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Srivastava Lab

UMAP plot – by group (DimPlot-style) or by feature (FeaturePlot-style)

Source: R/generics.R, R/visualization.R
PlotUMAP.Rd

Two modes, switched by feature:

  • Group mode (default, feature = NULL): cells coloured discretely by a metadata column – like Seurat's DimPlot.

  • Feature mode (feature supplied): cells coloured on a continuous scale by a PSI event ID, junction or transcript ID, gene name, or numeric metadata column – like Seurat's FeaturePlot. The palette adapts to the feature type (diverging RdBu [0,1] for PSI; sequential for counts and expression).

Two modes, switched by feature:

  • Group mode (default, feature = NULL): cells coloured discretely by a metadata column – like Seurat's DimPlot. Pass label = TRUE to add group labels at cluster centroids.

  • Feature mode (feature supplied): cells coloured on a continuous scale by a PSI event ID, junction or transcript ID, gene name, or numeric metadata column – like Seurat's FeaturePlot. The palette adapts to the feature type: diverging RdBu [0,1] for PSI; sequential for counts and expression.

Usage

PlotUMAP(
  object,
  feature = NULL,
  reduction = "umap",
  dims = c(1L, 2L),
  group_by = "seurat_clusters",
  pt_size = 0.5,
  na_colour = "grey80",
  label = FALSE,
  title = NULL,
  ...
)

# S4 method for class 'MatisseObject'
PlotUMAP(
  object,
  feature = NULL,
  reduction = "umap",
  dims = c(1L, 2L),
  group_by = "seurat_clusters",
  pt_size = 0.5,
  na_colour = "grey80",
  label = FALSE,
  title = NULL,
  ...
)

Arguments

object

A MatisseObject with a UMAP reduction.

feature

Character. Optional feature to plot – a PSI event ID (e.g. "SE:chr1:100-200:300-400:+"), a junction or transcript ID, a gene name, or a numeric cell-metadata column. NULL (the default) selects group mode.

reduction

Character. Name of the dimensionality reduction to use. Default: "umap".

dims

Integer vector of length 2 selecting which dimensions to plot. Default: c(1, 2).

group_by

Character. Metadata column to colour by in group mode. Default: "seurat_clusters". Ignored in feature mode.

pt_size

Numeric. Point size. Default: 0.5.

na_colour

Character. Colour for cells with no data. Default: "grey80".

label

Logical. Group-mode only – add group labels at cluster centroids. Default: FALSE.

title

Character. Plot title. Defaults to the feature name in feature mode and NULL in group mode.

...

Additional arguments (see PlotUMAP).

Value

A ggplot object.

A ggplot object.