plot_marker_express_ALL: Plot the top marker genes for ALL cell types
In LieberInstitute/DeconvoBuddies: Helper Functions for LIBD Deconvolution

View source: R/plot_marker_express_ALL.R

plot_marker_express_ALL

R Documentation

Plot the top marker genes for ALL cell types

Description

This function plots the top n marker genes for a all cell types based off of the stats table from get_mean_ratio() in a multi-page PDF file. The gene expression is plotted as violin plot with plot_gene_express() and adds annotations to each plot.

Usage

plot_marker_express_ALL(
  sce,
  stats,
  pdf_fn = NULL,
  n_genes = 10,
  rank_col = "MeanRatio.rank",
  anno_col = "MeanRatio.anno",
  gene_col = "gene",
  cellType_col = "cellType",
  color_pal = NULL,
  plot_points = FALSE
)

Arguments

`sce`	SummarizedExperiment-class object
`stats`	A `data.frame()` generated by `get_mean_ratio()` and/or `findMarkers_1vAll()`.
`pdf_fn`	A `character()` of the pdf filename to plot to, if `NULL` returns all plots
`n_genes`	An `integer(1)` of number of markers you'd like to plot
`rank_col`	The `character(1)` name of column to rank genes by in `stats`.
`anno_col`	The `character(1)` name of column containing annotation in `stats`.
`gene_col`	The `character(1)` name of column containing gene name in `stats` should be the same syntax as `rownames(sce)`.
`cellType_col`	The `character(1)` name of `colData()` column containing cell type for `sce` data. It should match `cellType.target` in `stats`.
`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")

## load example marker stats
data("marker_test")

# Plot marker gene expression to PDF, one page per cell type in stats
pdf_file <- tempfile("test_marker_expression_ALL", fileext = ".pdf")

plot_marker_express_ALL(
    sce_DLPFC_example,
    cellType_col = "cellType_broad_hc",
    stat = marker_test,
    pdf_fn = pdf_file
)

if (interactive()) browseURL(pdf_file)

LieberInstitute/DeconvoBuddies documentation built on Nov. 1, 2024, 11:58 a.m.