plotexpmap {RaceID}

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
)

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.

Value

None