Visualization

6.10. Visualization#

This section covers some tools to visualize your data and model.

6.10.1. Use Seaborn Style on Matplotlib Plots#

Seaborn style looks nicer than the default style of matplotlib, but matplotlib is more customizable. If you want to apply seaborn style on matplotlib plots, use seaborn.set_theme().

import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns

# Set seaborn style
sns.set_theme()

# Data for plotting
t = np.arange(0.0, 2.0, 0.01)
s = 1 + np.sin(2 * np.pi * t)

# Plot the data
plt.figure(figsize=(7, 5))
plt.plot(t, s)

plt.show()

../_images/45a20abc2969cf36fd4d7400cc383a2d91e6bba802ba3e7bd8e36fdfa05a60cf.png

6.10.2. Graphviz: Create a Flowchart to Capture Your Ideas in Python#

Visualizing complex data and systems is difficult. Creating diagrams by hand is slow and prone to mistakes, especially with large datasets.

Graphviz offers an easy method to generate graphs using a declarative language.

Here’s a short code example to demonstrate the utility of Graphviz:

from graphviz import Graph 

# Instantiate a new Graph object
dot = Graph('Data Science Process', format='png')

# Add nodes
dot.node('A', 'Get Data')
dot.node('B', 'Clean, Prepare, & Manipulate Data')
dot.node('C', 'Train Model')
dot.node('D', 'Test Data')
dot.node('E', 'Improve')

# Connect these nodes
dot.edges(['AB', 'BC', 'CD', 'DE'])

# Save chart
dot.render('data_science_flowchart', view=True)

'data_science_flowchart.png'

dot

../_images/5859a5ced5445e2fc2e751a9385fa1c0ce28d760de9ab1a437c58f2ba13d53eb.svg

Link to graphviz

6.10.3. folium: Create an Interactive Map in Python#

If you want to create a map provided the location in a few lines of code, try folium. Folium is a Python library that allows you to create an interactive map.

import folium
m = folium.Map(location=[45.5236, -122.6750])

tooltip = 'Click me!'
folium.Marker([45.3288, -121.6625], popup='<i>Mt. Hood Meadows</i>',
              tooltip=tooltip).add_to(m)
m 

Make this Notebook Trusted to load map: File -> Trust Notebook

View the document of folium here.

6.10.4. dtreeviz: Visualize and Interpret a Decision Tree Model#

If you want to find an easy way to visualize and interpret a decision tree model, use dtreeviz.

from dtreeviz.trees import dtreeviz
from sklearn import tree
from sklearn.datasets import load_wine

wine = load_wine()
classifier = tree.DecisionTreeClassifier(max_depth=2)
classifier.fit(wine.data, wine.target)

vis = dtreeviz(
    classifier,
    wine.data,
    wine.target,
    target_name="wine_type",
    feature_names=wine.feature_names,
)

vis.view()

The image below shows the output of dtreeviz when applying it on DecisionTreeClassifier.

Link to dtreeviz.

6.10.5. supertree: Interactive Decision Tree Visualization for Python#

Visualizing complex decision trees with static plots can make it hard to analyze and explain model decisions.

supertree is a Python package that addresses this by providing interactive and user-friendly decision tree visualizations within notebooks.

Key features include:

Zooming and panning through large trees
Collapsing and expanding selected nodes

from sklearn.tree import DecisionTreeClassifier
from sklearn.datasets import load_iris
from supertree import SuperTree # <- import supertree :)

# Load the iris dataset
iris = load_iris()
X, y = iris.data, iris.target

# Train model
model = DecisionTreeClassifier()
model.fit(X, y)

# Initialize supertree
super_tree = SuperTree(model, X, y, iris.feature_names, iris.target_names)

# show tree in your notebook
super_tree.show_tree()

Link to supertree.

6.10.6. HiPlot - High Dimensional Interactive Plotting#

If you are tuning hyperparameters of your machine learning model, it can be difficult to understand the relationships between different combinations of hyperparameters and a specific metric.

That is when HiPlot comes in handy. HiPlot allows you to discover patterns in high-dimensional data using parallel plots like below.

import hiplot as hip
data = [{'lr': 0.001, 'loss': 10.0, 'r2': 0.8, 'optimizer': 'SGD'},
        {'lr': 0.01, 'loss': 2.5, 'r2': 0.9, 'optimizer': 'Adam'},
        {'lr': 0.1, 'loss': 4, 'r2': 0.86, 'optimizer': 'Adam'}]
hip.Experiment.from_iterable(data).display()

HiPlot

Loading HiPlot...

