PlotlyとCufflinks

PlotlyとCufflinks#

Warning

2024/05/09現在，cufflinksは3年前からメンテナンスが止まっているようです．そのため，このノートを参考にcufflinksを勉強し始める必要はありません．

このノートは記録のためだけに公開されています．

可視化プラットフォームPlotlyとpd.DataFrameから簡単にPlotlyを使うためのラッパーcufflinks#

Plotlyを使うことで，HTML,CSS, Javascriptなどの力を借りたインタラクティブなグラフを作成できます．PlotlyはそのままPythonライブラリとして公開されていますが，PandasのDataFrameから手軽にプロットできるcufflinksというライブラリが別途公開されているので，ここではこれの使い方を確認していきます．

インストール#

インストールは以下のCommand。

pip install plotly
pip install cufflinks

データの準備#

まずはデータを読み込みます。

import warnings
warnings.filterwarnings('ignore')

from sklearn import datasets
from sklearn.manifold import TSNE
import pandas as pd
import cufflinks as cf
import numpy as np

cf.go_offline()

digits = datasets.load_digits()
digits.data.shape

(1797, 64)

df = pd.DataFrame(digits.data)
df["label"] = digits["target"]
df.head()

	2	3	4	5	9	...	58	59	60	61	62	label
0	5.0	13.0	9.0	1.0	0.0	...	6.0	13.0	10.0	0.0	0.0	0
1	0.0	12.0	13.0	5.0	0.0	...	0.0	11.0	16.0	10.0	0.0	1
2	0.0	4.0	15.0	12.0	0.0	...	0.0	3.0	11.0	16.0	9.0	2
3	7.0	15.0	13.0	1.0	8.0	...	7.0	13.0	13.0	9.0	0.0	3
4	0.0	1.0	11.0	0.0	0.0	...	0.0	2.0	16.0	4.0	0.0	4

5 rows × 65 columns

cufflinksで2d scatter plot#

X2 = TSNE(n_components=2,verbose=True).fit_transform(df.values)

embed2d = pd.DataFrame(X2, columns=list("XY"))
embed2d["label"] = df["label"]
embed2d.head()

[t-SNE] Computing 91 nearest neighbors...
[t-SNE] Indexed 1797 samples in 0.000s...

[t-SNE] Computed neighbors for 1797 samples in 0.319s...
[t-SNE] Computed conditional probabilities for sample 1000 / 1797
[t-SNE] Computed conditional probabilities for sample 1797 / 1797
[t-SNE] Mean sigma: 11.619740

[t-SNE] KL divergence after 250 iterations with early exaggeration: 60.883373

[t-SNE] KL divergence after 1000 iterations: 0.741524

	X	Y	label
0	-2.675452	57.514252	0
1	12.662912	-9.085543	1
2	-15.789229	-18.999388	2
3	-36.275799	5.813906	3
4	43.600700	-9.102531	4

embed2d.iplot(
    kind="scatter", 
    x="X", y="Y",
    xTitle="X", yTitle="Y",
    categories="label",
    title="T-SNE 2D demo",
    mode='markers',
    )

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[6], line 1
----> 1 embed2d.iplot(
      2     kind="scatter", 
      3     x="X", y="Y",
      4     xTitle="X", yTitle="Y",
      5     categories="label",
      6     title="T-SNE 2D demo",
      7     mode='markers',
      8     )

File ~/workspace/prpy/.venv/lib/python3.11/site-packages/cufflinks/plotlytools.py:798, in _iplot(self, kind, data, layout, filename, sharing, title, xTitle, yTitle, zTitle, theme, colors, colorscale, fill, width, dash, mode, interpolation, symbol, size, barmode, sortbars, bargap, bargroupgap, bins, histnorm, histfunc, orientation, boxpoints, annotations, keys, bestfit, bestfit_colors, mean, mean_colors, categories, x, y, z, text, gridcolor, zerolinecolor, margin, labels, values, secondary_y, secondary_y_title, subplots, shape, error_x, error_y, error_type, locations, lon, lat, asFrame, asDates, asFigure, asImage, dimensions, asPlot, asUrl, online, **kwargs)
    796 else:
    797 	_size=size
--> 798 _data=Scatter3d(x=_x,y=_y,mode=mode,name=_,
    799 			marker=dict(color=colors[_],symbol=symbol,size=_size,opacity=opacity,
    800 							line=dict(width=width)),textfont=tools.getLayout(theme=theme)['xaxis']['titlefont'])
    801 if '3d' in kind:
    802 	_data=Scatter3d(x=_x,y=_y,z=_z,mode=mode,name=_,
    803 			marker=dict(color=colors[_],symbol=symbol,size=_size,opacity=opacity,
    804 							line=dict(width=width)),textfont=tools.getLayout(theme=theme)['xaxis']['titlefont'])

