bio3d: plot.geostas – R documentation

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bio3d

plot.geostas

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.