plot3D.umap: plot3D.umap

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

plot3D.umap

Description

Plot a 3D umap based on one of the metadata columns. Uses plotly. Based on github.com/Dragonmasterx87.

Usage

plot3D.umap(
  obj = combined.obj,
  category = GetNamedClusteringRuns(obj = obj, v = FALSE)[1],
  annotate.by = category,
  suffix = NULL,
  dotsize = 1.25,
  col.names = c("umap_1", "umap_2", "umap_3"),
  ...
)

Arguments

obj	The Seurat object for which the 3D umap plot will be generated. Default: combined.obj
category	The metadata column based on which the 3D UMAP will be plotted. Default: First returned result from GetNamedClusteringRuns(obj) function.
annotate.by	The cluster or grouping to be used for automatic annotation. Default: First returned result from GetNamedClusteringRuns(obj) function.
suffix	A suffix added to the filename. Default: NULL
dotsize	The size of the dots in the plot. Default: 1.25
...	Pass any other parameter to the internally called plotly::plot_ly.

Examples

## Not run: 
if (interactive()) {
  plot3D.umap(category = "integrated_snn_res.0.1", obj = combined.obj)
}

## End(Not run)

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