Plot3D.ListOfCategories: Plot3D.ListOfCategories

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

Plot3D.ListOfCategories

Description

This function plots and saves a list of 3D UMAP or tSNE plots using plotly.

Usage

Plot3D.ListOfCategories(
  obj = combined.obj,
  annotate.by = "integrated_snn_res.0.7",
  cex = 1.25,
  default.assay = c("integrated", "RNA")[2],
  ListOfCategories = c("v.project", "experiment", "Phase", "integrated_snn_res.0.7"),
  SubFolderName = ppp("plot3D", substitute_deparse(ListOfCategories))
)

Arguments

obj	A Seurat object for which the plot is to be created. Default: 'combined.obj'.
annotate.by	Character vector specifying the metadata column to be used for annotating the plot. Default: 'integrated_snn_res.0.7'.
cex	Numeric value specifying the point size on the plot. Default: 1.25.
default.assay	Character vector specifying the assay to be used. Default: 'RNA' (second element in the vector c("integrated", "RNA")).
ListOfCategories	Character vector specifying the categories to be included in the plot. Default categories are "v.project", "experiment", "Phase", "integrated_snn_res.0.7".
SubFolderName	String specifying the name of the subfolder where the plots will be saved. By default, it's created using the function ppp("plot3D", substitute_deparse(ListOfCategories)).

Examples

## Not run: 
if (interactive()) {
  categ3Dplots <- c("v.project", "experiment", "Phase", "integrated_snn_res.0.7", "Area", "Individual", "Type")
  Plot3D.ListOfCategories(obj = combined.obj, ListOfCategories = categ3Dplots)
}

## End(Not run)

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