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

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