umapHiLightSel: Highlight Selected Clusters on UMAP

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Highlight Selected Clusters on UMAP

Description

Generates a UMAP plot from a Seurat object with specified clusters highlighted. It saves the resulting UMAP plot directly to the current working directory.

Usage

umapHiLightSel(
  obj = combined.obj,
  COI = c("0", "2", "4"),
  ident = GetClusteringRuns()[1],
  h = 7,
  w = 5,
  show_plot = TRUE,
  ...
)

Arguments

obj	Seurat object to be visualized; Default: combined.obj.
COI	Vector of cluster IDs to highlight on the UMAP plot; Default: c("0", "2", "4").
ident	Name of the metadata column containing cluster IDs; Default: GetClusteringRuns()[1].
h	Height of the plot; Default: 7.
w	Width of the plot; Default: 5.
show_plot	Logical; if TRUE, the plot will be displayed in the RStudio viewer; Default: TRUE.
...	Additional arguments to be passed to the DimPlot function.#'

Value

Saves a UMAP plot highlighting specified clusters to the current working directory. The function itself does not return an object within R.

See Also

DimPlot

Examples

## Not run: 
if (interactive()) {
  # GetClusteringRuns()[1] "integrated_snn_res.0.1"
  umapHiLightSel(obj = combined.obj, COI = c("0", "1"), ident = GetClusteringRuns()[1])
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.