plotEigengeneNetworksWithWords: plotEigengeneNetworksWithWords

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

plotEigengeneNetworksWithWords

Description

Plot an eigengene dendrogram with word annotation

Usage

plotEigengeneNetworksWithWords(
  MEs,
  colors,
  nboot = 100,
  numberOfWords = 10,
  geneNumLimit = 1000,
  geneVecType = "ENSEMBL",
  useWC = FALSE,
  border = TRUE,
  type = "words",
  wcScale = 3,
  candidateNodes = NULL,
  takeIntersect = TRUE,
  showType = "ID",
  textSize = 3.5,
  horiz = FALSE,
  dendPlot = "pvclust",
  dhc = NULL,
  wcArgs = list(),
  useDf = NULL,
  useWGCNA = TRUE,
  spacer = 0.005,
  wrap = NULL,
  highlight = NULL,
  argList = list(),
  useFunc = NULL,
  normalizeByClusterNum = TRUE,
  returnGlobOnly = FALSE,
  tipWC = FALSE,
  tipWCNodes = NULL,
  imageDir = NULL,
  wh = 5,
  al = TRUE,
  offset = 0.2,
  tipSize = 0.3,
  asp = 1.5,
  horizontalSpacer = 0,
  useRandomColor = FALSE,
  bg.colour = NULL,
  useggfx = NULL,
  ggfxParams = list(),
  autoSize = TRUE
)

Arguments

MEs	module eigengene data (data.frame of row as sample and col as gene cluster IDs)
colors	named vector of cluster
nboot	pvclust bootstrap number
numberOfWords	number of words to be included in pyramid plots
geneNumLimit	clusters with gene number above this threshold are ignored
geneVecType	type of IDs in 'colors'
useWC	plot wordcloud instead of pyramid plot
border	whether to draw border on pyramid plots
type	"words" or "enrich"
wcScale	max_size of wordcloud
candidateNodes	if NULL, all nodes are investigated
takeIntersect	take intersection or frequent words
showType	when "enrich", which labels to show
textSize	text size in pyramid plots
horiz	horizontal plot or not
dendPlot	type of dendrogram plot if dendPlot=="ggtree", provide those accepted by ggtree function to 'dhc'.
dhc	user-specified dendrogram
wcArgs	argument list, pass to ggwordcloud
useDf	data.frame to subset when manual function is specified "query" column will be used to subset
useWGCNA	pad named color vector with prefix "ME"
spacer	spacing for grob
wrap	wrap string
highlight	words to highlight
argList	passed to refseq()
useFunc	if not specified, use RefSeq summary data
normalizeByClusterNum	normalize frequency by ID numbers or not
returnGlobOnly	default to FALSE
tipWC	using ggtree, show WC on tip
tipWCNodes	node names to plot
imageDir	image directory to output WC
wh	width and height of wordcloud
al	positional argument to passed to ggtree::geom_tiplab (ggimage::geom_image)
offset	positional argument to passed to ggtree::geom_tiplab (ggimage::geom_image)
tipSize	positional argument to passed to ggtree::geom_tiplab (ggimage::geom_image)
asp	aspect ratio for ggimage::geom_image
horizontalSpacer	horizontal spacer for annotation
useRandomColor	use random color on wordclouds
bg.colour	use shadowtext for wordcloud, override border to FALSE
useggfx	filter in ggfx to apply to wordcloud, default to NULL
ggfxParams	parameters to pass to ggfx geom
autoSize	scale the size of text based on grob width

Details

The function accepts the module eigengene (ME) data.frame and named vector of genes with ME information and returns the dendrogram with textual information. The input is the typical output of WGCNA.

Value

plot of dendrogram between module eigengenes with word annotations

Examples

mod <- returnExample()
plotEigengeneNetworksWithWords(mod$MEs, mod$colors)

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