File ~/workspace/prpy/.venv/lib/python3.11/site-packages/plotly/graph_objs/_scatter3d.py:2694, in Scatter3d.__init__(self, arg, connectgaps, customdata, customdatasrc, error_x, error_y, error_z, hoverinfo, hoverinfosrc, hoverlabel, hovertemplate, hovertemplatesrc, hovertext, hovertextsrc, ids, idssrc, legend, legendgroup, legendgrouptitle, legendrank, legendwidth, line, marker, meta, metasrc, mode, name, opacity, projection, scene, showlegend, stream, surfaceaxis, surfacecolor, text, textfont, textposition, textpositionsrc, textsrc, texttemplate, texttemplatesrc, uid, uirevision, visible, x, xcalendar, xhoverformat, xsrc, y, ycalendar, yhoverformat, ysrc, z, zcalendar, zhoverformat, zsrc, **kwargs)
   2692 _v = name if name is not None else _v
   2693 if _v is not None:
-> 2694     self["name"] = _v
   2695 _v = arg.pop("opacity", None)
   2696 _v = opacity if opacity is not None else _v

File ~/workspace/prpy/.venv/lib/python3.11/site-packages/plotly/basedatatypes.py:4874, in BasePlotlyType.__setitem__(self, prop, value)
   4870         self._set_array_prop(prop, value)
   4872     # ### Handle simple property ###
   4873     else:
-> 4874         self._set_prop(prop, value)
   4875 else:
   4876     # Make sure properties dict is initialized
   4877     self._init_props()

File ~/workspace/prpy/.venv/lib/python3.11/site-packages/plotly/basedatatypes.py:5218, in BasePlotlyType._set_prop(self, prop, val)
   5216         return
   5217     else:
-> 5218         raise err
   5220 # val is None
   5221 # -----------
   5222 if val is None:
   5223     # Check if we should send null update

File ~/workspace/prpy/.venv/lib/python3.11/site-packages/plotly/basedatatypes.py:5213, in BasePlotlyType._set_prop(self, prop, val)
   5210 validator = self._get_validator(prop)
   5212 try:
-> 5213     val = validator.validate_coerce(val)
   5214 except ValueError as err:
   5215     if self._skip_invalid:

File ~/workspace/prpy/.venv/lib/python3.11/site-packages/_plotly_utils/basevalidators.py:1104, in StringValidator.validate_coerce(self, v)
   1102         v = str(v)
   1103     else:
-> 1104         self.raise_invalid_val(v)
   1106 if self.no_blank and len(v) == 0:
   1107     self.raise_invalid_val(v)

File ~/workspace/prpy/.venv/lib/python3.11/site-packages/_plotly_utils/basevalidators.py:296, in BaseValidator.raise_invalid_val(self, v, inds)
    293             for i in inds:
    294                 name += "[" + str(i) + "]"
--> 296         raise ValueError(
    297             """
    298     Invalid value of type {typ} received for the '{name}' property of {pname}
    299         Received value: {v}
    300 
    301 {valid_clr_desc}""".format(
    302                 name=name,
    303                 pname=self.parent_name,
    304                 typ=type_str(v),
    305                 v=repr(v),
    306                 valid_clr_desc=self.description(),
    307             )
    308         )

ValueError: 
    Invalid value of type 'numpy.int64' received for the 'name' property of scatter3d
        Received value: 0

    The 'name' property is a string and must be specified as:
      - A string
      - A number that will be converted to a string

cufflinksで3d scatter plot#

X3 = TSNE(n_components=3,verbose=True).fit_transform(df.values)
embed3d = pd.DataFrame(X3, columns=list("XYZ"))
embed3d["label"] = df["label"]
embed3d.head()

[t-SNE] Computing 91 nearest neighbors...
[t-SNE] Indexed 1797 samples in 0.007s...
[t-SNE] Computed neighbors for 1797 samples in 0.516s...
[t-SNE] Computed conditional probabilities for sample 1000 / 1797
[t-SNE] Computed conditional probabilities for sample 1797 / 1797
[t-SNE] Mean sigma: 8.132731
[t-SNE] KL divergence after 250 iterations with early exaggeration: 61.700394
[t-SNE] Error after 1000 iterations: 0.611338

	X	Y	Z	label
0	2.644546	22.259514	-1.929261	0
1	-10.827566	-4.184731	8.216836	1
2	-0.487536	-3.023013	13.081998	2
3	7.301555	7.178536	3.457083	3
4	-17.475632	1.376311	-1.810267	4

embed3d.iplot(kind="scatter3d", x="X", y="Y", z="Z", mode="markers", categories="label", title="T-SNE 3D demo")

その他、よく使うグラフの作り方#

toy1 = pd.DataFrame(np.random.random((100,6)), 
                    columns=("特徴1","特徴2","特徴3","特徴4","特徴5","特徴6"))

toy1.iplot()

toy1.iplot(subplots=True, subplot_titles=True)

toy1.scatter_matrix()

x = cf.datagen.sinwave(10,.25)
x.iplot(kind="surface")