plotFeature: Plot feature

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

Plot feature

Description

Plot feature

Usage

plotFeature(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotFeature(
  object,
  features,
  reduction = "UMAP",
  color = getOption(x = "acid.continuous.color", default =
    ggplot2::scale_color_gradient(low = "gray75", high = "purple")),
  pointSize = getOption(x = "acid.point.size", default = 1L),
  pointAlpha = getOption(x = "acid.point.alpha", default = 0.9),
  pointsAsNumbers = getOption(x = "acid.points.as.numbers", default = FALSE),
  label = getOption(x = "acid.label", default = FALSE),
  labelSize = getOption(x = "acid.label.size", default = 6L),
  dark = getOption(x = "acid.dark", default = FALSE),
  legend = getOption(x = "acid.legend", default = TRUE),
  expression = c("mean", "sum")
)

Arguments

object	Object.
features	character. Features to plot (e.g. gene expression, PC scores, number of genes detected).
reduction	vector(1). Dimension reduction name or index position.
color	ScaleDiscrete. Desired ggplot2 color scale. Must supply discrete values. When set NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual(). To set the discrete color palette globally, use: options("acid.color.discrete" = ggplot2::scale_color_viridis_d())
pointSize	numeric(1). Point size for dots in the plot. In the range of 1-3 is generally recommended.
pointAlpha	numeric(1) (0-1). Alpha transparency level.
pointsAsNumbers	logical(1). Plot the points as numbers (TRUE) or dots (FALSE).
label	logical(1). Superimpose sample text labels on the plot.
labelSize	integer(1). Size of the text label.
dark	logical(1). Plot against a dark background using the acid_theme_light() ggplot2 theme.
legend	logical(1). Include plot legend.
expression	character(1). Calculation to apply. Uses match.arg() internally and defaults to the first argument in the character vector.
...	Additional arguments.

Value

ggplot (1 feature) or list (multiple features).

Note

Updated 2021-03-03.

See Also

• Seurat::FeaturePlot().

Examples

data(SingleCellExperiment_Seurat, package = "AcidTest")

## SingleCellExperiment ====
object <- SingleCellExperiment_Seurat
plotFeature(
    object = object,
    features = c("nCount_RNA", "nFeature_RNA", "PC_1", "PC_2"),
    reduction = "UMAP"
)

acidgenomics/minimalism documentation built on April 1, 2024, 10:34 a.m.