plot.bio3d {bio3d}R Documentation

Plots with marginal SSE annotation

Description

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

Usage

plot.bio3d(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 lines, ‘b’, ‘c’) for points joined by lines, ‘s’ and ‘S’ for stair steps and ‘h’ for histogram-like vertical lines. Finally, ‘n’ does not produce any points or lines.
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.

Details

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

Value

Called for its effect.

Note

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

Author(s)

Barry Grant

References

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

See Also

plot.default, dssp, stride

Examples

##-- SSE setup --#
pdb <- read.pdb(  system.file("examples/1bg2.pdb", package="bio3d") )
sse <- dssp(pdb, resno=FALSE)

##-- Or load previous dataset
data(kinesin)
attach(kinesin)

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

## Not run: 
## Tidy short helices
torm <- sse$helix$length < 4
sse$helix$length <- sse$helix$length[!torm]
sse$helix$start <- sse$helix$start[!torm]
sse$helix$end <- sse$helix$end[!torm]

##-- Read a FASTA alignment file
aln <- read.fasta( system.file("examples/kinesin_xray.fa",package="bio3d") )

## Plot of residue conservation (similarity) with secondary structure
plot.bio3d( conserv(aln)[!is.gap(aln$ali[1,])],  sse=sse )


##- Gaps relative to rep.stru
data(kinesin)
rep.stru <- 1
gap.atom.inds <- which(aln$ali[rep.stru,] == "-")
gap.xyz.inds  <- atom2xyz(gap.atom.inds)

## RMSF and B-factors
coords <- xyz[,-gap.xyz.inds]
bfac <- pdbs$b[,-gap.atom.inds]
r <- rmsf(coords)

##- Plot
plot.bio3d(r)
plot.bio3d(r, type="o", sse=sse)
plot.bio3d(r, sse=sse, helix.col="purple", sheet.col="orange")

## End(Not run)

[Package bio3d version 1.0-6 Index]