visPlot

Source: R/visPlot.R

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

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")

#> Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
visPlot(mouseBrainSubsetSCE, "counts", "scatterplot", "age", "Cmtm5")

#> Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
visPlot(mouseBrainSubsetSCE, "counts", "heatmap", "level1class",
        c("Cmtm5", "C1qa"))