igplot: simple plot of igraph object

In shkonishi/cornet: Cunstruction of correlation network form transcriptome data

Description

Shortening several 'plot.igraph' options, and these has initial value.

Usage

igplot(g, lay, connected, v.l, v.l.c, v.l.cx, v.f.c, v.s, v.c, v.l.f, v.shp,
    e.c, e.w, e.lty, ...)

Arguments

g	igraph object
lay	layout function of igraph, if 'lay="all"', all layout functions were performed.
connected	logical: default is true, connected vertex was shown.
v.c, v.f.c, v.l, v.l.c, v.l.cx, v.s, v.l.f, v.shp,	vertex parameters, v.c(vertex.color), v.f.c(vertex.frame.color), v.l(vertex.label), v.l.c(vertex.label.color), v.l.cx(vertex.label.cex), v.s(vertex.size), v.l.f(vertex.label.family), v.shp(vertex.shape)
e.c, e.w, e.lty	edge parameters, e.c(edge.color), e.w(edge.width), e.lty(edge.lty)
...	other arguments of plot.igraph. E.g. margin, frame, and main

Examples

# sample data
dat <- data.frame(
 S1 = c(43.26, 166.6, 12.53, 28.77, 114.7, 119.1, 118.9, 3.76, 32.73, 17.46),
 S2 = c(40.89, 41.87, 39.55, 191.92, 79.7, 80.57, 156.69, 2.48, 11.99, 56.11),
 S3 = c(5.05, 136.65, 42.09, 236.56, 99.76, 114.59, 186.95, 136.78, 118.8, 21.41)
 )
rownames(dat) <- paste0("G", 1:10)

# correlation matrix
cormat <- round(cor(t(dat)),2)

# threshold graph
res <- cornet::corgraph(mat=cormat)
g1 <- res[[1]]
cornet::igplot(g=g1, v.s=15)

# complete graph
g2 <- cornet::matoedge(cormat)
 ewid <- abs(igraph::E(g2)$weight)
 ecol <-  ifelse(igraph::E(g2)$weight < 0 , "steelblue3", "grey80")
cornet::igplot(g = g2, lay=igraph::layout.circle, v.s = 15, e.c = ecol, e.w = ewid*4)

shkonishi/cornet documentation built on May 30, 2019, 7:09 p.m.