Visualise Malignant and Non-Malignant Subsets

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.

cnaScatterPlot(cna, cor.method = "pearson", threshold = NULL,
  cor.threshold = threshold, signal.threshold = threshold,
  group = NULL, group.col = "magenta", cex = 0.5, hline = NULL,
  vline = NULL, bySample = FALSE, samples = NULL, sep = "-|_",
  excludeFromAvg = 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'
threshold	PARAM_DESCRIPTION, Default: NULL
cor.threshold	PARAM_DESCRIPTION, Default: threshold
signal.threshold	PARAM_DESCRIPTION, Default: NULL
group	PARAM_DESCRIPTION, Default: NULL
group.col	PARAM_DESCRIPTION, Default: 'magenta'
hline	PARAM_DESCRIPTION, Default: NULL
vline	PARAM_DESCRIPTION, Default: NULL
bySample	PARAM_DESCRIPTION, Default: FALSE
samples	a character vector of sample names list of character vectors (cell/column names). Can be provided if the cna matrix contains multiple samples of cells, i.e. multiple tumours, such that the cell-group correlations are calcualted for each group/tumour in turn. Default: FALSE
sep	if bySample is TRUE and samples are NULL, split cell IDs by <sep> and take the first substring to be the sample name. Default: '-|_'
excludeFromAvg	a character vector of cell IDs to exclude from the average tumour profile. Default: NULL
...	other arguments passed to base plot
samples	PARAM_DESCRIPTION, Default: NULL

Value

a base R plot

Details

DETAILS

Examples

# NOT RUN {
if(interactive()){
 #EXAMPLE1
 }
# }