returnPyramid: returnPyramid

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

returnPyramid

Description

Return pyramid plots

Usage

returnPyramid(
  L,
  R,
  geneVec,
  geneVecType,
  numberOfWords = 25,
  widths = c(0.3, 0.6, 0.3),
  lowCol = "blue",
  showType = "ID",
  useRandomColor = FALSE,
  highCol = "red",
  highlight = NULL,
  wcScale = 3,
  type = "words",
  wrap = 15,
  textSize = 3.5,
  useggfx = NULL,
  normalizeByClusterNum = TRUE,
  takeIntersect = TRUE,
  useWC = FALSE,
  wcArgs = list(),
  bg.colour = NULL,
  orgDb = org.Hs.eg.db,
  argList = list(),
  useFunc = NULL,
  useDf = NULL,
  xmin = NULL,
  xmax = NULL,
  autoSize = TRUE
)

Arguments

L	genes in the cluster
R	genes in the other cluster
geneVec	gene-named vector of node names in dendrogram
geneVecType	type of the name of geneVec (default: ENSEMBL)
numberOfWords	the number of words to plot
widths	parameters to pass to patchwork
lowCol	gradient low color
showType	which labels to show in enrich
useRandomColor	use random colors on wordclouds
highCol	gradient high color
highlight	words to highlight
wcScale	if useWC, number of size scaling (max_size)
type	"words" or "enrich"
wrap	wrap the strings
textSize	text size in pyramid plots
useggfx	use ggfx on plot
normalizeByClusterNum	normalize frequency by ID numbers or not
takeIntersect	take intersection or frequent words
useWC	return wordcloud
wcArgs	argument list for ggwordcloud
bg.colour	background color for wordclouds
orgDb	organism database to use in enrich
argList	parameters passed to refseq()
useFunc	function to summarize text
useDf	data.frame to subset when manual function is specified
xmin	used for adjusting text size
xmax	used for adjusting text size
autoSize	size the text based on grob width

Details

Returns the pyramid plots of text frequencies between clusters. Used internally in getWordsOnDendro.

Value

list of pyramid plot grobs and its positions

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.