plot.dmat.Rd
Plot a distance matrix (DM) or a difference distance matrix (DDM).
# S3 method for dmat plot(x, key = TRUE, resnum.1 = c(1:ncol(x)), resnum.2 = resnum.1, axis.tick.space = 20, zlim = range(x, finite = TRUE), nlevels = 20, levels = pretty(zlim, nlevels), color.palette = bwr.colors, col = color.palette(length(levels)  1), axes = TRUE, key.axes, xaxs = "i", yaxs = "i", las = 1, grid = TRUE, grid.col = "yellow", grid.nx = floor(ncol(x)/30), grid.ny = grid.nx, center.zero = TRUE, flip=TRUE, ...)
x  a numeric distance matrix generated by the function


key  logical, if TRUE a color key is plotted. 
resnum.1  a vector of residue numbers for annotating the x axis. 
resnum.2  a vector of residue numbers for annotating the y axis. 
axis.tick.space  the separation between each axis tick mark. 
zlim  z limits for the distances to be plotted. 
nlevels  if 
levels  a set of levels used to partition the range of 'z'. Must be *strictly* increasing (and finite). Areas with 'z' values between consecutive levels are painted with the same color. 
color.palette  a color palette function, used to assign colors in the plot. 
col  an explicit set of colors to be used in the plot. This argument overrides any palette function specification. 
axes  logical, if TRUE plot axes are drawn. 
key.axes  statements which draw axes on the plot key. It overrides the default axis. 
xaxs  the x axis style. The default is to use internal labeling. 
yaxs  the y axis style. The default is to use internal labeling. 
las  the style of labeling to be used. The default is to use horizontal labeling. 
grid  logical, if TRUE overlaid grid is drawn. 
grid.col  color of the overlaid grid. 
grid.nx  number of grid cells in the x direction. 
grid.ny  number of grid cells in the y direction. 
center.zero  logical, if TRUE levels are forced to be equidistant around zero, assuming that zlim ranges from less than to more than zero. 
flip  logical, indicating whether the second axis should be fliped. 
...  additional graphical parameters for image. 
Called for its effect.
Grant, B.J. et al. (2006) Bioinformatics 22, 26952696.T
Much of this function is based on the filled.contour
function
by Ross Ihaka.
Barry Grant
This function is based on the layout
and legend key code in the
function filled.contour
by Ross Ihaka. As with
filled.contour
the output is a combination of two plots: the
legend and (in this case) image
(rather than a contour plot).
# Read PDB file pdb < read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) # DM d < dm(pdb,"calpha") # Plot DM ##filled.contour(d, nlevels = 4) ##plot(d) plot(d, resnum.1 = pdb$atom[pdb$calpha,"resno"], color.palette = mono.colors, xlab="Residue Number", ylab="Residue Number")if (FALSE) { # Download and align two PDB files pdbs < pdbaln( get.pdb( c( "4q21", "521p"), path=tempdir(), overwrite=TRUE)) # Get distance matrix a < dm.xyz(pdbs$xyz[1,]) b < dm.xyz(pdbs$xyz[2,]) # Calculate DDM c < a  b # Plot DDM plot(c,key=FALSE, grid=FALSE) plot(c, axis.tick.space=10, resnum.1=pdbs$resno[1,], resnum.2=pdbs$resno[2,], grid.col="black", xlab="Residue No. (4q21)", ylab="Residue No. (521p)") }