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.
Usage
data(integrinMediatedCellAdhesion)
Details
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.
data(integrinMediatedCellAdhesion)
if (require("Rgraphviz") & interactive())
plot(IMCAGraph, attrs=IMCAAttrs$defAttrs,
nodeAttrs=IMCAAttrs$nodeAttrs, subGList=IMCAAttrs$subGList)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(graph)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/graph/IMCA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: integrinMediatedCellAdhesion
> ### Title: KEGG Integrin Mediated Cell Adhesion graph
> ### Aliases: IMCA IMCAAttrs IMCAGraph integrinMediatedCellAdhesion
> ### Keywords: datasets
>
> ### ** Examples
>
> data(integrinMediatedCellAdhesion)
> #if (require("Rgraphviz") & interactive())
> plot(IMCAGraph, attrs=IMCAAttrs$defAttrs,
+ nodeAttrs=IMCAAttrs$nodeAttrs, subGList=IMCAAttrs$subGList)
>
>
>
>
>
> dev.off()
null device
1
>