ggcna: Plot a CNA heatmap

In jlaffy/infercna: Infer Copy Number Alterations And Clonality In (Single-Cell) RNA-seq Data

Plot a CNA heatmap

Description

Uses 'ggplot::geom_raster' to generate a plot of copy number aberration (CNA) values. Delineates chromosomes and chromosome arms, and provides options for clustering cells or groups of cells (e.g., cell types, samples, or subclones) prior to plotting.

Usage

ggcna(
  m,
  reorder = FALSE,
  reorder.by = NULL,
  groups = NULL,
  interorder = TRUE,
  genome = "hg19",
  dist.method = "euclidean",
  cluster.method = "complete",
  hide = c("21", "Y"),
  limits = c(-1, 1),
  y.angle = 90,
  legend.title = NULL,
  title = "Copy-number aberrations",
  axis.text.size = 12,
  legend.height = 0.3,
  legend.width = 0.5,
  cols = NULL,
  ...
)

Arguments

m	CNA matrix (genes by cells). <m> can be generated using 'infercna::infercna'.
reorder	reorder cells using hierarchical clustering, Default: FALSE
reorder.by	reorder cells by genes on select chromosomes or chromosome arms, e.g., c("7", "10", "1p", "19q"). Default: NULL
groups	groups of cells to delineate and label on the plot (e.g., cell types, samples, or subclones). If <reorder> is TRUE, ordering will be performed within groups, Default: NULL
interorder	reorder by hierarchical clustering betweeen groups, Default: TRUE
genome	set genome to use ('hg19' or 'hg38'), Default: 'hg19'
dist.method	distance metric for reordering, Default: 'euclidean'
cluster.method	linkage method for reordering, Default: 'complete'
hide	hide x-axis labels for specific chromosomes (e.g., small chromosomes whose labels would overlap flanking labels), Default: c("21", "Y")
limits	for the colour key; replaces out of bounds values with the nearest limit. Default: c(-1, 1)
y.angle	y-axis labels' angle, Default: 90
legend.title	legend title, Default: NULL
title	plot title, Default: 'Copy-number aberrations'
axis.text.size	x and y axes label size, Default: 12
legend.height	legend bar height, Default: 0.3
legend.width	legend bar width, Default: 0.5
cols	custom colour palette (character vector), Default: NULL
...	other arguments to pass to 'scalop::graster'.

Details

DETAILS

Value

a 'ggplot' object

Examples

cna = infercna::infercna(mgh125, isLog=T, refCells=refCells)
malCells = list(Malignant=setdiff(colnames(mgh125), unlist(refCells)))
groups = c(malCells, refCells)
p = ggcna(m, reorder=T, groups=refCells)

jlaffy/infercna documentation built on Jan. 26, 2024, 11:24 p.m.