mcell_mc2d_plot_by_factor: Plot mc+cells using pre-defined mc colorization, breakdown by...

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

Plot mc+cells using pre-defined mc colorization, breakdown by given metadata field (e.g. patient)

Description

Plot mc+cells using pre-defined mc colorization, breakdown by given metadata field (e.g. patient)

Usage

mcell_mc2d_plot_by_factor(
  mc2d_id,
  mat_id,
  meta_field,
  meta_data_vals = NULL,
  single_plot = T,
  filter_values = NULL,
  filter_name = NULL,
  ncols = NULL,
  neto_points = F,
  colors = NULL,
  base_dir = NULL,
  filt_mc = NULL,
  na_color = "white"
)

Arguments

mc2d_id	mc2d object to use for plot
mat_id	mat object matching mc2d_id that contains the cells metadata information
meta_field	field name (in mat cell_metadata slot) to split cells by
meta_data_vals	actual named vector (names are cells, values are the metadata to factor on), if this is not null, the meta_field is not used
single_plot	output all panels in a single plot or plot per panel (T)
filter_values	to filter meta_field values by (NULL)
filter_name	name to add to plots (NULL)
ncols	number of panels in column (if single_plot is true), automatically calculate if NULL
neto_points	plot without a box and a title (relevant if single_plot=F)

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