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Allow the use of custom linkage/distance functions for creating dendrograms. #577

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Merged
merged 2 commits into from
Oct 21, 2016
Merged

Allow the use of custom linkage/distance functions for creating dendrograms. #577

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4ab398f
Allow the use of custom linkage/distance function in dendrograms.
grst Oct 5, 2016
7f94b93
Update tools.py
jackparmer Oct 21, 2016
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22 changes: 15 additions & 7 deletions plotly/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6051,14 +6051,18 @@ def create_distplot(hist_data, group_labels,

@staticmethod
def create_dendrogram(X, orientation="bottom", labels=None,
colorscale=None):
colorscale=None, distfun=scs.distance.pdist,
linkagefun=lambda x: sch.linkage(x, 'complete')):
"""
BETA function that returns a dendrogram Plotly figure object.

:param (ndarray) X: Matrix of observations as array of arrays
:param (str) orientation: 'top', 'right', 'bottom', or 'left'
:param (list) labels: List of axis category labels(observation labels)
:param (list) colorscale: Optional colorscale for dendrogram tree
:param (function) distfun: Function to compute the pairwise distance from the observations
:param (function) linkagefun: Function to compute the linkage matrix from the pairwise distances

clusters

Example 1: Simple bottom oriented dendrogram
Expand Down Expand Up @@ -6114,7 +6118,8 @@ def create_dendrogram(X, orientation="bottom", labels=None,
if len(s) != 2:
exceptions.PlotlyError("X should be 2-dimensional array.")

dendrogram = _Dendrogram(X, orientation, labels, colorscale)
dendrogram = _Dendrogram(X, orientation, labels, colorscale,
distfun=distfun, linkagefun=linkagefun)

return {'layout': dendrogram.layout,
'data': dendrogram.data}
Expand Down Expand Up @@ -7041,7 +7046,8 @@ class _Dendrogram(FigureFactory):
"""Refer to FigureFactory.create_dendrogram() for docstring."""

def __init__(self, X, orientation='bottom', labels=None, colorscale=None,
width="100%", height="100%", xaxis='xaxis', yaxis='yaxis'):
width="100%", height="100%", xaxis='xaxis', yaxis='yaxis',
distfun=scs.distance.pdist, linkagefun=lambda x: sch.linkage(x, 'complete')):
# TODO: protected until #282
from plotly.graph_objs import graph_objs
self.orientation = orientation
Expand All @@ -7064,7 +7070,7 @@ def __init__(self, X, orientation='bottom', labels=None, colorscale=None,
self.sign[self.yaxis] = -1

(dd_traces, xvals, yvals,
ordered_labels, leaves) = self.get_dendrogram_traces(X, colorscale)
ordered_labels, leaves) = self.get_dendrogram_traces(X, colorscale, distfun, linkagefun)

self.labels = ordered_labels
self.leaves = leaves
Expand Down Expand Up @@ -7173,12 +7179,14 @@ def set_figure_layout(self, width, height):

return self.layout

def get_dendrogram_traces(self, X, colorscale):
def get_dendrogram_traces(self, X, colorscale, distfun, linkagefun):
"""
Calculates all the elements needed for plotting a dendrogram.

:param (ndarray) X: Matrix of observations as array of arrays
:param (list) colorscale: Color scale for dendrogram tree clusters
:param (function) distfun: Function to compute the pairwise distance from the observations
:param (function) linkagefun: Function to compute the linkage matrix from the pairwise distances
:rtype (tuple): Contains all the traces in the following order:
(a) trace_list: List of Plotly trace objects for dendrogram tree
(b) icoord: All X points of the dendrogram tree as array of arrays
Expand All @@ -7192,8 +7200,8 @@ def get_dendrogram_traces(self, X, colorscale):
"""
# TODO: protected until #282
from plotly.graph_objs import graph_objs
d = scs.distance.pdist(X)
Z = sch.linkage(d, method='complete')
d = distfun(X)
Z = linkagefun(d)
P = sch.dendrogram(Z, orientation=self.orientation,
labels=self.labels, no_plot=True)

Expand Down