mcell_mc_plot_submc_marks: plot a marker heat map for a subset of metacells - selecting...

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

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

Description

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

Usage

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

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