plot.dmat: Plot Distance Matrix

In bio3d: Biological Structure Analysis

Plot Distance Matrix

Description

Plot a distance matrix (DM) or a difference distance matrix (DDM).

Usage

## 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, ...)

Arguments

x	a numeric distance matrix generated by the function dm.
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 is not specified, the range of 'z' values is divided into approximately this many levels.
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.

Value

Called for its effect.

Note

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).

Author(s)

Barry Grant

References

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.

See Also

dm, filled.contour, contour, image

Examples

# 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)

bio3d documentation built on Oct. 27, 2022, 1:06 a.m.