Plot Distance Matrix
Plot a distance matrix (DM) or a difference distance matrix (DDM).
## S3 method for class '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.
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).
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.T
Much of this function is based on the filled.contour function
by Ross Ihaka.
# 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")
## Not run:
# 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)")
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.