bio3d (version 2.1-2)

plot.bio3d: Plots with marginal SSE annotation

Description

Draw a standard scatter plot with optional secondary structure in the marginal regions.

Usage

## S3 method for class 'bio3d':
plot(x, y = NULL, type = "h", main = "", sub = "", xlim = NULL, ylim = NULL, 
                 ylim2zero = TRUE, xlab = NULL, ylab = NULL, axes = TRUE, 
                 ann = par("ann"), col = par("col"), sse = NULL, top = TRUE, bot = TRUE, 
                 helix.col = "gray20", sheet.col = "gray80", sse.border = FALSE, ...)

Arguments

x

the x coordinates for the plot. Any reasonable way of defining the coordinates is acceptable. See the function xy.coords for details.

y

the y coordinates for the plot, see above.

type

one-character string giving the type of plot desired. The following values are possible, (for details, see plot): p for points, l for lines, o for overplotted points and line

main

a main title for the plot, see also title.

sub

a sub-title for the plot.

xlim

the x limits (x1,x2) of the plot. Note that x1 > x2 is allowed and leads to a reversed axis.

ylim

the y limits of the plot.

ylim2zero

logical, if TRUE the y-limits are forced to start at zero.

xlab

a label for the x axis, defaults to a description of x.

ylab

a label for the y axis, defaults to a description of y.

axes

a logical value indicating whether both axes should be drawn on the plot. Use graphical parameter xaxt or yaxt to suppress just one of the axes.

ann

a logical value indicating whether the default annotation (title and x and y axis labels) should appear on the plot.

col

The colors for lines and points. Multiple colours can be specified so that each point is given its own color. If there are fewer colors than points they are recycled in the standard fashion. Lines are plotted in the first colour specified.

sse

secondary structure object as returned from dssp or stride.

top

logical, if TRUE rectangles for each sse are drawn towards the top of the plotting region.

bot

logical, if TRUE rectangles for each sse are drawn towards the bottom of the plotting region.

helix.col

The colors for rectangles representing alpha helices.

sheet.col

The colors for rectangles representing beta strands.

sse.border

The border color for all sse rectangles.

...

other graphical parameters.

Value

• Called for its effect.

Details

See the functions plot.default, dssp and stride for further details.

References

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

See Also

plot.default, dssp, stride

Examples

## Plot of B-factor values along with secondary structure from PDB
pdb <- read.pdb( "1bg2" )
plot.bio3d(pdb$atom[pdb$calpha,"b"], sse=pdb, ylab="B-factor")

## Calculate secondary structure
#sse <- stride(pdb, resno=FALSE)
sse <- dssp(pdb, resno=FALSE)

## Plot of B-factor values along with calculated secondary structure
plot.bio3d(pdb$atom[pdb$calpha,"b"], sse=sse, ylab="B-factor", typ="l",
col="blue", lwd=2)