R: Plot Geostas Results

plot.geostas {bio3d} | R Documentation

## Plot Geostas Results

### Description

Plot an atomic movement similarity matrix with domain annotation

### Usage

    ## S3 method for class 'geostas'
    plot(x, at=seq(0, 1, 0.1), main="AMSM with Domain Assignment",
                             col.regions=rev(heat.colors(200)),
                             margin.segments=x$grps, ...)

### Arguments

`x` | an object of type `geostas` as obtained by the ‘geostas’ function.
`at` | numeric vector specifying the levels to be colored.
`main` | a main title for the plot.
`col.regions` | color vector. See `contourplot` for more information.
`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.
`...` | additional graphical parameters for `plot.dccm` and `contourplot`.

### Details

This is a wrapper function for `plot.dccm` with appropriate adjustments for plotting atomic movement similarity matrix obtained from function `geostas`.

See the `plot.dccm` for more details.

### Value

Called for its effect.

### Author(s)

Barry Grant, Lars Skjaerven

### References

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

### See Also

`plot.dccm`, `geostas`

[Package bio3d version 2.3-3 Index]