plotKnot3D: 3D plot of a polygonal link

In FedericoComoglio/Rknots: Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures

Description

3D plot of a polygonal link

Usage

plotKnot3D(points3D, ends = c(), text = FALSE, showNC = FALSE, colors = list(), ...)

Arguments

points3D	an N x 3 matrix of the x, y, z coordinates of a polygonal link
ends	a vector of positive integers defining the separators of the polygonal link. Default empty (polygonal knot)
text	logical, if TRUE the numbering of the points is shown
showNC	logical, if TRUE the N-terminus and C-terminus of a protein are labeled in red
colors	a list of color vectors, one for each component. Each vector i can be of length 1, containing the color to be used for the component i or of length equal to the number of points of the component i, thus specifying the color to be used for each edge. If not supplied, single colors from 1 to n are used, where n is the number of link components
...	other parameters for lines3d or spheres3d

Value

Called for its effect.

Note

This is a low-level function.

Author(s)

Federico Comoglio, [e-mail]

See Also

plotDiagram

Examples

## Not run: 
##3D plot of the Hopf link

hopf <- matrix(c(0.000084, -1.667027, -0.000300,
    0.179585, 0.249735, 0.991541,
    -0.179478, 0.250355, -0.991211,
    0.000084, -1.667027, -0.000300,
    -0.991561, -0.250457, 0.179413,
    -0.000415, 1.666817, 0.000107,
    0.991784, -0.249435, -0.179541,
    -0.991561, -0.250457, 0.179413),
    ncol = 3, byrow = TRUE)
			
plotKnot3D(hopf, ends = 4, text = FALSE, showNC = FALSE, lwd = 5, radius = 0.05)

##Stevedore knot
data(Rolfsen.table, package = "Rknots")
stevedore <- Rolfsen.table$"6.1"
plotKnot3D(stevedore, ends = c(), text = FALSE, showNC = FALSE, 
    radius = 0.05, lwd = 5)

#The same plot, without specifying any parameter for the rgl primitive shapes 
# (the default sphere radius is 1).
plotKnot3D(stevedore, ends = c(), text = FALSE)

## End(Not run)

FedericoComoglio/Rknots documentation built on May 6, 2019, 4:35 p.m.