plotQuantMap: Plotting noise-related quantaties of local pruned k-nearest neighbourhoods

Description

Plotting noise-related quantaties of local pruned k-nearest neighbourhoods in the dimensional reduction representation chosen for quantKnn or as boxplot across clusters.

Usage

plotQuantMap(
  x,
  n,
  object,
  box = FALSE,
  cluster = NULL,
  set = NULL,
  logsc = FALSE,
  cex = 0.5,
  ...
)

Value

None

Arguments

x: List object returned by quantKnn function.
n: Component name of x. One of "noise.av", "noise.ratio", "local.corr", "umi".
object: SCseq class object.
box: Logical. If TRUE, then data are shown as boxplot across clusers. Default is FALSE and a dimensional reduction representation is shown.
cluster: Valid cluster number or vector of cluster numbers, contained in object@cpart. If given and box=TRUE then the median of the feature values across clusters in cluster is indicated as a black solid line in the boxplot. Default is NULL.
set: Ordered set of valid cluster numbers. If box equals TRUE than data will only be plotted for these clusters in the given order. Default is NULL and data for all clutsers will be shown.
logsc: logical. If TRUE, then feature values are log2-transformed. Default is FALSE.
cex: Real positive number. Size of data points. Default is 0.5.
...: Additional parameters of plotfeatmap if box=FALSE (e.g., um or fr to select dimensional reduction representation, see help(plotfeatmap)), or of plotB (e.g., ylim, see help(plotB)).