plotfeatmap: Highlighting feature values in a dimensional reduction representation

Description

This functions highlights feature values in a two-dimensional t-SNE map, UMAP, or a Fruchterman-Rheingold graph layout of the singe-cell transcriptome data.

Usage

plotfeatmap(
  object,
  g,
  n = NULL,
  logsc = FALSE,
  fr = FALSE,
  um = FALSE,
  cells = NULL,
  cex = 1,
  map = TRUE,
  leg = TRUE,
  flo = NULL,
  ceil = NULL
)

Value

None

Arguments

object: SCseq class object.
g: Vector of real numbered features to highlight in the dimensional reduction representation, NAs will be highlighted in grey.
n: String of characters representing the title of the plot. Default is NULL and the first element of g is chosen.
logsc: logical. If TRUE, then feature values are log2-transformed. Default is FALSE. and untransformed values are shown.
fr: logical. If TRUE then plot Fruchterman-Rheingold layout. Default is FALSE.
um: logical. If TRUE then plot umap dimensional reduction representation. Default is FALSE.
cells: Vector of valid cell names corresponding to column names of slot ndata of the SCseq object. Gene expression is ony shown for this subset.
cex: size of data points. Default value is 1.
map: logical. If TRUE then data points are shown. Default value is TRUE.
leg: logical. If TRUE then the legend is shown. Default value is TRUE.
flo: Numeric. Lower bound for feature values. All values smaller then flo are replaced by flo. #' Default is NULL and no fllo is applied.
ceil: Numeric. Upper bound for feature values. All values larger then ceil are replaced by ceil. Default is NULL and no ceil is applied.