Creates a circular interactive plot of the path through the protein.
Plot.Protein(graph, path, vertex.size = 5, color.palette = "heat")
The graph object returned by GraphClust ($protein.graph).
The path returned by GraphClust ($candidate.path).
How large you want each vertex to be.
Possible options are: "heat", "gray", "topo", "cm".
This will plot the amino acids in a circular directed graph. The vertices can be dragged around to enhance the visual representation. This is meant to complement the Plot.Protein.Linear function in iPAC which is also applicable in this package.
This function is based on the “tkplot" function in igraph. Please see the documentation for that package for the necessary requirements. Special thanks to Dr. G\'abor Cs\'ardi (creator of the igraph package) for his help.
Gregory Ryslik and Hongyu Zhao (2012). iPAC: Identification of Protein Amino acid Clustering. R package version 1.1.3. http://www.bioconductor.org/.
Csardi G, Nepusz T: The igraph software package for complex network research, InterJournal, Complex Systems 1695. 2006. http://igraph.sf.net.
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## Not run: #Loads the mutational and positional data CIF<-"http://www.pdb.org/pdb/files/3GFT.cif" Fasta<-"http://www.uniprot.org/uniprot/P01116-2.fasta" KRAS.Positions<-get.Positions(CIF,Fasta, "A") data(KRAS.Mutations) #gets the cluster results and graph object my.graph.clusters <- GraphClust(KRAS.Mutations,KRAS.Positions$Positions, insertion.type = "cheapest_insertion",alpha = 0.05, MultComp = "Bonferroni") Plot.Protein(my.graph.clusters$protein.graph, my.graph.clusters$candidate.path, vertex.size=5, color.palette="heat") ## End(Not run)
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