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Added parameter to choose color_threshold #1075

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Added parameter to choose color_threshold #1075

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77ae57b
Added parameter to choose color_threshold
Elpiro Jul 27, 2018
6e7ae79
Update _dendrogram.py
Elpiro Sep 19, 2018
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29 changes: 15 additions & 14 deletions plotly/figure_factory/_dendrogram.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
def create_dendrogram(X, orientation="bottom", labels=None,
colorscale=None, distfun=None,
linkagefun=lambda x: sch.linkage(x, 'complete'),
hovertext=None):
hovertext=None, color_threshold='default'):
"""
BETA function that returns a dendrogram Plotly figure object.

Expand All @@ -30,6 +30,7 @@ def create_dendrogram(X, orientation="bottom", labels=None,
:param (function) linkagefun: Function to compute the linkage matrix from
the pairwise distances
:param (list[list]) hovertext: List of hovertext for constituent traces of dendrogram
:param (double) color_threshold: Value at which the separation of clusters will be made
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Please align with :param above


clusters

Expand Down Expand Up @@ -88,20 +89,19 @@ def create_dendrogram(X, orientation="bottom", labels=None,

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

return graph_objs.Figure(data=dendrogram.data,
layout=dendrogram.layout)
return graph_objs.Figure(data=dendrogram.data, layout=dendrogram.layout)


class _Dendrogram(object):
"""Refer to FigureFactory.create_dendrogram() for docstring."""

def __init__(self, X, orientation='bottom', labels=None, colorscale=None,
width=np.inf, height=np.inf, xaxis='xaxis', yaxis='yaxis',
width="100%", height="100%", xaxis='xaxis', yaxis='yaxis',
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"100%" is not a valid height/width and it looks like this is causing your test failure.

Where you trying to change some behavior here? I'm not sure why the old value was inf. I think the default should probably be just None, which will let the rending approach (plot, iplot, or FigureWidget) decide how to size the figure.

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"100%" isn't a valid for a width/height. This is what's causing your test failure. I think this should probably be None, which will let the rendering approaches (plot, iplot, or FigureWidget) decide what size to use.

distfun=None,
linkagefun=lambda x: sch.linkage(x, 'complete'),
hovertext=None):
hovertext=None, color_threshold='default'):
self.orientation = orientation
self.labels = labels
self.xaxis = xaxis
Expand All @@ -127,8 +127,9 @@ def __init__(self, X, orientation='bottom', labels=None, colorscale=None,
(dd_traces, xvals, yvals,
ordered_labels, leaves) = self.get_dendrogram_traces(X, colorscale,
distfun,
linkagefun,
hovertext)
linkagefun,
hovertext,
color_threshold)
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Why is there no closing parenthesis here?


self.labels = ordered_labels
self.leaves = leaves
Expand All @@ -144,7 +145,7 @@ def __init__(self, X, orientation='bottom', labels=None, colorscale=None,
self.zero_vals.sort()

self.layout = self.set_figure_layout(width, height)
self.data = dd_traces
self.data = graph_objs.Data(dd_traces)
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graph_objs.Data is deprecated in version 3. Just stick with dd_traces as a list or tuple.


def get_color_dict(self, colorscale):
"""
Expand Down Expand Up @@ -237,7 +238,7 @@ def set_figure_layout(self, width, height):

return self.layout

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

Expand All @@ -262,7 +263,8 @@ def get_dendrogram_traces(self, X, colorscale, distfun, linkagefun, hovertext):
d = distfun(X)
Z = linkagefun(d)
P = sch.dendrogram(Z, orientation=self.orientation,
labels=self.labels, no_plot=True)
labels=self.labels, no_plot=True,
color_threshold = color_threshold)
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please align with labels= above


icoord = scp.array(P['icoord'])
dcoord = scp.array(P['dcoord'])
Expand All @@ -288,12 +290,11 @@ def get_dendrogram_traces(self, X, colorscale, distfun, linkagefun, hovertext):
hovertext_label = None
if hovertext:
hovertext_label = hovertext[i]
trace = dict(
type='scatter',
trace = graph_objs.Scatter(
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Let's stick with dict (See below)

x=np.multiply(self.sign[self.xaxis], xs),
y=np.multiply(self.sign[self.yaxis], ys),
mode='lines',
marker=dict(color=colors[color_key]),
marker=graph_objs.Marker(color=colors[color_key]),
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Stick with dict or use graph_objs.scatter.Marker. graph_objs.Marker is deprecated in version 3

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graph_objs.Marker is deprecated. So this should either stay a dict, or be graph_objs.scatter.Marker. Given the dendrogram performance discussion in #1052, I think we should avoid using graph_objs here and stick with dicts. This would also be consistent with my goals described in #1079

text=hovertext_label,
hoverinfo='text'
)
Expand Down