plotfeatmap: Highlighting feature values in a dimensional reduction...

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

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
)

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.

Value

None

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.