plot_red: Plots a geometric visualization of the given k-cone reduced...
In cdiener/dycone: dycone - analyze the dynamic landscape of metabolome data

Description Usage Arguments Details Value See Also Examples

Plotting the reduced k-cone is a two step procedure. Where the k-cones are first projected into the two most informative dimensions by PCA. In case the basis is very large this is followed by clustering of the basis vectors to reduce overlap in the projection. In the plot, arrows denote the basis vectors, or 'extreme rays' of the respective k-cones and the shaded area denotes the interior of the k-cone into which all feasible k vectors must fall.

1 2	plot_red(basis_list, arrows = TRUE, col = NULL, n_cl = NULL, r_names = NULL)

`basis_list`	A list of basis to be reduced.
`arrows`	Whether to draw the individual basis vectors or just the interior of the cone.
`col`	If NULL colors are automatically generated from a green to red palette. If not NULL must be of the same length as basis_list and denotes the colors used to draw the individual basis.
`n_cl`	The numbers of clusters to be used. If there are more than 1000 basis vectors per basis, clustering is always performed since calculation of the convex hull (interior area of the cone) is extremely lengthy otherwise.
`r_names`	Optional vector of names for the reactions (rows of the basis). If given those will be used to annotate the axes with the names of the six reactions carrying the largest absolute loadings in the respective principal component.

Due to the dimension reduction and clustering plot_red is not a fast function and plotting might take a few minutes for large cones.

Nothing. Just plots :O

plot_basis for heatmap of the basis.

S <- matrix(c(1,0,0,1,-1,0, 0, -1), nrow=2)
rownames(S) <- c('A', 'B')
V <- polytope_basis(S)
plot_red(list(V)) # A single basis is fine as long as it is a list