Plot normalized accessibility of peaks over metacells, ordered by clustering

Usage

plot_atac_peak_map(
  atac_mc,
  atac_mc_clust = NULL,
  peak_clust = NULL,
  peak_annotation = NULL,
  filename = NULL,
  dev = png,
  main = atac_mc@id,
  colors = colorRampPalette(c("blue4", "white", "red4"))(100),
  ...
)

Arguments

atac_mc

McPeaks object

atac_mc_clust

output of gen_atac_mc_clust (for meaningful visuals, make sure this is ordered by cluster)

peak_clust

output of gen_atac_peak_clust or other clustering of peaks (for meaningful visuals, make sure this is ordered by cluster)

peak_annotation

(optional) a list of a named vector and a dataframe conforming to the pheatmap annotation_colors and annotation_row conventions

filename

(optional) path and filename of where to save the figure; if unspecified, figure isn't saved

dev

(optional; default - png) graphical device to save figure with

colors

(optional) colorRampPalette vector of colors for scaling colors in heatmap

...

Arguments passed on to save_pheatmap

width: the width of the device.
height: the height of the device.
res: The nominal resolution in ppi which will be recorded in the bitmap file, if a positive integer. Also used for units other than the default, and to convert points to pixels.

Value

a pheatmap figure.

Examples

if (FALSE) {
peak_clust <- gen_atac_peak_clust(my_mcatac, 16)
plot_atac_peak_map(my_mcatac, order(my_mcatac@metadata$cell_type), order(peak_clust), "./my_figures/my_mcatac_heatmap.png")

## Peak annotation example
is_dyn <- setNames(as.numeric(rownames(my_mcatac@mat) %in% my_mcatac_dynamic_peaks_only@peaks$peak_name), rownames(my_mcatac@mat))
pa1 <- list("is_dyn" = setNames(c("black", "red"), c(0, 1)))
pa2 <- tibble::column_to_rownames(enframe(is_dyn, name = "peak_name", value = "is_dyn"), "peak_name")
pa <- list(pa1, pa2)
plot_atac_peak_map(my_mcatac, atac_mc_clust = order(my_mcatac@metadata$cell_type), peak_annotation = pa)
}