Plot.Protein.Linear {iPAC} | R Documentation |
Plot.Protein.Linear creates a visual representation of the protein reordering by showing the protein in linear form and setting the color based upon the remapped amino acid position.
Plot.Protein.Linear(path, colCount, cex=0.5, height = 1,width = 1, title = "Protein Reordering", color.palette = "heat")
path |
The remapped protein using only those amino acids for which mutational data is available. |
colCount |
How many columns you want in the plot |
cex |
How large you want the text to be. See R graphical parameters for more information. |
height |
The height of the resulting box that outlines the amino acid number. |
width |
The width of the resulting box that outlines the amino acid number. |
title |
The title that you want the graph to display. |
color.palette |
One of of the standard color palettes available in R. The options are "heat", "gray", "topo", and "cm". |
The terminal you are running this on must be able to create an R graphical device.
This method is still in beta. If any bugs found, please email the package authors.
#Extract the data from a CIF file and match it up with the canonical protein sequence. #Here we use the 3GFT structure from the PDB, which corresponds to the KRAS protein. CIF<-"https://files.rcsb.org/view/3GFT.cif" Fasta<-"https://www.uniprot.org/uniprot/P01116-2.fasta" KRAS.Positions<-get.Positions(CIF,Fasta, "A") #Load the mutational data for KRAS. Here the mutational data was obtained from the #COSMIC database (version 58). data(KRAS.Mutations) #Show the remapped order using the MDS remapper. new.ordering<-get.Remapped.Order(KRAS.Mutations, KRAS.Positions$Positions) #Create the Plots. Note that Amino Acid 61 is missing if get.AlignedPositions #was used. Thus Amino Acid 61 is missing in the plots below. Plot.Protein.Linear(new.ordering, 25, color.palette = "heat") Plot.Protein.Linear(new.ordering, 25, color.palette = "gray")