plotCeldaViolin: Feature Expression Violin Plot

In celda: CEllular Latent Dirichlet Allocation

Description

Outputs a violin plot for feature expression data.

Usage

plotCeldaViolin(x, ...)

## S4 method for signature 'SingleCellExperiment'
plotCeldaViolin(
  x,
  features,
  useAssay = "counts",
  altExpName = "featureSubset",
  exactMatch = TRUE,
  plotDots = TRUE,
  dotSize = 0.1
)

## S4 method for signature 'matrix'
plotCeldaViolin(
  x,
  celdaMod,
  features,
  exactMatch = TRUE,
  plotDots = TRUE,
  dotSize = 0.1
)

Arguments

x	Numeric matrix or a SingleCellExperiment object with the matrix located in the assay slot under useAssay. Rows represent features and columns represent cells.
...	Ignored. Placeholder to prevent check warning.
features	Character vector. Uses these genes for plotting.
useAssay	A string specifying which assay slot to use if x is a SingleCellExperiment object. Default "counts".
altExpName	The name for the altExp slot to use. Default "featureSubset".
exactMatch	Logical. Whether an exact match or a partial match using grep() is used to look up the feature in the rownames of the counts matrix. Default TRUE.
plotDots	Boolean. If TRUE, the expression of features will be plotted as points in addition to the violin curve. Default TRUE.
dotSize	Numeric. Size of points if plotDots = TRUE. Default 0.1.
celdaMod	Celda object of class "celda_G" or "celda_CG". Used only if x is a matrix object.

Value

Violin plot for each feature, grouped by celda cluster

Examples

data(sceCeldaCG)
plotCeldaViolin(x = sceCeldaCG, features = "Gene_1")
data(celdaCGSim, celdaCGMod)
plotCeldaViolin(x = celdaCGSim$counts,
   celdaMod = celdaCGMod,
   features = "Gene_1")

celda documentation built on Nov. 8, 2020, 8:24 p.m.