R: Plot Distance Matrix

plot.dmat {bio3d} | R Documentation

## 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)

[Package bio3d version 2.3-4 Index]