visualizeModule: Visualization of module

In HiCociety: Inferring Chromatin Interaction Modules from 3C-Based Data

Visualization of module

Description

It draws a triangle heatmap and arcplot of a module

Usage

visualizeModule(
  hicpath,
  HC.object,
  moduleNum,
  resolution,
  hic.norm,
  heatmap.color.range = NULL,
  heatmap.color = colorRampPalette(c("white", "red")),
  arc.depth = 10,
  arc.color = "gray80",
  nbnom.param = 0.99,
  txdb = "TxDb.Mmusculus.UCSC.mm10.knownGene",
  gene.strand.arrow.lwd = 3,
  gene.strand.lwd = 6,
  col.forward.gene = "purple",
  col.reverse.gene = "pink",
  highlight.centrality = FALSE,
  highlight.cent.col = FALSE,
  highlight.node = NULL,
  highlight.node.col = NULL,
  show.sig.int = TRUE,
  netinfo
)

Arguments

hicpath	Path to the .hic file
HC.object	The object name from hic2community result
moduleNum	The row index of module to draw
resolution	Resolution of HiC data
hic.norm	Normalization method. If not, set 'NONE'
heatmap.color.range	Min and max value of contact frequency, e.g., c(0,10)
heatmap.color	Color for heatmap. For example, colorRampPalette(c("white","red))
arc.depth	Height of arc plot
arc.color	Arc color
nbnom.param	Negative binomial probability cutoff. Higher cutoff gives less number of arcs.
txdb	Character. One of Txdb list obtained from get_txdb().
gene.strand.arrow.lwd	Numeric. Line width of arrowhead indicating the strands of genes. Same as arr.lwd option in Arrows function in shape package.
gene.strand.lwd	Numeric. Line width of arrow body indicating the strands of genes. Same as lwd option in Arros function in shape package.
col.forward.gene	Character. Color of arrows within gene track for forward genes.
col.reverse.gene	Character. Color of arrows within gene track for reverse genes
highlight.centrality	Boolean input to set if highlight eigenvector centrality node.
highlight.cent.col	The color of arcs stemming from the centrality node.
highlight.node	The coordiante of a node of which the user will highlight the arcs stemming from this node. Default=NULL
highlight.node.col	The color of arcs stemming from the node which the user highlight.
show.sig.int	Boolean. If TRUE, it marks significant contact on the triangle heatmap.
netinfo	Boolean. If TRUE, it shows network information of the module as text in the plot.

Details

Visualization of module

Value

No return value; the function generates a plot.

Author(s)

Sora Yoon, PhD

Examples

# A slow example that takes too long to run, wrapped in donttest{}

myhic = system.file('extdata','example.hic',package = 'HiCocietyExample')
HC.object = hic2community(myhic, "19", 5000, 0.975, 2000000, par.noise=1,
'louvain', n_cores=2)
mNum = 1
visualizeModule(hicpath = myhic, HC.object = HC.object, moduleNum = mNum,
resolution = 5000,
hic.norm = 'NONE', heatmap.color.range=c(0,10),
heatmap.color = colorRampPalette(c('white','red')),
arc.depth=10, arc.color = "gray80", nbnom.param=0.99,
txdb = 'TxDb.Mmusculus.UCSC.mm10.knownGene',
gene.strand.arrow.lwd = 3, gene.strand.lwd = 3,
col.forward.gene = 'purple', col.reverse.gene = 'pink',
highlight.centrality=FALSE, highlight.cent.col=FALSE,
highlight.node=NULL, highlight.node.col=NULL,
show.sig.int=FALSE, netinfo=FALSE)

HiCociety documentation built on Feb. 16, 2026, 5:10 p.m.