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Published byIan McMillan Modified over 3 years ago

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Rgraphviz Lightning talk to Boston area R users group Jeff Marcus 7/13/2011

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Introduction Rgraphviz allows you to visualize graphs (nodes and arcs) Good detailed presentation at materials/2009/SeattleApr09/graph/biocGraphs.pdf Some applications –Social networks –Biological pathways, protein interactions –My use: callflow analysis in speech recognition applications Rgraphviz part of Bioconductor project Built around Graphviz, AT&T opensource graph visualization software

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Example using graph package library(graph) library(Rgraphviz) nodes <- c("A", "B", "C", "D") edge.list <- list( A=list(edges=c("A", "B", "C")), B=list(edges=("C")), C=list(edges=c(C","D")), D=list(edges=B")) g <- new("graphNEL", nodes=nodes, edgeL=edge.list, edgemode="directed") Rgraphviz::plot(g) Note: graphNEL is a class in the graph package that extends virtual graph class. Efficient for smallish graphs with not too many edges

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Igraph package Package igraph has richer set of graph manipulation functions and is better suited to large graphs Must convert igraph to graphNEL for Rgraphviz library(igraph) # igraph has many ways to construct graphs ig <- igraph::graph.data.frame (data.frame( from=c("a","a","a","b", "c", "c", "d"), to=c("a","b","c","c", "c", "d", "b"))) g <- igraph.to.graphNEL (ig) # Same graph as before Rgraphviz::plot(g)

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Rgraphviz layout control Very fine-grained control of layout –Overall layout (dot, neato, etc., each useful for different purposes) –Node shapes –Node and edge colors –Edge thicknesses –Ability to plot subgraphs as well Rgraphviz essentially an API around graphviz so need to consult graphviz documentation for details Caution: I found that many but not all graphviz features supported

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Example: callflow graph Rgraphviz can produce legible graphs much more complex than this one

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Installation You will need to first install graphviz See https://wiki.duke.edu/display/DUKER/Install+RGr aphviz+under+Windows for details for Windows installation. https://wiki.duke.edu/display/DUKER/Install+RGr aphviz+under+Windows

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