This functions highlights gene expression in a two-dimensional t-SNE map or a Fruchterman-Rheingold graph layout of the singe-cell transcriptome data.
plotexpmap(object, g, n = NULL, logsc = FALSE, imputed = FALSE,
fr = FALSE, cells = NULL, cex = 1, map = TRUE, leg = TRUE)SCseq class object.
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.
String of characters representing the title of the plot. Default is NULL and the first element of g is chosen.
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.
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.
logical. If TRUE then plot t-SNE map, else plot Fruchterman-Rheingold layout.
Vector of valid cell names corresponding to column names of slot ndata of the SCseq object. Gene expression is ony shown for
this subset.
size of data points. Default value is 1.
logical. If TRUE then data points are shown. Default value is TRUE.
logical. If TRUE then the legend is shown. Default value is TRUE.
None