heatmapOntoClust: Create a heatmap of ontology clusters

In altintasali/ontoClust: Cluster Gene Ontology Terms

Description

Create a heatmap of ontology clusters

Usage

heatmapOntoClust(
  oc,
  clusterColors = NULL,
  cluster_cols = FALSE,
  rowNames = c("id", "description")[2],
  cellwidth = 8,
  cellheight = 8,
  treeheight_row = 30,
  treeheight_col = 30,
  legend = FALSE,
  filename = NA,
  silent = FALSE,
  ...
)

Arguments

oc	Output from getOntoClust
clusterColors	A character vector with length of clusters (rows). If NULL (default), rainbow colors will be used.
cluster_cols	Logical to cluster link communities (columns).
rowNames	Display text for ontologies. It can be either id Ontology ID description Description of the ontology ID (default)
cellwidth	Width each cell. Default is 8.
cellheight	Height each cell. Default is 8.
treeheight_row	Height of the tree on rows (ontology clusters). Default is 30.
treeheight_col	Height of the tree on columns (link communities). Default is 30.
legend	Legend for black/white colors. Default is FALSE.
filename	Default NULL. If provided with .pdf or .png extensions, function generates a PDF or PNG output file.
silent	Default FALSE. If TRUE, the function does not plot the heatmap to the graphics device.
...	Additional parameters for pheatmap

Value

pheatmap object

Examples

ontology.id <- sample_data$GOBP$ID[1:50]
network <- createOntologyNetwork(ontology.id, method = "jaccard", weighted = FALSE)
lc <- getLC(network)
oc <- getOntoClust(lc)
heatmapOntoClust(oc)

altintasali/ontoClust documentation built on Dec. 19, 2021, 1:36 a.m.