scGODotPlot: scGODotPlot visualization

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

scGODotPlot visualization

Description

scGODotPlot visualization for all clusters

Usage

scGODotPlot(
  object = NULL,
  key = NULL,
  clusters = NULL,
  direction = "up",
  ont = "BP",
  padj.cutoff = 0.01,
  order.genes = FALSE,
  colors = NULL,
  font.size = 8,
  top_n = 5,
  extra = NULL
)

Arguments

object	Seurat object
key	The keyword that is stored in object@misc$key
clusters	Vectors of clusters to display, default clusters=NULL means all clusters
direction	Regulation direction to use, only 'up' or 'down' is allowed
ont	Ontology to use, only 'BP', 'CC', or 'MF' is allowed
padj.cutoff	The cutoff of adjusted Pvalue, default padj.cutoff=0.01
order.genes	Order GO results by the number of significant genes, default is FALSE
colors	Colors to specify, default cols = c('white', 'red')
font.size	Font size of axis
top_n	Only top_n entries to plot
extra	Extra slot used to fetch GOs

Value

A ggplot object

Examples

scGODotPlot(object = H3N2_small,
  key = "Infected_vs_Bystander.GO",
  ont = "BP",
  top_n = 6,
  direction = "up",
  cluster = "0",
  font.size = 8
)

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