UMAP plot coloured by any feature — PlotUMAP • Matisse

Overlays the value of a feature on the UMAP embedding stored in the embedded Seurat object. Pass a PSI event ID, a junction ID, a gene name, or a cell-metadata column. The colour scale adapts automatically: diverging RdBu [0,1] for PSI; sequential viridis for counts and expression.

Overlays the value of a feature on the UMAP embedding stored in the embedded Seurat object. The colour scale adapts to the feature type: diverging RdBu [0,1] for PSI events; sequential viridis for junction counts and gene expression.

Usage

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

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

Arguments

object: A MatisseObject with a UMAP reduction.
feature: Character. Feature to plot. May be a PSI event ID (e.g. "SE:chr1:100-200:300-400:+"), a junction or transcript ID, a gene name, or a cell-metadata column.
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).
pt_size: Numeric. Point size. Default: 0.5.
na_colour: Character. Colour for cells with no data. Default: "grey80".
title: Character. Plot title. Defaults to the feature name.
...: Additional arguments (see PlotUMAP).

Value

A ggplot object.