<hiplot.ipython.IPythonExperimentDisplayed at 0x10b683730>

Link to HiPlot.

6.10.7. missingno.dendogram: Visualize Correlation Between Missing Data#

Missing values can sometimes tell you how strongly the presence or absence of one variable affects the presence of another. To visualize the correlation between different columns based on the missing values, use missingno.dendogram.

from sklearn.datasets import fetch_openml

soybean = fetch_openml(name="soybean", as_frame=True)['data']

import missingno as msno

msno.dendrogram(soybean)

<AxesSubplot:>

../_images/462e08d1f593f372abec32e4009fa7386f60bce2af8c2b7c221ae21921b4d31b.png

The dendrogram uses a hierarchical clustering algorithm to bin variables against one another by their nullity correlation. Cluster leaves which linked together at a distance of zero fully predict one another’s presence. In the graph above, the nullity of seed-discolor fully predicts the nullity of germination.

Link to missingno.

6.10.8. matplotlib-venn: Create a Venn Diagram Using Python#

If you want to draw a venn diagram using Python, try matplotlib-venn. To create a venn diagram using matplotlib-venn, you can specify the size of each region:

import matplotlib.pyplot as plt
from matplotlib_venn import venn2

venn2(subsets = (8, 10, 5), set_labels = ('Are Healthy', 'Do Exercise'))
plt.show()

../_images/72f8c00a41f913796c4bd7ac06311887f3b7b549d76b021ae05e83b524be6fa0.png

… or specify the elements in each set:

venn2([set(['A', 'B', 'C', 'D']), set(['D', 'E', 'F'])], set_labels=['Group1', 'Group2'])
plt.show()

../_images/25cd552d6977e850379ca40b3409cd8c719a149642c41342a8d56b87056fecf2.png

You can also draw three cicles using venn3:

from matplotlib_venn import venn3
venn3(subsets = (5, 5, 3, 5, 3, 3, 2), set_labels = ('Are Healthy', 'Do Exercise', 'Eat Well'))
plt.show()

../_images/f8c3511b5bdb1fca374ee0dc7fc408eb4fbb03aac4c730d03659cf732ba8f62b.png

Link to matplotlib-venn.

6.10.9. squarify: Plot Treemap in Python#

A treemap splits a rectangle into sub-rectangles, whose sizes are proportional to their values. To plot a treemap in Python, use squarify.

import matplotlib.pyplot as plt
import squarify   
import pandas as pd

df = pd.DataFrame({'count': [8, 4, 3], 'role': ['DS', 'DE', 'DA']})

# Plot
squarify.plot(sizes=df['count'], label=df['role'])
plt.axis('off')
plt.show()

../_images/0ae67755ddd655afe5ad9827f2fbc2ddb764cd577ebe479210e94aac6633ccad.png

Link to squarify.

6.10.10. UMAP: Dimension Reduction in Python#

It can be difficult to visualize a multi-dimensional dataset. Luckily, UMAP allows you to reduce the dimension of your dataset and create a 2D views of your data.

To understand how UMAP works, let’s try with the fruit dataset. In this dataset, we have the features of different fruits, such as mass, width, height, and color score. Our task is to classify which fruit a sample belongs to based on its features.

import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)

from sklearn.preprocessing import StandardScaler
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd

%matplotlib inline

Let’s start with loading and visualizing the data.

data = pd.read_table("https://raw.githubusercontent.com/susanli2016/Machine-Learning-with-Python/master/fruit_data_with_colors.txt")
data.head(10)

	fruit_label	fruit_name	fruit_subtype	mass	width	height	color_score
0	1	apple	granny_smith	192	8.4	7.3	0.55
1	1	apple	granny_smith	180	8.0	6.8	0.59
2	1	apple	granny_smith	176	7.4	7.2	0.60
3	2	mandarin	mandarin	86	6.2	4.7	0.80
4	2	mandarin	mandarin	84	6.0	4.6	0.79
5	2	mandarin	mandarin	80	5.8	4.3	0.77
6	2	mandarin	mandarin	80	5.9	4.3	0.81
7	2	mandarin	mandarin	76	5.8	4.0	0.81
8	1	apple	braeburn	178	7.1	7.8	0.92
9	1	apple	braeburn	172	7.4	7.0	0.89

sns.pairplot(data.drop(columns=['fruit_label', 'fruit_subtype']), hue='fruit_name')
plt.show()

