plot_clones: Plot cluster/clone information

In dkzhang777/SlideCNA: Calls Copy Number Alterations from Slide-Seq Data

Plot cluster/clone information

Description

This function plots cluster dendrograms, spatial assignment, and the CNV heat map

Usage

plot_clones(
  cnv_data,
  md,
  k,
  type,
  chrom_colors,
  text_size,
  title_size,
  legend_size_pt,
  legend_height_bar,
  hc_function = "ward.D2",
  plot_directory,
  spatial = TRUE
)

Arguments

cnv_data	list object of cnv data from SlideCNA::prep_cnv_dat()
md	data.table of metadata of each bead
k	integer of number of clusters/clones
type	character string, being "all" if using all binned beads, or "malig" if just malignant binned beads
chrom_colors	vector of colors labeled by which chromosome they correspond to
text_size	Ggplot2 text size
title_size	Ggplot2 title size
legend_size_pt	Ggplot2 legend_size_pt
legend_height_bar	Ggplot2 legend_height_bar
hc_function	character string for which hierarchical clustering function to use
plot_directory	output plot directory path
spatial	TRUE if using spatial information

Value

A hierarchical clustering object of the clusters

dkzhang777/SlideCNA documentation built on Jan. 25, 2025, 5:53 p.m.