Plot3D.ListOfGenes: Plot3D.ListOfGenes

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

Plot3D.ListOfGenes

Description

Plot and save list of 3D UMAP or tSNE plots using plotly.

Usage

Plot3D.ListOfGenes(
  obj = combined.obj,
  annotate.by = "integrated_snn_res.0.7",
  opacity = 0.5,
  cex = 1.25,
  default.assay = c("integrated", "RNA")[2],
  ListOfGenes = c("BCL11B", "FEZF2", "EOMES", "DLX6-AS1", "HOPX", "DDIT4"),
  SubFolderName = ppp("plot3D", substitute_deparse(ListOfGenes))
)

Arguments

obj	Seurat object to be used for the plot. Default: combined.obj
annotate.by	Variable to annotate the clusters by. Default: 'integrated_snn_res.0.7'
opacity	Opacity for the plot points. Default: 0.5
cex	Point size for the plot. Default: 1.25
default.assay	Default assay to be used from the Seurat object. Default: second entry from c("integrated", "RNA")
ListOfGenes	List of genes to be plotted. Default: c("BCL11B", "FEZF2", "EOMES", "DLX6-AS1", "HOPX", "DDIT4")
SubFolderName	Name of the subfolder where the plots will be saved. Default: a subfolder named 'plot3D' concatenated with the list of genes.

Examples

## Not run: 
if (interactive()) {
  CellTypeMarkers <- c("PGK1", "CTIP2" = "BCL11B", "FEZF2", "EOMES", "DLX6-AS1", "HOPX", "DDIT4", "TOP2A", "PTGDS", "EDNRB", "EGFR", "SCGN", "NR2F2", "EMX2", "GAD2", "DLX2", "SATB2")
  Plot3D.ListOfGenes(obj = combined.obj, ListOfGenes = CellTypeMarkers)
}

## End(Not run)

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