../_images/e06e74134a420e3616c31ec312773a4e44501c63efae6143bb7397f7e0d8456d.png

We can see some distinctions between different fruits in the pairwise feature scatterplot matrix. Now to visualize all 4 features in a 2D plot, we start with creating a UMAP object.

import umap

reducer = umap.UMAP()

/Users/khuyentran/book/venv/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm

Next, we scale the features so that they are all on the same scale.

features = data.iloc[:, 3:].values
scaled_features = StandardScaler().fit_transform(features)

Lastly, we use the UMAP object to reduce the dimension of the dataset and plot the features as a scatter plot.

embedding = reducer.fit_transform(scaled_features)
embedding.shape

(59, 2)

pd.DataFrame(embedding, columns=['Dimension 1', 'Dimension 2']).to_csv('~/Downloads/embedding.csv')

plt.style.use('dark_background')

colors = ["#72BEFA", "#E583B6", "#72FCDB", "white"]
color_list = [colors[label - 1] for label in data.fruit_label]

plt.scatter(
    embedding[:, 0],
    embedding[:, 1],
    c=color_list,
    s=80,
)
plt.show()

../_images/873242685f5edbcace0a49ecf078284b33e202baf8b43b5476005e5151380b74.png

Now we can see some distinctions in features between 4 different fruits in a 2D plot.

Link to UMAP.

6.10.11. Evidently: Detect and Visualize Data Drift#

Data drift is unexpected changes in model input data that can lead to model performance degradation. Since your code is built around the characteristics of your data, it is important to detect data drift when it occurs. Evidently allows you to do exactly in a few lines of code.

In the code below, we use Evidently to detect changes in feature distribution.

import pandas as pd
from sklearn import datasets

from evidently.dashboard import Dashboard
from evidently.tabs import DataDriftTab

california = datasets.fetch_california_housing()
california = pd.DataFrame(california.data, columns = california.feature_names)

california_data_drift_report = Dashboard(tabs=[DataDriftTab])
california_data_drift_report.calculate(california[:1000], california[1000:], column_mapping = None)

california_data_drift_report.show()

gif

Find other features of Evidently here.

6.10.12. Mermaid: Create Class Diagrams for Your Python Classes Using Text and Code#

If you want to create class diagrams to explain your Python classes, use Mermaid. Mermaid lets you create diagrams and visualizations using text and code.

For example, writing this piece of code on Mermaid Live Editor:

 classDiagram
      Animal <|-- Dog
      Animal <|-- Cat
      Animal <|-- Fish
      Animal : int age
      Animal : str gender
      Animal: is_mammal()
      Animal: is_pet()
      class Dog{
          str fur_color
          bark()
          run()
      }
      class Cat{
          str fur_color
          meow()
          run()
      }
      class Fish{
          str scale_color
          swim()
      }

… will create a diagram like below:

6.10.13. Mermaid: Create Flow Chart Using Code#

Mermaid also allows you to create a flow chart using simple code logic.

For example, writing this piece of code on Mermaid Live Editor:

graph TD
    A[Should you go to work today?] --> B(Do you like working?)
    B --Yes--> C{Go to work}
    B --No--> D(Are you feeling sick?)
    D --Yes--> E{Go to the doctor}
    D --No--> F(Do you have a lot of work to do?)
    F --Yes--> H(And you don't want to go?)
    F --No--> H  
    H --Yes, I don't want to-->I(You signed up for this. Get dressed and go to work!) 
    

… will create a diagram like below:

Find other diagrams you can create with Mermaid here.

6.10.14. pretty-confusion-matrix: Plot a Pretty and Comprehensible Confusion Matrix#

It can be difficult to understand a confusion matrix, especially when there are many classes in the target.

import numpy as np
from sklearn.metrics import confusion_matrix

y_test = np.array([1, 2, 3, 4, 5])
prediction = np.array([3, 2, 4, 3, 5])

confusion_matrix(y_test, prediction)

array([[0, 0, 1, 0, 0],
       [0, 1, 0, 0, 0],
       [0, 0, 0, 1, 0],
       [0, 0, 1, 0, 0],
       [0, 0, 0, 0, 1]])

To make your confusion matrix prettier and easier to understand, use pretty_confusion_matrix.

from pretty_confusion_matrix import pp_matrix_from_data


cmap = 'PuRd'
pp_matrix_from_data(y_test, prediction, cmap=cmap)

../_images/429e18aa9b5fa0af41216e9e890d7cfb414dc917914c284e24a62e2ad3ce6254.png

Link to pretty confusion matrix.

