R: DCCM Plot

plot.dccm {bio3d} | R Documentation

## DCCM Plot

### Description

Plot a dynamical cross-correlation matrix.

### Usage

    ## S3 method for class 'dccm'
    plot(x, resno=NULL, sse=NULL, colorkey=TRUE,
                        at=c(-1, -0.75, -0.5,  -0.25, 0.25, 0.5, 0.75, 1),
                        main="Residue Cross Correlation",
                        helix.col = "gray20", sheet.col = "gray80",
                        inner.box=TRUE, outer.box=FALSE,
                        xlab="Residue No.", ylab="Residue No.",
                        margin.segments=NULL, segment.col=vmd_colors(), segment.min=1, ...)

### Arguments

`x` | a numeric matrix of atom-wise cross-correlations as output by the ‘dccm’ function.
`resno` | an optional vector with length equal to that of `x` that will be used to annotate the x- and y-axis. This is typically a vector of residue numbers. Can be also provided with a ‘pdb’ object, in which ‘resno’ of all C-alpha atoms will be used. If NULL residue positions from 1 to the length of `x` will be used. See examples below.
`sse` | secondary structure object as returned from `dssp`, `stride` or `read.pdb`.
`colorkey` | logical, if TRUE a key is plotted.
`at` | numeric vector specifying the levels to be colored.
`main` | a main title for the plot.
`helix.col` | The colors for rectangles representing alpha helices.
`sheet.col` | The colors for rectangles representing beta strands.
`inner.box` | logical, if TRUE an outer box is drawn.
`outer.box` | logical, if TRUE an outer box is drawn.
`xlab` | a label for the x axis.
`ylab` | a label for the y axis.
`margin.segments` | a numeric vector of cluster membership as obtained from cutree() or other community detection method. This will be used for bottom and left margin annotation.
`segment.col` | a vector of colors used for each cluster group in margin.segments.
`segment.min` | a single element numeric vector that will cause margin.segments with a length below this value to be excluded from the plot.
`...` | additional graphical parameters for contourplot.

### Details

See the ‘contourplot’ function from the lattice package for plot customization options, and the functions `dssp` and `stride` for further details.

### Value

Called for its effect.

### Note

Be sure to check the correspondence of your ‘sse’ object with the ‘cij’ values being plotted as no internal checks are currently performed.

### Author(s)

Barry Grant

### References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

### See Also

`plot.bio3d`, `plot.dmat`, `filled.contour`, `contour`, `image` `plot.default`, `dssp`, `stride`

### Examples

    ## Not run:
      ##-- Read example trajectory file
      trtfile <- system.file("examples/hivp.dcd", package="bio3d")
      trj <- read.dcd(trtfile)

      ## Read reference PDB and trim it to match the trajectory
      pdb <- trim(read.pdb("1W5Y"), 'calpha')

      ## select residues 24 to 27 and 85 to 90 in both chains
      inds <- atom.select(pdb, resno=c(24:27,85:90))

      ## lsq fit of trj on pdb
      xyz <- fit.xyz(pdb$xyz, trj, fixed.inds=inds$xyz, mobile.inds=inds$xyz)

      ## Dynamic cross-correlations of atomic displacements
      cij <- dccm(xyz)

      ## Default plot
      plot.dccm(cij)

      ## Change the color scheme and the range of colored data levels
      plot.dccm(cij, contour=FALSE, col.regions=bwr.colors(200), at=seq(-1,1,by=0.01) )

      ## Add secondary structure annotation to plot margins
      plot.dccm(cij, sse=pdb)

      ## Add additional margin annotation for chains
      ## Also label x- and y-axis with PDB residue numbers
      ch <- ifelse(pdb$atom$chain=="A", 1,2)
      plot.dccm(cij, resno=pdb, sse=pdb, margin.segments=ch)

      ## Plot with cluster annotation from dynamic network analysis
      #net <- cna(cij)
      #plot.dccm(cij, margin.segments=net$raw.communities$membership)

      ## Focus on major communities (i.e. exclude those below a certain total length)
      #plot.dccm(cij, margin.segments=net$raw.communities$membership, segment.min=25)

    ## End(Not run)

[Package bio3d version 2.4-0 Index]