plotEigengeneNetworksWithWords: plotEigengeneNetworksWithWords

plotEigengeneNetworksWithWordsR Documentation

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 May 31, 2024, 4:42 p.m.