scVizMeta: scVizMeta function

In ncrna/Yeskit: Yet Another Single-Cell Analysis Toolkit (Yeskit)

scVizMeta function

Description

Visualize MetaData in low dimensional embedding

Usage

scVizMeta(
  object = NULL,
  signature = NULL,
  pt.size = NULL,
  reduction = NULL,
  title = NULL,
  split.by = NULL,
  ncol = NULL,
  raster = TRUE,
  palette = "YlOrRd",
  interval = c(Max = 1e+05, Hyper = 10000, Abundant = 1000, Large = 500, 
    Medium = 100, Small = 10, Single = 1, None = 0)
)

Arguments

object	Seurat object
signature	Name of one gene set
pt.size	Adjust point size to plot, default pt.size=0.5
reduction	Which dimensionality reduction to use, default is 'umap'
title	Text for the plot title, default title=NULL
split.by	Name of a metadata column to split plot by
ncol	Number of columns for display the plots
raster	Convert points to raster format, default is TRUE
palette	A palette name from RColorBrewer package
interval	set MetaData intervals to plot

Details

visualize data from MetaData slot

Value

A ggplot object

References

Inspired by Borcherding et al, F1000Research (2020)

Examples

data("H3N2_small")
scVizMeta(object = H3N2_small,
  reduction = "umap",
  signature = "H3N2",
  split.by = "sample",
  pt.size = 1,
  interval = c(
    Abundant = 1000, 
    Large = 500, 
    Medium = 100, 
    Small = 10, 
    Single = 1, 
    None = 0
  )
)

ncrna/Yeskit documentation built on Nov. 4, 2024, 10:32 p.m.