mcell_mc_plot_hierarchy: plot super strucutre: super clust mc footprint, and selected...

In tanaylab/metacell: Meta cell analysis for single cell RNA-seq data

plot super strucutre: super clust mc footprint, and selected genes

Description

plot super strucutre: super clust mc footprint, and selected genes

Usage

mcell_mc_plot_hierarchy(
  mc_id,
  graph_id,
  mc_order,
  sup_mcs,
  width,
  height,
  fig_fn = NULL,
  min_nmc = 2,
  shades = colorRampPalette(c("white", "pink", "red", "black", "brown", "orange")),
  plot_grid = T,
  show_mc_ids = F
)

Arguments

mc_id	id of metacell object
graph_id	id of graph for (Re-) constructing confusion matrix
mc_order	the mc ordering (e.g., hc$order using the output of mcell_mc_hclust_confu)
sup_mcs	the list you get from mcell_mc_hierarchy (for now)
width	width of figure in pixels
height	height of figure in pixels
fig_fn	figure name (NULL will create a figure named [mc_id]_supmc_confu in the figure directory)
min_nmc	minimal number of mc in supmc set, smaller gruops will not be plotted
shades	heatmap color palette
plot_grid	plot vertical grid in the heatmap
show_mc_ids	plot mc ids below the heatmap

tanaylab/metacell documentation built on Jan. 29, 2025, 1:34 a.m.