Plot gene expression violin plots for top marker genes for one cell type

Source: R/plot_marker_express.R

This function plots the top n marker genes for a specified cell type based off of the stats table from get_mean_ratio2(). The gene expression is plotted as violin plot with plot_gene_express and adds annotations to each plot.

plot_marker_express(
  sce,
  stats,
  cell_type,
  n_genes = 4,
  rank_col = "MeanRatio.rank",
  anno_col = "MeanRatio.anno",
  gene_col = "gene",
  cellType_col = "cellType",
  color_pal = NULL,
  plot_points = FALSE,
  ncol = 2
)

Arguments

sce

SummarizedExperiment-class object

stats

A data.frame() generated by get_mean_ratio() and/or findMarkers_1vAll().

cell_type

A character() target cell type to plot markers for

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).

ncol

An integer(1) specifying the number of columns for the facet in the final plot. Defaults to 2.

Value

A ggplot2 object created with plot_gene_express(). It is a scater::plotExpression() style violin plot for selected marker genes.

See also

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

Examples

## Download the processed study data from
## <https://github.com/LieberInstitute/Human_DLPFC_Deconvolution>.
if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
#> 2024-12-16 18:01:06.973173 loading file /github/home/.cache/R/BiocFileCache/30161ee4ad2_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1

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

## Plot the top markers for Astrocytes
plot_marker_express(
    sce = sce_DLPFC_example,
    stat = marker_test,
    cellType_col = "cellType_broad_hc",
    cell_type = "Astro",
    gene_col = "gene"
)