Plot a heatmap of marker genes fold change over metacells given an McPeaks object

This is a thin wrapper around plot_rna_markers_mat which computes the marker matrix and uses the correct metadata fields in the McPeaks object.

Usage

plot_rna_markers(atac_mc, n_genes = 100, force_cell_type = TRUE, ...)

Arguments

atac_mc

a McPeaks object with RNA expression (using add_mc_rna)

n_genes

maximal number of genes to return. Default: 100

force_cell_type

do not split cell types when ordering the metacells. Default: TRUE

...

Arguments passed on to plot_rna_markers_mat

mat

a heatmap of marker genes fold change over metacells (e.g. output of get_rna_marker_matrix)

metacell_types

a data frame with a field called "metacell" and a field called "cell_type" (optional)

cell_type_colors

a data frame with a field called "cell_type" and a field called "color" (optional)

low_color

a color for low fold change

high_color

a color for high fold change

mid_color

a color for mid fold change

midpoint

midpoint for the color scale (default: 0)

min_lfp

minimum log2 fold change (default: -3). Value below this will be set to min_lfp.

max_lfp

maximum log2 fold change (default: 3). Value above this will be set to max_lfp.

plot_legend

TRUE to plot a legend of the cell types (default: TRUE)

top_cell_type_bar

add a cell type annotation also at the top of the heatmap (default: TRUE)

gene_colors

a named list with a color for each marker gene (optional)

col_names

show column names (metacells)

interleave

show the gene names (rows) interleaved

annotation_title

title for cell type annotation. Default: "Cell type"

top_annotation_title

title for top cell type annotation. Default: "Cell type"

title

title for the plot

row_names

The names that will be used as the Y-axis labels. A NULL (the defualt) indicates that the original matrix rownames are used. A FALSE indicates that no Y-axis labels should be displayed.

plot_right

Whether to put the Y-axis labels at the right side of the heatmap (as well as at the left hand side)

col_names_orient

Orientation of the X-axis label

Examples

if (FALSE) {
plot_rna_markers(atac_mc)
}