plotexpmap: Highlighting gene expression in a dimensional reduction representation

Description

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

Usage

plotexpmap(
  object,
  g,
  n = NULL,
  logsc = FALSE,
  imputed = FALSE,
  fr = FALSE,
  um = FALSE,
  cells = NULL,
  cex = 0.5,
  map = TRUE,
  leg = TRUE,
  noise = FALSE
)

Value

None

Arguments

object: SCseq class object.
g: Individual gene name or vector with a group of gene names corresponding to a subset of valid row names of the ndata slot of the SCseq object.
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 gene expression values are log2-transformed after adding a pseudo-count of 0.1. Default is FALSE and untransformed values are shown.
imputed: logical. If TRUE and imputing was done by calling compdist with knn > 0, then imputed expression values are shown. If FALSE, then raw counts are shown. Default is FALSE.
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 0.5.
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.
noise: logical. If TRUE then display local gene expression variability instead of gene expression (requires VarID analysis)/ Default value is FALSE.