Description Usage Details Source Examples
A graph representing the integrin-mediated cell adhesion pathway from
KEGG, as well as a list of attributes for use in plotting the
graph with Rgraphviz
.
1 |
The integrinMediatedCellAdhesion
data set contains two objects:
The first is IMCAGraph
, which is an object of class
graph-NEL
and represents the hsa04510 graph from KEGG
.
The second is IMCAAttrs
, which is a list of four elements. The
first element, defAttrs
corresponds to the attrs
arguments of agopen
and
plot.graph
. The
second element is nodeAttrs
which corresponds to the
nodeAttrs
argument in the same two functions from
Rgraphviz
. The third element, subGList
corresponds to
the subGList
argument in those functions. Lastly, the fourth
element, LocusLink
provides a named list where the names are
the nodes and the values are vectors of LocusLink ID values which
correspond to those nodes.
The values from defAttrs
, nodeAttrs
and subGList
in the IMCAAttrs
list are part of an ongoing attempt by
Bioconductor to provide the set of options to most accurately recreate
the actual visual image of the pathway from the KEGG site using
Rgraphviz
. Users may try out their own combination of
attributes and settings for their own needs, but these represent our
own efforts at as closely recreating the image as possible.
http://www.genome.ad.jp/kegg/pathway/hsa/hsa04510.html
1 2 3 4 | data(integrinMediatedCellAdhesion)
if (require("Rgraphviz") & interactive())
plot(IMCAGraph, attrs=IMCAAttrs$defAttrs,
nodeAttrs=IMCAAttrs$nodeAttrs, subGList=IMCAAttrs$subGList)
|
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: Rgraphviz
Loading required package: grid
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.