plotexpmap {RaceID} | R Documentation |
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
[Package
RaceID version 0.3.7
Index]