Feature Expression Violin Plot

Outputs a violin plot for feature expression data.

plotCeldaViolin(
  x,
  celdaMod,
  features,
  displayName = NULL,
  useAssay = "counts",
  altExpName = "featureSubset",
  exactMatch = TRUE,
  plotDots = TRUE,
  dotSize = 0.1
)

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

# S4 method for ANY
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.

celdaMod

Celda object of class "celda_G" or "celda_CG". Used only if x is a matrix object.

features

Character vector. Uses these genes for plotting.

displayName

Character. The column name of rowData(x) that specifies the display names for the features. Default NULL, which displays the row names. Only works if x is a SingleCellExperiment object.

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.

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")