RedeR (version 1.20.0)

att: Map and set edge and vertex attributes to RedeR application.

Description

These functions map data frames containing edge/vertex attributes to an igraph object and set attributes to RedeR.

Usage

att.setv(g, from, to='nodeColor', pal=1, cols=NULL, na.col=grey(0.7), xlim=c(20,100,1), shapes=NULL, breaks=NULL, categvec=NULL, nquant=NULL, isrev=FALSE, getleg=TRUE, roundleg=1, title=NULL)
att.sete(g, from, to='edgeColor', pal=1, cols=NULL, na.col=grey(0.7), xlim=c(20,100,1), shapes=NULL, breaks=NULL, categvec=NULL, nquant=NULL, isrev=FALSE, getleg=TRUE, roundleg=1, title=NULL)
att.mapv(g, dat, refcol=1)
att.mape(g, dat, refcol=c(1,2))

Arguments

g

An igraph object.

from

An attribute name available in 'g' .

to

A valid RedeR attribute name (see addGraph or type 'att.setv()' or 'att.sete()').

breaks

A numeric vector of two or more breakpoints to be applied to the attribute values.

pal

Default color palette. Options: 1 or 2.

xlim

A numeric vector with three boundaries: c(, , ). It corresponds to boundary values to be apply to numeric attributes (e.g. nodeSize). Default: c(20,100,1).

cols

Vector of colors (either hexadecimals or valid R color names).

na.col

A color representing eventual NAs. Default: grey(0.7)

shapes

A string vector with valid RedeR shapes (see addGraph or type 'att.setv()' or 'att.sete()').

categvec

Optional: levels to encode attributes as a factor .

nquant

Optional: number of breakpoints to split attribute values by quantiles .

isrev

Optional: reversed version of attribute values .

getleg

Optional: return legend values .

dat

A data frame with the attributes to be mapped to 'g'.

refcol

The reference columns in the 'data' object with either node ids (one column ) or edge ids (two columns ).

roundleg

Integer indicating the number of decimal places (round) in the legend of numerical attributes

title

Optional: legend title

Value

Map/set RedeR attributes to igraph objects.

See Also

addGraph

Examples

data(ER.deg)

sg <- ER.deg$ceg  # an igraph object
dt <- ER.deg$dat  # a data frame object

# maps the data frame to the igraph object
sg <- att.mapv(g=sg, dat=dt, refcol=1)

# Sets graph attributes to RedeR!

# sets gene symbol do nodeAlias attribute
sg <- att.setv(sg, from="Symbol", to="nodeAlias")

# sets numerical value to nodeColor attribute
sg <- att.setv(sg, from="logFC.t3", to="nodeColor", breaks=seq(-1,1,0.2), pal=2)

# sets numerical value to nodeSize attribute
sg <- att.setv(sg, from="ERbdist", to="nodeSize", nquant=10, isrev=TRUE, xlim=c(5,40,1))