene_list`.
`color_pal`	A named `character(1)` vector that contains a color pallet matching the `cell_type` values.
`plot_points`	A `logical(1)` 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).

Value

A PDF file with violin plots for the expression of top marker genes for all cell types.

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)

LieberInstitute/DeconvoBuddies documentation built on Dec. 16, 2024, 10:32 p.m.