ontologyDotPlot: ontologyDotPlot

In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

ontologyDotPlot

Description

Dot plots for visualizing GREAT results

Usage

ontologyDotPlot(
  object,
  top = 5,
  topics = "all",
  ontology = "GO Biological Process",
  var.y = "ID",
  var.col = "Binom_Adjp_BH",
  var.size = "Binom_Fold_Enrichment",
  order.by = "Binom_Fold_Enrichment",
  col.low = "brown1",
  col.mid = "floralwhite",
  col.high = "dodgerblue",
  min.size = 2,
  max.size = 10
)

Arguments

object	Initialized cisTopic object, after [e-mail] has been filled.
top	Number of top terms per topic to visualize
topics	Topics to plot. By default, all of them; if not a vector with the topic numbers must be provided.
ontology	Ontology from which terms are selected to visualize.
var.y	Varible (factor) to visualize in the y axis. By default it is ID, but it can be also name.
var.col	Variable whose values will be visualized with the color scale
var.size	Variable whose values will be visualized with the size scale
order.by	Order terms in the y axis (descendent order) based on given variable
col.low	Lower color in the color scale
col.mid	Middle color in the color scale
col.high	Higher color in the color scale
min.size	Minimum dot size
max.size	Maximum dot size

Value

Dot plot with the topics, terms and the selected enrichments to visualize

aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.