cnaScatterPlot: Visualise Malignant and Non-Malignant Subsets

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

Visualise Malignant and Non-Malignant Subsets

Description

Visualise Malignant and Non-Malignant Subsets of cells. This is achieved by plotting, for each cell, its CNA signal over its CNA correlation. Please see 'infercna::cnaSignal' and 'infercna::cnaCor' for details.

Usage

cnaScatterPlot(
  cna,
  cor.method = "pearson",
  gene.quantile = NULL,
  gene.quantile.for.corr = gene.quantile,
  gene.quantile.for.signal = gene.quantile,
  groups = NULL,
  groups.col = scalop::discrete_colours[1:length(groups)],
  border.col = "black",
  alpha = 0.3,
  cex = 0.8,
  pch = 20,
  hline = NULL,
  vline = NULL,
  refCells = NULL,
  samples = NULL,
  ...
)

Arguments

cna	a matrix of gene rows by cell columns containing CNA values.
cor.method	character string indicating the method to use for the pairwise correlations. E.g. 'pearson', 'spearman'. Default: 'pearson'
gene.quantile	calculate CNA measures including only top / "hotspot" genes according to their squared CNA values across all cells. Value between 0 and 1 denoting the quantile of genes to include. Default: NULL
gene.quantile.for.corr	as above but for CNA correlations specifically. Default: gene.quantile
gene.quantile.for.signal	as above but for CNA signal specifically. Default: gene.quantile
groups	character vector of cell IDs to colour. Default: NULL
groups.col	colour to colour groups by. Default: 'magenta'
border.col	colour for point border. Default: 'black'
alpha	colour transparency. Default: 0.3
hline	y-intercept line. Default: NULL
vline	x-intercept line. Default: NULL
refCells	a character vector of cell ids to exclude from average CNA profile that each cell is correlated to. You can pass reference normal cell ids to this argument if these are known. Default: NULL
samples	if CNA correlations should be calculated within cell subgroups, provide i) a list of cell id groups, ii) a character vector of sample names to groups cells by, iii) TRUE to extract sample names from cell ids and subsequently groups. Default: NULL
...	other arguments passed to base plot

Value

a base R plot. If return value is saved to a variable, instead returns data points for cna correlations and cna signal in list form.

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