scVolcanoPlot: scVolcanoPlot

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

scVolcanoPlot

Description

Volcano Plot for DGEs

Usage

scVolcanoPlot(
  object = NULL,
  key = NULL,
  cluster = NULL,
  padj = 0.05,
  logFC = 0.585,
  cols = NULL,
  pt.size = NULL,
  species.by = NULL,
  top_n = NULL,
  labels = NULL,
  label.size = NULL,
  box = TRUE,
  raster = TRUE
)

Arguments

object	A seurat object.
key	The DE matrix are stored in object@misc$key
cluster	Cluster specified by the user
padj	Cutoff of adjusted pvalue
logFC	Log2FoldChange in DGEs
cols	Colours to pain the dots, default cols=c('#808080', '#810F7C', '#006D2C', '#000000')
pt.size	Size of the dots, default pt.size=1
species.by	Species which is used to divid cells into two groups
top_n	Number of up- and down-regulated genes to show
labels	An array of gene names to show
label.size	Font size of the labels, default label.size=2.5
box	Draws a rectangle behind the labels, default is TRUE
raster	Convert points to raster format, default is TRUE

Value

A ggplot object

Examples

data("H3N2_small")
scVolcanoPlot(object = H3N2_small,
  key = "Infected_vs_Bystander",
  cluster = "0",
  top_n = 5
)

ncrna/Yeskit documentation built on Oct. 27, 2023, 2:13 a.m.