title: "Introduction to KEGGlincs" author: "Shana White" date: "03/23/2017"
by Shana White
#Make sure that the following bioconductor packages are installed source("http://bioconductor.org/biocLite.R") biocLite(c("hgu133a.db", "KEGGgraph", "KEGGREST", "KOdata")) #Download package biocLite("KEGGlincs") #Load/activate package for use library(KEGGlincs)
KEGGlincs is an R package that provides a seamless interface for viewing detailed versions of KEGG pathways in Cytoscape such that the exact relationships (edges) that exist between pathway elements (nodes) are visualized in a meaningful manner.
This package is intended to be used as a tool to accurately regenerate KEGG pathways with expanded edges that are marked-up (in terms of color or color+width) to portray specific edge attributes. Specifically, - the edges are expanded to represent all relationships between genes encoded by the KGML file but not necessarily represented in the original [KEGG] pathway. This 'expansion' occurs either because: - one node may represent many [often paralogous] genes. - a node is of type 'group' and represents two or more genes that are part of the same functional complex. - the edge attributes represented can be specified by the user as either: - Functional - the exact type and [in some cases] subtype of the relationship defined by the KGML file. - Data driven - based on quantitative experimental evidence for gene-gene relationships generated by experimental data. As an added feature and motivating example, this package gives users an opportunity to use LINCS L1000 knock-out data in order to analyze/visualize the pathway edges as they pertain to specific cell lines.
Aside from edge-specific annotation/mark-up, a unique feature of this package lies in the ability for users to generate graph objects in R and send them to Cytoscape for an interactive visualization experience via utilities developed by the cyREST team.
The following example showcases the ideas described above.
Note: An open Cytoscape session is required for pathway visualization; i.e. make sure that Cytoscape is open before running the following commands
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