XGR (version 1.1.4)

xPCHiCplot: Function to visualise promoter capture HiC data using different network layouts

Description

xPCHiCplot is supposed to visualise promoter capture HiC data using different network layouts.

Usage

xPCHiCplot(g, node.info = c("smart", "none", "GR", "GR_SNP",
"GR_SNP_target",
"SNP_target"), node.colors = c("skyblue", "pink1"), nodes.query = NULL,
newpage = TRUE, signature = TRUE, glayout = layout_with_kk,
vertex.frame.color = NA, vertex.size = NULL, vertex.color = NULL,
vertex.shape = "sphere", vertex.label = NULL, vertex.label.cex = NULL,
vertex.label.font = 2, vertex.label.dist = 0.3,
vertex.label.color = "black", edge.arrow.size = 0.5, edge.width = NULL,
edge.color = "grey", ...)

Arguments

g

an object of both classes "igraph" and "PCHiC" (part of the results from xDefineHIC)

node.info

tells the information used to label nodes. It can be one of "none" for no node labeling, "GR" for only using genomic regions (GR), "GR_SNP" for using GR and SNP (if any), "GR_SNP_target" for using GR and SNP (if any) and target genes (if any), "SNP_target" for using SNP (if any) and target genes (if any), and "smart" (by default) for only using GR if both SNP and target genes are not available (otherwise GR will be hidden)

node.colors

colors used to flag which nodes contain SNP or not. By default, a node harboring an SNP will be colored in 'skyblue' and the node without an SNP in 'pink'

nodes.query

nodes in query for which edges attached to them will be displayed. By default, it sets to NULL meaning no such restriction

newpage

logical to indicate whether to open a new page. By default, it sets to true for opening a new page

signature

logical to indicate whether the signature is assigned to the plot caption. By default, it sets TRUE

glayout

either a function or a numeric matrix configuring how the vertices will be placed on the plot. If layout is a function, this function will be called with the graph as the single parameter to determine the actual coordinates. This function can be one of "layout_nicely" (previously "layout.auto"), "layout_randomly" (previously "layout.random"), "layout_in_circle" (previously "layout.circle"), "layout_on_sphere" (previously "layout.sphere"), "layout_with_fr" (previously "layout.fruchterman.reingold"), "layout_with_kk" (previously "layout.kamada.kawai"), "layout_as_tree" (previously "layout.reingold.tilford"), "layout_with_lgl" (previously "layout.lgl"), "layout_with_graphopt" (previously "layout.graphopt"), "layout_with_sugiyama" (previously "layout.kamada.kawai"), "layout_with_dh" (previously "layout.davidson.harel"), "layout_with_drl" (previously "layout.drl"), "layout_with_gem" (previously "layout.gem"), "layout_with_mds". A full explanation of these layouts can be found in http://igraph.org/r/doc/layout_nicely.html

vertex.frame.color

the color of the frame of the vertices. If it is NA, then there is no frame

vertex.size

the size of each vertex. If it is a vector, each vertex may differ in size

vertex.color

the fill color of the vertices. If it is NA, then there is no fill color

vertex.shape

the shape of each vertex. It can be one of "circle", "square", "csquare", "rectangle", "crectangle", "vrectangle", "pie" (http://igraph.org/r/doc/vertex.shape.pie.html), "sphere", and "none"

vertex.label

the label of the vertices. If it is NA, then there is no label. The default vertex labels are the name attribute of the nodes

vertex.label.cex

the font size of vertex labels.

vertex.label.font

the font of vertex labels. It is interpreted the same way as the the 'font' graphical parameter: 1 is plain text, 2 is bold face, 3 is italic, 4 is bold and italic and 5 specifies the symbol font.

vertex.label.dist

the distance of the label from the center of the vertex. If it is 0 then the label is centered on the vertex. If it is 1 then the label is displayed beside the vertex.

vertex.label.color

the color of vertex labels.

edge.arrow.size

the size of the arrows for the directed edge. The default value is 0.5.

edge.width

the width of the directed edge. If NULL, the width edge is proportional to CHiCAGO scores (quantifying the strength of physical interactions).

edge.color

the color of the directed edge. The default value is 'grey'.

...

additional graphic parameters. See http://igraph.org/r/doc/plot.common.html for the complete list.

Value

an igraph object

See Also

xDefineHIC

Examples

# NOT RUN {
# Load the library
library(XGR)
# }
# NOT RUN {
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
# }
# NOT RUN {
# a) provide the SNPs with the significance info
data(ImmunoBase)
data <- names(ImmunoBase$AS$variants)

# b) extract HiC-gene pairs given a list of AS SNPs
PCHiC <- xDefineHIC(data, include.HiC="Monocytes", GR.SNP="dbSNP_GWAS",
RData.location=RData.location)
head(PCHiC$df)

# c) visualise the interaction (a directed graph: bait->prey)
g <- PCHiC$ig
## a node with SNPs colored in 'skyblue' and the one without SNPs in 'pink'
## the width in an edge is proportional to the interaction strength
xPCHiCplot(g, vertex.shape="sphere")
xPCHiCplot(g, glayout=layout_in_circle, vertex.shape="sphere")

# d) control node labelling info
xPCHiCplot(g, node.info="GR_SNP_target")
xPCHiCplot(g, node.info="GR_SNP")
xPCHiCplot(g, node.info="SNP_target")
xPCHiCplot(g, node.info='SNP_target', vertex.label.cex=0.5)
# }