getWordsOnDendro: getWordsOnDendro

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

getWordsOnDendro

Description

Get grobs to plot on the dendrogram with the position information

Usage

getWordsOnDendro(
  dhc,
  geneVec,
  geneNumLimit = 1000,
  geneVecType = "ENSEMBL",
  useWC = FALSE,
  useRandomColor = FALSE,
  numberOfWords = 25,
  showType = "ID",
  wcArgs = list(),
  highlight = NULL,
  textSize = 3.5,
  wcScale = 3,
  wrap = NULL,
  candidateNodes = NULL,
  takeIntersect = TRUE,
  useDf = NULL,
  bg.colour = NULL,
  type = "words",
  argList = list(),
  useFunc = NULL,
  useggfx = NULL,
  normalizeByClusterNum = TRUE,
  autoSize = TRUE
)

Arguments

dhc	dendrogram
geneVec	gene-named vector of node names in dendrogram
geneNumLimit	when the gene number is above this threshold, pyramid plots are not produced
geneVecType	type of the name of geneVec (default: ENSEMBL)
useWC	use wordcloud
useRandomColor	use random colors on wordclouds
numberOfWords	the number of words to plot (default: 25)
showType	when "enrich", which labels to show
wcArgs	argument list for ggwordcloud
highlight	words to highlight
textSize	text size in pyramid plots
wcScale	max_size of wordcloud
wrap	wrap the strings
candidateNodes	if NULL, all nodes are investigated
takeIntersect	take intersection or frequent words
useDf	data.frame to subset when manual function is specified
bg.colour	background color for wordcloud
type	"words" or "enrich"
argList	passed to refseq
useFunc	function to summarize text
useggfx	use ggfx on resulting plot
normalizeByClusterNum	normalize frequency by ID numbers or not
autoSize	size the text based on grob width

Details

The function accepts the dendrogram and named vector of genes with associated clusters and returns the list of plots with the positional information. Used internally in 'plotEigengeneNetworksWithWords'.

Value

list of pyramid plot grobs and its positions

Examples

mod <- returnExample()
result <- hclust(dist(t(mod$MEs)))
dhc <- result |>
    as.dendrogram() |>
    dendextend::hang.dendrogram()
geneVec <- paste0("ME", mod$colors)
names(geneVec) <- names(mod$colors)
getWordsOnDendro(dhc, geneVec, numberOfWords = 2)

noriakis/wcGeneSummary documentation built on April 22, 2024, 7:12 a.m.