Description Usage Arguments Value Author(s) See Also Examples
These functions map data frames containing edge/vertex attributes to an igraph object and set attributes to RedeR.
1 2 3 4 | 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))
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g |
An igraph object. |
from |
An attribute name available in 'g' <string>. |
to |
A valid RedeR attribute name (see |
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(<lower boundary>, <upper boundary>, <NA>). 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 |
categvec |
Optional: levels to encode attributes as a factor <vector>. |
nquant |
Optional: number of breakpoints to split attribute values by quantiles <integer>. |
isrev |
Optional: reversed version of attribute values <logical>. |
getleg |
Optional: return legend values <logical>. |
dat |
A data frame with the attributes to be mapped to 'g'. |
refcol |
The reference column in the 'data' object with either node ids (one column <integer>) or edge ids (two columns <vector of two integers>). |
roundleg |
Integer indicating the number of decimal places (round) in the legend of numerical attributes |
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title |
Optional: legend title |
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Map/set RedeR attributes to igraph objects.
Mauro Castro
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | 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))
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