API References
Comparing low vs. high dimensions/embeddings.
- flameplot.flameplot.compare(mapX, mapY, nn=250, n_steps=5, verbose=3)
Comparison of two embeddings.
Decription
Quantification of local similarity across two maps or embeddings, such as PCA and t-SNE. To compare the embedding of samples in two different maps using a scale dependent similarity measure. For a pair of maps X and Y, we compare the sets of the, respectively, kx and ky nearest neighbours of each sample.
- param mapX
Mapping of first embedding.
- type mapX
numpy array
- param data2
Mapping of second embedding.
- type data2
numpy array
- param nn
number of neirest neighbor to compare between the two maps. This can be set based on the smalles class size or the aveage class size. The default is 250.
- type nn
integer, optional
- param n_steps
The number of evaluation steps until reaching nn, optional. If higher, the resolution becomes lower and vice versa. The default is 5.
- type n_steps
integer
- param verbose
print messages. The default is 3.
- type verbose
integer, optional
- returns
scores : array with the scores across various nearest neighbors (nn).
nn : nearest neighbors
n_steps : The number of evaluation steps until reaching nn.
- rtype
dict()
Examples
>>> # Load data >>> X, y = flameplot.import_example() >>> >>> # Compute embeddings >>> embed_pca = decomposition.TruncatedSVD(n_components=50).fit_transform(X) >>> embed_tsne = manifold.TSNE(n_components=2, init='pca').fit_transform(X) >>> >>> # Compare PCA vs. tSNE >>> scores = flameplot.compare(embed_pca, embed_tsne, n_steps=25) >>> >>> # plot PCA vs. tSNE >>> fig = flameplot.plot(scores, xlabel='PCA', ylabel='tSNE') >>>
References
- flameplot.flameplot.import_example(data='digits', url=None, sep=',')
Import example dataset from github source.
Import one of the few datasets from github source or specify your own download url link.
- Parameters
data (str) – Name of datasets: ‘digits’
url (str) – url link to to dataset.
verbose (int, optional) – Print progress to screen. The default is 3. 0: None, 1: ERROR, 2: WARN, 3: INFO (default), 4: DEBUG, 5: TRACE
- Returns
Dataset containing mixed features.
- Return type
pd.DataFrame()
- flameplot.flameplot.plot(out, cmap='jet', xlabel=None, ylabel=None, reverse_cmap=False)
Make plot.
- Parameters
out (dict) – output of the compare() function.
cmap (string, optional) – colormap. The default is ‘jet’.
- Return type
fig.
- flameplot.flameplot.scatter(Xcoord, Ycoord, **args)
Scatterplot.
- Parameters
Xcoord (numpy array) – 1D Coordinates.
Ycoord (numpy array) – 1D Coordinates.
**args (TYPE) – See scatterd for all possible arguments.
- Return type
fig.
- flameplot.flameplot.wget(url, writepath)