plot.core {bio3d} | R Documentation |
Plots the total ellipsoid volume of core positions versus core size at each iteration of the core finding process.
plot.core(x, y = NULL, type = "h", main = "", sub = "", xlim = NULL, ylim = NULL, xlab = "Core Size (Number of Residues)", ylab = "Total Ellipsoid Volume (Angstrom^3)", axes = TRUE, ann = par("ann"), col = par("col"), ...)
x |
a list object obtained with the function
core.find from which the ‘volume’
component is taken as the x coordinates for the plot. |
y |
the y coordinates for the plot. |
type |
one-character string giving the type of plot desired. |
main |
a main title for the plot, see also ‘title’. |
sub |
a sub-title for the plot. |
xlim |
the x limits of the plot. |
ylim |
the y limits of the plot. |
xlab |
a label for the x axis. |
ylab |
a label for the y axis. |
axes |
a logical value indicating whether both axes should be drawn. |
ann |
a logical value indicating whether the default annotation (title and x and y axis labels) should appear on the plot. |
col |
The colors for lines and points. Multiple colours can be specified so that each point is given its own color. If there are fewer colors than points they are recycled in the standard fashion. |
... |
extra plotting arguments. |
Called for its effect.
The produced plot can be useful for deciding on the core/non-core boundary.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## Not run: ##-- Read kinesin alignment and structures aln <- read.fasta(system.file("examples/kinesin_xray.fa",package="bio3d")) pdb.path = system.file("examples/",package="bio3d") pdbs <- read.fasta.pdb(aln, pdb.path = pdb.path, pdbext = ".ent") ## Find core core <- core.find(pdbs, #write.pdbs = TRUE, verbose=TRUE) ## End(Not run) ## Not run: ##-- OR read previously saved kinesin data data(kinesin) attach(kinesin) col=rep("black", length(core$volume)) col[core$volume<2]="pink"; col[core$volume<1]="red" plot(core, col=col) print(core) ## End(Not run)