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Scatter plot of UMAP dimensionality reduction

Source: R/plotUMAP.R
plotUMAP.Rd

Graphs the output of the UMAP dimensionality reduction as a scatterplot using the 'DimPlot()' function from the Seurat package. Gene sets are colored and labeled by their cluster. When there is only one source in the data (default), each point will be shaped by the direction of the enrichment score of the gene set. When there are two sources in the data, each point will be shaped by the source indicating whether the gene set was found significant in either or both sources. With three or more sources, points are not shaped.

Usage

plotUMAP(
  geneSetsList,
  resolution = NULL,
  removeClusterId = FALSE,
  interactive = FALSE,
  highlightClusterNo = NULL,
  pointSize = 2,
  pointAlpha = 1/3,
  labelSize = 3,
  labelAlpha = 1,
  highlightPointAlpha = 2/3,
  highlightPointSize = 4,
  highlightLabelAlpha = 1,
  highlightLabelSize = 5
)

Arguments

geneSetsList

'gsList' object with clusters and labels.

resolution

The cluster resolution to plot. Default NULL uses the active resolution: the optimal resolution found by clusterGeneSets(), or the one last set with updateResolution() or updateClusterLabels().

removeClusterId

Logical, if TRUE the cluster number will be removed from each cluster label. Default: FALSE.

interactive

Logical, indicating whether to plot an interactive UMAP plot. Default: FALSE. If TRUE, an interactive plot is made with 'HoverLocator()' from the Seurat package; hovering over a point shows its gene set and cluster.

highlightClusterNo

A vector with the cluster numbers of the clusters (at the resolution) to highlight in the plot.

pointSize

Size of points. Default is 2.

pointAlpha

Transparency of points. Default is 1/3.

labelSize

Size of the cluster labels. Default is 3.

labelAlpha

Transparency of the cluster labels. Default is 1.

highlightPointAlpha

Transparency of the points of highlighted clusters. Default is 2/3.

highlightPointSize

Size of the points of highlighted clusters. Default is 4.

highlightLabelAlpha

Transparency of the labels of highlighted clusters. Default is 1.

highlightLabelSize

Size of the labels of highlighted clusters. Default is 5.

Value

A ggplot object (a patchwork from 'Seurat::DimPlot()'), or a plotly object when interactive = TRUE.

Examples

plotUMAP(exampleGsList)

plotUMAP(exampleGsList, highlightClusterNo = 0, removeClusterId = TRUE)