6.10.15. matplotx: Useful Extensions for Matplotlib#

Have you ever wanted to create matplotlib plot in dark mode? If so, use matplotx.

For example, to use Dracula style, add:

plt.style.use(matplotx.styles.dracula)

to the code.

import numpy as np
import matplotlib.pyplot as plt
import matplotx
from IPython.core.pylabtools import figsize

# Create data
np.random.seed(2)
N = 50
x = np.random.rand(N)
y = np.random.rand(N)
colors = np.random.rand(N)
area = (30 * np.random.rand(N))**2  # 0 to 15 point radii

# Use dracula style
plt.style.use(matplotx.styles.dracula)

# Create a scatter plot
plt.scatter(x, y, s=area, c=colors)
figsize(10, 10)
plt.show()

../_images/562e4cfb44a6740158208c39b6f2067da9b73a1660ad32d01290bb156f12d811.png

Other styles that matplotx provides are:

‘aura’,
‘ayu’,
‘challenger_deep’,
‘dracula’,
‘dufte’,
‘dufte_bar’,
‘duftify’,
‘github’,
‘gruvbox’,
‘nord’,
‘onedark’,
‘pacoty’,
‘pitaya_smoothie’,
‘solarized’,
‘tab10’,
‘tab20’,
‘tab20r’,
‘tokyo_night’

Each style might have dark and light mode. For example, to use the dark mode version of aura style, type:

matplotx.styles.aura['dark']

{'lines.color': 'edecee',
 'patch.edgecolor': 'edecee',
 'text.color': 'edecee',
 'axes.facecolor': '15141b',
 'axes.edgecolor': 'edecee',
 'axes.labelcolor': 'edecee',
 'xtick.color': 'edecee',
 'ytick.color': 'edecee',
 'legend.framealpha': 0,
 'grid.color': 'edecee',
 'figure.facecolor': '15141b',
 'figure.edgecolor': '15141b',
 'savefig.facecolor': '15141b',
 'savefig.edgecolor': '15141b',
 'boxplot.boxprops.color': 'edecee',
 'boxplot.capprops.color': 'edecee',
 'boxplot.flierprops.color': 'edecee',
 'boxplot.flierprops.markeredgecolor': 'edecee',
 'boxplot.whiskerprops.color': 'edecee',
 'axes.prop_cycle': cycler('color', ['#82e2ff', '#ffca85', '#61ffca', '#ff6767', '#a277ff', '#f694ff', '#6d6d6d'])}

Link to matplotx.

6.10.16. ipysankeywidget: IPython Sankey Diagram Widget#

Sankey diagram is a flow diagram that depicts flows, where the width of the lines is proportional to the flow rate. If you want to quickly create a Sankey diagram in your Jupyter Notebook, use ipysankeywidget.

import pandas as pd
from ipysankeywidget import SankeyWidget

df = pd.DataFrame(
    {
        "source": ["Anna", "Josh", "Anna", "Ben", "Ben"],
        "target": ["New York", "New York", "Chicago", "San Jose", "Milwaukee"],
        "type": [
            "bussiness trip",
            "family visit",
            "vacation",
            "family visit",
            "bussiness trip",
        ],
        "value": [2, 3, 1, 3, 2],
    }
)

flows = df.to_dict("records")
SankeyWidget(links=flows).auto_save_png("diagram.png")

Link to ipysankeywidget.

6.10.17. ipyvizzu: Add Animation to Your Charts with Ease#

Sometimes you might want to add animations to your chart to show your audience the transition between one plot to another plot. However, it can be complicated to do that with matplotlib or Javascript.

With ipyvizzu, you can easily add animations to your plot in couples of lines of code inside your Jupyter Notebook.

