plot3D.umap.gene: plot3D.umap.gene

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

plot3D.umap.gene

Description

Plot a 3D umap with gene expression. Uses plotly. Based on github.com/Dragonmasterx87.

Usage

plot3D.umap.gene(
  gene = "TOP2A",
  obj = combined.obj,
  annotate.by = GetNamedClusteringRuns(obj = obj, v = FALSE)[1],
  quantileCutoff = 0.99,
  def.assay = c("integrated", "RNA")[2],
  suffix = NULL,
  alpha = 0.5,
  dotsize = 1.25,
  col.names = c("umap_1", "umap_2", "umap_3"),
  assay = "RNA",
  ...
)

Arguments

gene	The gene of interest. Default: 'TOP2A'
obj	The Seurat object for which the 3D umap plot will be generated. Default: combined.obj
annotate.by	The cluster or grouping to be used for automatic annotation. Default: First returned result from GetNamedClusteringRuns(obj) function.
quantileCutoff	Cutoff value for the quantile for clipping outliers in the gene expression data. Default: 0.99
def.assay	The default assay to be used. Choose between "integrated" and "RNA". Default: "RNA"
suffix	A suffix added to the filename. Default: NULL
alpha	Opacity of the points in the plot. Default: 0.5
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.gene(obj = combined.obj, gene = "DDIT4", quantileCutoff = .95)
  plot3D.umap.gene(obj = combined.obj, gene = "percent.mito", quantileCutoff = .95) # for continous meta variables
  plot3D.umap.gene(obj = combined.obj, gene = "nFeature_RNA", quantileCutoff = .95) # for continous meta variables
}

## End(Not run)

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