plotnet: plotNet

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

plotNet

Description

Plot the network stored in the biotext object with changing the visualization parameters.

Usage

plotNet(
  x,
  layout = "nicely",
  edgeLink = TRUE,
  edgeLabel = FALSE,
  showLegend = FALSE,
  fontFamily = "sans",
  tagPalette = NULL,
  catColors = NULL,
  queryColor = "grey",
  pal = c("blue", "red"),
  colorize = FALSE,
  discreteColorWord = FALSE,
  useSeed = 42,
  autoScale = FALSE,
  scaleRange = c(5, 10),
  scaleEdgeWidth = c(1, 3),
  naEdgeColor = "grey",
  colorText = FALSE,
  asis = FALSE
)

## S4 method for signature 'biotext'
plotNet(
  x,
  layout = "nicely",
  edgeLink = FALSE,
  edgeLabel = FALSE,
  showLegend = FALSE,
  fontFamily = "sans",
  tagPalette = NULL,
  catColors = NULL,
  queryColor = "grey",
  pal = c("blue", "red"),
  colorize = FALSE,
  discreteColorWord = FALSE,
  useSeed = 42,
  autoScale = FALSE,
  scaleRange = c(5, 10),
  scaleEdgeWidth = c(1, 3),
  naEdgeColor = "grey",
  colorText = FALSE,
  asis = FALSE
)

Arguments

x	biotextgraph object
layout	the layout for the network, defaul to "nicely". It can be one of the layouts implemented in 'igraph' and 'ggraph', such as 'kk' (Kamada-Kawai), 'nicely' (automatic selection of algorithm), 'drl' (the force-directed DrL layout). The options are available at: https://igraph.org/r/doc/layout_.html
edgeLink	if FALSE, use geom_edge_diagonal. if TRUE, geom_edge_link. Default to TRUE.
edgeLabel	if TRUE, plot the edge label (default: FALSE)
showLegend	whether to show legend in the network
fontFamily	font family to use, default to "sans".
tagPalette	tag palette when 'tag' is TRUE. It is also used for dependency network using udpipe, and tagging colorization for word cloud. Default to NULL, which indicates automatically set.
catColors	colors for words and texts when colorize is TRUE and discreteColorWord is TRUE
queryColor	color for associated queries with words
pal	palette for color gradient in correlation network. should be a vector of length two like c("red","blue").
colorize	color the word nodes by their frequency, and the other nodes by their category. if colorize=FALSE and addFreqToGene=TRUE, gene nodes are colorized according to the minimum frequency of the words in the network
discreteColorWord	colorize words by "Words" category, not frequency.
useSeed	random seed
autoScale	scale the label and node size automatically for the large network.
scaleRange	scale for label and node size in the network.
scaleEdgeWidth	scale for edge width
naEdgeColor	edge colors for NA values (linking query with the category other than text)
colorText	color text label based on frequency in the network
asis	plot the original network (default to FALSE)

Details

The function accepts the already calculated biotext object and outputs the visualization based on the specified parameters.

Value

biotext object with network visualization changed

Examples

library(ggraph)
geneList <- c("DDX41","PNKP","ERCC1","IRF3","XRCC1")
test <- refseq(geneList)
plotNet(test, asis=TRUE)

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