mcell_mc_plot_marks: plot a marker heat map give a metacell object
In tanaylab/metacell: Meta cell analysis for single cell RNA-seq data

mcell_mc_plot_marks

R Documentation

plot a marker heat map give a metacell object

Description

plot a marker heat map give a metacell object

Usage

mcell_mc_plot_marks(
  mc_id,
  gset_id,
  mat_id = mc_id,
  fig_fn = NULL,
  lateral_gset_id = NULL,
  mc_ord = NULL,
  plot_cells = T,
  zero_median = T,
  add_genes = NULL,
  add_metadata = NULL,
  ext_metadata = NULL,
  md_level_colors = NULL,
  focus_mcs = NULL,
  gene_list = NULL,
  reorder_marks = F,
  fold_burn = 3
)

Arguments

`mc_id`	id of metacell object ina scdb
`gset_id`	markers to plot (e.g. using mcell_gset_from_mc_markers)
`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
`fig_fn`	file name for the figure (if null it will be call heat_marks in the fig directory)
`lateral_gset_id`	markers to plot on top (e.g. cell cycle)
`plot_cells`	by defulat this is TRUE and data is shown for single cells. If this is false, than metacells fold change values will be plotted
`zero_median`	if this is true then for each gene, all values below the median will be plotted as "0". It can save some noise but will make genes that are anit-enriched in some MC non visible.
`add_genes`	A list of marker genes to be added manually
`add_metadata`	name of metadata field to add below hte heat map
`ext_metadata`	values of metadata per cell to add (a anamed vector, with some or all of the cell names specified)
`md_level_colors`	what colors to use for the metadata levels, if present
`focus_mcs`	option list of MC IDs in case only some of the model should be plotted
`gene_list`	a list of gene names to replcace the markers from a gset_id