KEGG Integrin Mediated Cell Adhesion graph
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.
data(integrinMediatedCellAdhesion)
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.