A graph representing the integrin-mediated cell adhesion pathway from
KEGG, as well as a list of attributes for use in plotting 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
The second is
IMCAAttrs, which is a list of four elements. The
defAttrs corresponds to the
second element is
nodeAttrs which corresponds to the
nodeAttrs argument in the same two functions from
Rgraphviz. The third element,
subGList corresponds to
subGList argument in those functions. Lastly, the fourth
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
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.
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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
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