Multidimensional scaling¶
Utility functions for multidimensional scaling.
R must be installed, and the Python package rpy2 must be installed, e.g.:
$ apt-get install r-base
$ pip install rpy2
See also the examples at:
- anhima.mds.smacof(dist_square, **kwargs)[source]¶
Multidimensional scaling using the SMACOF (Scaling by Majorizing a Complicated Function) algorithm.
Parameters: dist_square : array_like, shape (n_samples, n_samples)
A distance matrix in square form.
kwargs : additional keyword arguments
Additional keyword arguments are passed through to sklearn.manifold.MDS().
Returns: coords : ndarray, shape (n_samples, n_components)
An array whose rows give the coordinates of the points chosen to represent the dissimilarities.
See also
anhima.dist.pairwise_distance, anhima.mds.classical, sklearn.manifold.MDS, anhima.pca.pca
- anhima.mds.classical(dist_square, k=2)[source]¶
Classical multidimensional scaling via the R cmdscale function.
Parameters: dist_square : array_like, shape (n_samples, n_samples)
A distance matrix in square form.
k : integer, optional
The maximum dimension of the space which the data are to be represented in; must be in {1, 2, ..., n-1}.
Returns: coords : ndarray, shape (n_samples, k)
An array whose rows give the coordinates of the points chosen to represent the dissimilarities.
- anhima.mds.plot_coords(coords, dimx=1, dimy=2, ax=None, colors=u'b', sizes=20, labels=None, scatter_kwargs=None, annotate_kwargs=None)[source]¶
Scatter plot of transformed coordinates from multidimensional scaling.
Parameters: coords : ndarray, shape (n_samples, n_components)
The transformed coordinates.
dimx : int, optional
The dimension to plot on the X axis. N.B., this is one-based, so 1 is the first dimension, 2 is the second dimension, etc.
dimy : int, optional
The dimension to plot on the Y axis. N.B., this is one-based, so 1 is the first dimension, 2 is the second dimension, etc.
ax : axes, optional
The axes on which to draw. If not provided, a new figure will be created.
colors : color or sequence of color, optional
Can be a single color format string, or a sequence of color specifications of length n_samples.
sizes : scalar or array_like, shape (n_samples), optional
Size in points^2.
labels : sequence of strings
If provided, will be used to label points in the plot.
scatter_kwargs : dict-like
Additional keyword arguments passed through to plt.scatter.
annotate_kwargs : dict-like
Additional keyword arguments passed through to plt.annotate when labelling points.
Returns: ax : axes
The axes on which the plot was drawn.
See also