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A wrapper around scater::plotReducedDim().

Source: R/visualization.R
plotReducedDim_mod.Rd

A wrapper around scater::plotReducedDim().

Usage

plotReducedDim_mod(
  sce,
  dimred,
  colour_by = NULL,
  point_size = 1,
  point_alpha = 0.8,
  title = "",
  subtitle = "",
  use_default_ggplot_palette = TRUE,
  colour_gradient = list(low = "lightgrey", high = "blue"),
  legend_title = NULL,
  add_cells_per_cluster = TRUE,
  ...
)

Arguments

sce

A SingleCellExperiment object.

dimred, colour_by, point_size, point_alpha, ...

Passed to scater::plotReducedDim().

title, subtitle, legend_title

A character scalar.

use_default_ggplot_palette

A logical scalar: if TRUE, use the default ggplot2 palette (ggplot2::scale_color_hue()).

colour_gradient

A named list with low and high colors for continuous variables.

add_cells_per_cluster

A logical scalar: if TRUE and colour_by variable is (coercible to) factor, add number of cells per each level to color legend labels.

Value

A ggplot2 object.