fractDotPlot: Dotplot of gene expression across clusters or samples

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

Dotplot of gene expression across clusters or samples

Description

This is a plotting function for visualizing gene expression across subsets of clusters or samples. The diameter of a dot reflects the fraction of cells expressing a gene, and the color indicates the expression z-score across all clusters or samples.

Usage

fractDotPlot(
  object,
  genes,
  cluster = NULL,
  samples = NULL,
  subset = NULL,
  zsc = FALSE,
  logscale = TRUE,
  cap = Inf,
  flo = -Inf
)

Arguments

object	SCseq class object.
genes	vector of valid gene names corresponding to row names of slot ndata. The expression for this genes is shown.
cluster	vector of valid cluster numbers contained in slot cpart. Default is NULL. If not given, then the samples argument is expected. If both are given, only the samples argument is considered. If both are NULL, then cluster is initialized with all clusters.
samples	vector of sample names for all cells. Length and order has to correspond to colnames of slot ndata. Default is NULL.
subset	vector of unique sample names to show in the expression dotplot. Each sample names in subset has to occur in samples. Default is NULL. If not given and samples is not NULL, the subset is intialized with all sample names occuring in samples.
zsc	logical. If TRUE then a z-score transformation is applied. Default is FALSE.
logscale	logical. If TRUE then a log2 transformation is applied. Default is TRUE.
cap	real number. Upper limit for the expression, log2 expression, or z-score. Values larges then cap are replaced by cap.
flo	real number. Lower limit for the expression, log2 expression, or z-score. Values smaller then flo are replaced by flo.

Value

None

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