visPlot: visPlot

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description

Given a plotting method with condition and gene list, return the respective visualization plot(s).

Usage

visPlot(
  inSCE,
  useAssay,
  method,
  condition = NULL,
  glist,
  facetWrap = TRUE,
  scaleHMap = TRUE,
  convertFactor = FALSE
)

Arguments

inSCE	Input SingleCellExperiment object.
useAssay	The assay to use in the visualization plot. Required
method	Visualization method. Available options are boxplot, scatterplot, or heatmap. Required
condition	colData annotation of the experiment. Required
glist	selected genes for visualization. Maximum 25 genes. Required
facetWrap	facet wrap according to genes for boxplot, scatterplot and barplot. Default is FALSE. Optional
scaleHMap	scale heatmap expression values. Default is TRUE. Optional
convertFactor	If the condition is not a factor, convert it to a factor before plotting. The default is FALSE

Value

A visualization plot

Examples

visPlot(mouseBrainSubsetSCE, "logcounts", "boxplot", "level1class", "C1qa")
visPlot(mouseBrainSubsetSCE, "counts", "scatterplot", "age", "Cmtm5")
visPlot(mouseBrainSubsetSCE, "counts", "heatmap", "level1class",
        c("Cmtm5", "C1qa"))

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.