View source: R/plot_marker_express_List.R
plot_marker_express_List | R Documentation |
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
)
sce |
SummarizedExperiment-class object |
gene_list |
A named list containing the names of genes to plot |
pdf_fn |
A |
cellType_col |
The |
gene_name_col |
The |
color_pal |
A named |
plot_points |
A logical indicating whether to plot points over the violin,
defaults to |
A pdf with violin plots for the expression of top marker genes for all cell types
Other expression plotting functions:
plot_gene_express()
,
plot_marker_express()
,
plot_marker_express_ALL()
## 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)
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