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

Source: R/plot_marker_express_List.R

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.

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.

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")
#> 2024-10-31 13:27:33.716845 loading file /github/home/.cache/R/BiocFileCache/66141272054e_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1

## 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"
)
#> $Inhib
#> 
#> $Astro
#> 
#> pdf 
#>   2 

if (interactive()) browseURL(pdf_file)