Plot a heatmap of marker genes fold change over metacells

Usage

plot_rna_markers_mat(
  mat,
  metacell_types = NULL,
  cell_type_colors = NULL,
  low_color = "blue",
  high_color = "red",
  mid_color = "white",
  midpoint = 0,
  min_lfp = -3,
  max_lfp = 3,
  plot_legend = TRUE,
  top_cell_type_bar = TRUE,
  gene_colors = NULL,
  col_names = FALSE,
  row_names = TRUE,
  col_names_orient = "slanted",
  plot_right = TRUE,
  interleave = TRUE,
  vertial_gridlines = FALSE,
  annotation_title = "Cell type",
  top_annotation_title = "Cell type",
  title = NULL
)

Arguments

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)
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.
col_names_orient: Orientation of the X-axis label
plot_right: Whether to put the Y-axis labels at the right side of the heatmap (as well as at the left hand side)
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
vertical_gridlines: show vertical gridlines

Value

a ggplot object with the heatmap (and legend if plot_legend is TRUE)

Examples

if (FALSE) {
m_rna <- get_rna_marker_matrix(atac_mc)
plot_rna_markers_mat(m_rna, atac_mc@metadata, atac_mc@metadata, col_names = F)
}