Plot.Protein

Description

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

Usage

1
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.

Note

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.

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
## 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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.