Plot Co-embedding UMAP for Genes and Cells

Source: R/caesar_plot.r

This function generates a UMAP plot for co-embedding genes and cells in a Seurat object. It allows for customization of point colors, shapes, and text labels, and can display both gene and cell embeddings in the same plot.

CoUMAP.plot(
  seu,
  reduction = "caesarUMAP",
  gene_txtdata = NULL,
  ident = NULL,
  xy_name = reduction,
  dims = c(1, 2),
  cols = NULL,
  shape_cg = c(1, 5),
  pt_size = 1,
  pt_text_size = 5,
  base_size = 16,
  base_family = "serif",
  legend.point.size = 5,
  legend.key.size = 1.5,
  alpha = 0.8
)

Arguments

seu

A Seurat object containing the co-embedding data.

reduction

A character string specifying the name of the dimensional reduction to use for the UMAP plot. Default is "caesarUMAP".

gene_txtdata

A data frame containing gene names and labels to display as text on the plot. If NULL, no text labels are shown. Default is NULL.

ident

A character string specifying the column name in the Seurat object's metadata that contains cell type or cluster labels. If NULL, the default identities (Idents(seu)) are used. Default is NULL.

xy_name

A character string specifying the prefix for the UMAP axes. Default is the value of reduction.

dims

A numeric vector of length 2 specifying which dimensions to plot. Default is c(1, 2).

cols

A named vector of colors for clusters. If NULL, default colors are generated. Default is NULL.

shape_cg

A numeric vector of length 2 specifying the shapes for cells and genes. Default is c(1, 5).

pt_size

Numeric, specifying the size of the points for cells and genes. Default is 1.

pt_text_size

Numeric, specifying the size of the text labels for genes. Default is 5.

base_size

Numeric, specifying the base font size for the plot. Default is 16.

base_family

Character string specifying the font family for the plot. Default is "serif".

legend.point.size

Numeric, specifying the size of the points in the legend. Default is 5.

legend.key.size

Numeric, specifying the size of the legend keys. Default is 1.5.

alpha

Numeric, specifying the transparency level for cell points. Default is 0.8.

Value

A ggplot object representing the UMAP plot.

Details

The function creates a UMAP plot that shows both gene and cell embeddings. Gene embeddings can be optionally labeled with text, and the plot can be customized with different colors, shapes, and sizes.

See also

CoUMAP for obtain co-embedding UMAP.

Examples

data(toydata)

seu <- toydata$seu

seu <- CoUMAP(seu, gene.set = rownames(seu))
CoUMAP.plot(seu)