xVisNet: Function to visualise a graph object of class "igraph"

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Description

xVisNet is supposed to visualise a graph object of class "igraph". It also allows vertices/nodes color-coded according to the input pattern.

Usage

xVisNet(
g,
pattern = NULL,
colormap = c("yr", "jet", "gbr", "wyr", "br", "bwr", "rainbow", "wb"),
ncolors = 40,
zlim = NULL,
colorbar = TRUE,
newpage = TRUE,
signature = TRUE,
glayout = layout_with_kk,
vertex.frame.color = NA,
vertex.size = NULL,
vertex.color = NULL,
vertex.shape = NULL,
vertex.label = NULL,
vertex.label.cex = NULL,
vertex.label.dist = 0.3,
vertex.label.color = "blue",
vertex.label.family = "sans",
edge.arrow.size = 0.3,
...
)

Arguments

g	an object of class "igraph"
pattern	a numeric vector used to color-code vertices/nodes. Notably, if the input vector contains names, then these names should include all node names of input graph, i.e. V(g)$name, since there is a mapping operation. After mapping, the length of the patern vector should be the same as the number of nodes of input graph; otherwise, this input pattern will be ignored. The way of how to color-code is to map values in the pattern onto the whole colormap (see the next arguments: colormap, ncolors, zlim and colorbar)
colormap	short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta), and "ggplot2" (emulating ggplot2 default color palette). Alternatively, any hyphen-separated HTML color names, e.g. "lightyellow-orange" (by default), "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names
ncolors	the number of colors specified over the colormap
zlim	the minimum and maximum z/patttern values for which colors should be plotted, defaulting to the range of the finite values of z. Each of the given colors will be used to color an equispaced interval of this range. The midpoints of the intervals cover the range, so that values just outside the range will be plotted
colorbar	logical to indicate whether to append a colorbar. If pattern is null, it always sets to false
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 FALSE
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", and "layout_as_bipartite". 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. If the pattern is given, this setup will be ignored
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". If it sets to NULL, these vertices with negative will be "csquare" and the rest "circle".
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.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
vertex.label.family	the font family of vertex labels
edge.arrow.size	the size of the arrows for the directed edge. The default value is 1.
...	additional graphic parameters. See http://igraph.org/r/doc/plot.common.html for the complete list.

Value

invisible

Note

none

See Also

xSubneterGenes, xSubneterSNPs

Examples

## Not run: 
# 1) generate a ring graph
g <- make_ring(10, directed=TRUE)

# 2) visualise the graph
# 2a) visualise in one go
xVisNet(g=g, vertex.shape="sphere", glayout=layout_with_kk)
# 2b) visualise the graph with layout first calculated
glayout <- layout_(g, with_kk(), component_wise())
xVisNet(g=g, vertex.shape="sphere", glayout=glayout)
# 2c) visualise the graph with layout appended to the graph itself
g <- add_layout_(g, with_kk(), component_wise())
xVisNet(g=g, vertex.shape="sphere")

# 4) visualise the graph with vertices being color-coded by the pattern
pattern <- runif(vcount(g))
names(pattern) <- V(g)$name
xVisNet(g=g, pattern=pattern, colormap="bwr", vertex.shape="sphere")

# 5) use font family (Arial)
BiocManager::install("extrafont")
library(extrafont)
font_import()
fonttable()
## creating PDF files with fonts
loadfonts()
pdf("xVisNet_fonts.pdf", family="Arial Black")
xVisNet(g=g, newpage=FALSE, vertex.label.family="Arial Black",
signature=F)
dev.off()

## End(Not run)

XGR documentation built on Jan. 8, 2020, 5:06 p.m.