Wrapper around metaMDS and Rtsne
for dimensionality reduction with certain set parameters.
Usage
getFit(d, dim = 2, technique, perp = 30, seed = 8541)
Arguments
- d
distance matrix as a matrix
- dim
number of dimensions, by default 2. As argument k for
metaMDS and dims for Rtsne
- technique
either "mds" to run metaMDS,
"tsne" to run Rtsne or "umap" to run umap
- perp
perplexity value for Rtsne, default is 30.
This value is ignored when metaMDS is run.
- seed
seed to keep randomness at check
Details
metaMDS is run with trymax=20 and trace=FALSE
by default, so that the search for best solution is not printed.
Rtsne uses as default parameters
theta=0.0, check.duplicates = FALSE, max_iter = 1000.
