plot_var: Plot Metadata Variables

In whtns/seuratTools: Tools for Managing Seurat Objects

Plot Metadata Variables

Description

Plots static or interactive plot where each point represents a cell metadata variable whose position on the map depends on cell embeddings determined by the reduction technique used

Usage

plot_var(
  seu,
  group = "batch",
  embedding = "umap",
  dims = c(1, 2),
  highlight = NULL,
  pt.size = 1,
  return_plotly = FALSE,
  ...
)

Arguments

seu	A Seurat object
group	Name of one or more metadata columns to group (color) cells by.
embedding	The dimensional reduction technique to be used
dims	Dimensions to plot, must be a two-length numeric vector
highlight	A list of character or numeric vectors of cells to highlight
pt.size	Adjust point size on the plot
return_plotly	Convert plot to interactive web-based graph
...

Examples

# static mode
plot_var(human_gene_transcript_seu, group = "batch", return_plotly = FALSE)

# interactive plotly plot
plotly_plot <- plot_var(human_gene_transcript_seu, group = "batch")
print(plotly_plot)

whtns/seuratTools documentation built on Oct. 28, 2024, 7:18 a.m.