HiCociety (version 0.1.38)

visualizeModule: 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
)

Value

No return value; the function generates a plot.

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.

Author

Sora Yoon, PhD

Details

Visualization of module

Examples

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