UMAP plot coloured by any feature — PlotUMAP • Matisse

Overlays the value of a feature (PSI event, junction count, or gene expression) on the UMAP embedding stored in the embedded Seurat object. Pass an event ID for PSI, a junction ID for junction counts, or a gene name for expression.

Overlays the value of a feature on the UMAP embedding stored in the embedded Seurat object. Pass a PSI event ID to colour by splicing ratio, a junction ID to colour by junction read counts, or a gene name to colour by gene expression.

Usage

PlotUMAP(object, feature, ...)

# 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. Can be a PSI event ID (e.g. "SE:chr1:100-200:300-400:+"), a junction ID, or a gene name.
...: Additional arguments (see PlotUMAP).
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.

Value

A ggplot object.