plotMarker: Plot cell-type-specific gene markers

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

Plot cell-type-specific gene markers

Description

Visualize gene markers on a reduced dimension plot (e.g. t-SNE, UMAP).

Usage

plotMarker(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotMarker(
  object,
  genes,
  reduction = "UMAP",
  expression = c("mean", "sum"),
  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),
  labels = list(title = "auto", subtitle = NULL)
)

Arguments

object	Object.
genes	character. Gene identifiers.
reduction	vector(1). Dimension reduction name or index position.
expression	character(1). Calculation to apply. Uses match.arg() internally and defaults to the first argument in the character vector.
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.
labels	list. ggplot2 labels. See ggplot2::labs() for details.
...	Additional arguments.

Value

Show graphical output. Invisibly return a ggplot list.

Note

Updated 2023-08-10.

Author(s)

Michael Steinbaugh, Rory Kirchner

Examples

requireNamespace("Matrix", quietly = TRUE)
requireNamespace("SingleCellExperiment", quietly = TRUE)
data(SingleCellExperiment_Seurat, package = "AcidTest")

## SingleCellExperiment ====
object <- SingleCellExperiment_Seurat
counts <- SingleCellExperiment::counts(object)
sums <- sort(Matrix::rowSums(counts), decreasing = TRUE)
genes <- names(head(sums, n = 4L))
plotMarker(
    object = object,
    genes = genes,
    reduction = "UMAP"
)

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