plotCeldaViolin: Feature Expression Violin Plot
In campbio/celda: CEllular Latent Dirichlet Allocation

plotCeldaViolin

R Documentation

Feature Expression Violin Plot

Description

Outputs a violin plot for feature expression data.

Usage

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

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

## S4 method for signature '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")

campbio/celda documentation built on April 5, 2024, 11:47 a.m.