plot a marker heat map for a subset of metacells - selecting relevant genes for separation

plot a marker heat map for a subset of metacells - selecting relevant genes for separation

mcell_mc_plot_submc_marks(
  mc_id,
  mat_id,
  foc_mcs,
  fig_fn,
  n_max_marks = 10,
  add_genes = NULL,
  zero_median = F,
  h = 800,
  w = 600
)

Arguments

mc_id

id of metacell object ina scdb

mat_id

matrix object to us (default is the mc_id - assuming they use the same ID), if some cells in mc@mc are missing from the matrix, the function will generate an error

foc_mcs

list of metacell ids to focus on

fig_fn

file name for the figure (if null it will be call heat_marks in the fig directory)

zero_median

should median expression be used for trimming low umi counts

h

height

w

height

n_max_mark

number of markers for separation on each metacell

ddd_genes

specific list of genes to add to the marker list