plotKnot3D: 3D plot of a polygonal link In Rknots: Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures

Description

3D plot of a polygonal link

Usage

 `1` ```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, [email protected]

`plotDiagram`
 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26``` ```## 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) ```