GraphPAC (version 1.14.0)

Plot.Protein: Plot.Protein

Description

Creates a circular interactive plot of the path through the protein.

Usage

Plot.Protein(graph, path, vertex.size = 5, color.palette = "heat")

Arguments

graph

The graph object returned by GraphClust ($protein.graph).

path

The path returned by GraphClust ($candidate.path).

vertex.size

How large you want each vertex to be.

color.palette

Possible options are: "heat", "gray", "topo", "cm".

Details

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.

References

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.

Examples

## 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)