Plot RNA and ATAC marker matrix side by side — plot_atac_rna

plot an rna marker heatmap (right) together with an heatmap of fold change of ATAC peaks that are the most correlated to each marker gene (left, using get_genes_atac_fp).

Usage

plot_atac_rna_markers(
  atac_mc,
  n_genes = 100,
  force_cell_type = TRUE,
  plot_legend = TRUE,
  row_names = FALSE,
  ...
)

Arguments

atac_mc

a McPeaks/McTracks 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

plot_legend

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

row_names

show the row names of the heatmaps. Note that the space each plot takes might become uneven due to genes / peaks with longer names.

...

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.
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
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

Value

a ggplot object with the heatmap of RNA markers (right) and the heatmap of ATAC peaks (left). The ATAC matrix is ordered by the RNA matrix.

a ggplot object with the heatmaps

Examples

if (FALSE) {
plot_atac_rna_markers(atac_mc)
plot_atac_rna_markers(atac_mc, force_cell_type = FALSE)
plot_atac_rna_markers(atac_mc, n_genes = 200)
}