In the code below, I use ipyvizzu to visualize the relationship between animals that can lay eggs and animals that are airborne.

from sklearn.datasets import fetch_openml

zoo = fetch_openml(data_id=965)["frame"]

df = zoo[["eggs", "airborne"]]
df = df.astype("object")
df["eggs"] = df["eggs"].map({"false": "no eggs", "true": "has eggs"})
df["airborne"] = df["airborne"].map({"false": "not airborne", "true": "is airborne"})
df["Count"] = 1

df.head(10)

	eggs	airborne	Count
0	no eggs	not airborne	1
1	no eggs	not airborne	1
2	has eggs	not airborne	1
3	no eggs	not airborne	1
4	no eggs	not airborne	1
5	no eggs	not airborne	1
6	no eggs	not airborne	1
7	has eggs	not airborne	1
8	has eggs	not airborne	1
9	no eggs	not airborne	1

from ipyvizzu import Chart, Data, Config, Style

data = Data()
data.add_data_frame(df)

chart = Chart(width="640px", height="360px")

chart.animate(data)

chart.animate(
    Config({"x": "Count", "y": "eggs", "label": "Count", "title": "Animals in the zoo"})
)
chart.animate(
    Config(
        {
            "x": ["Count", "airborne"],
            "label": ["Count", "airborne"],
            "color": "airborne",
        }
    )
)

chart.animate(Config({"x": "Count", "y": ["eggs", "airborne"]}))

Link to ipyvizzu.

6.10.18. ipyvizzu-story: Create an Interactive Presentation in Your Jupyter Notebook#

If you want to create an interactive presentation using Python in your Jupyter Notebook, use ipyvizzu-story.

import seaborn as sns  

df = sns.load_dataset("penguins")
df = df[['species', 'sex']].dropna()
df = df.astype("object")
df["count"] = 1

df.head(10)

	species	sex	count
0	Adelie	Male	1
1	Adelie	Female	1
2	Adelie	Female	1
4	Adelie	Female	1
5	Adelie	Male	1
6	Adelie	Female	1
7	Adelie	Male	1
12	Adelie	Female	1
13	Adelie	Male	1
14	Adelie	Male	1

from ipyvizzu import Data, Config
from ipyvizzustory import Story, Slide, Step

data = Data()
data.add_data_frame(df)

story = Story(data=data)

slide1 = Slide(
    Step(
        Config(
            {
                "x": ["count", "sex"],
                "label": ["count", "sex"],
                "color": "sex",
            }
        )
    )
)
story.add_slide(slide1)

slide2 = Slide(
    Step(
        Config({"x": "count", "y": ["species", "sex"]}),
    )
)
story.add_slide(slide2)

story.play()

Link to ipyvizzu-store.

6.10.19. Lux: A Python API for Intelligent Visual Discovery#

Have you ever taken a while to come up with the visualizations for your data? With Lux, you can get some suggestions on what to visualize.

To use Lux, simply import it.

from sklearn.datasets import load_wine
import lux  

wine = load_wine(as_frame=True)['frame'] 

wine

wine.exported['Correlation'][0]

wine.exported['Occurrence'][0]

Link to Lux.

6.10.20. Add Statistical Significance Annotations on Seaborn Plots#

Have you ever looked at two box plots and wondered if there is a significant difference between the means of the two groups? statannotations makes it easy for you to add statistical significance annotations on seaborn plots.

import seaborn as sns 
from statannotations.Annotator import Annotator
import matplotlib.pyplot as plt 

df = sns.load_dataset('taxis')
df.head(10)

	pickup	dropoff	passengers	distance	fare	tip	total	color	payment	pickup_zone	dropoff_zone	pickup_borough	dropoff_borough
0	2019-03-23 20:21:09	2019-03-23 20:27:24	1	1.60	7.0	2.15	12.95	yellow	credit card	Lenox Hill West	UN/Turtle Bay South	Manhattan	Manhattan
1	2019-03-04 16:11:55	2019-03-04 16:19:00	1	0.79	5.0	0.00	9.30	yellow	cash	Upper West Side South	Upper West Side South	Manhattan	Manhattan
2	2019-03-27 17:53:01	2019-03-27 18:00:25	1	1.37	7.5	2.36	14.16	yellow	credit card	Alphabet City	West Village	Manhattan	Manhattan
3	2019-03-10 01:23:59	2019-03-10 01:49:51	1	7.70	27.0	6.15	36.95	yellow	credit card	Hudson Sq	Yorkville West	Manhattan	Manhattan
4	2019-03-30 13:27:42	2019-03-30 13:37:14	3	2.16	9.0	1.10	13.40	yellow	credit card	Midtown East	Yorkville West	Manhattan	Manhattan
5	2019-03-11 10:37:23	2019-03-11 10:47:31	1	0.49	7.5	2.16	12.96	yellow	credit card	Times Sq/Theatre District	Midtown East	Manhattan	Manhattan
6	2019-03-26 21:07:31	2019-03-26 21:17:29	1	3.65	13.0	2.00	18.80	yellow	credit card	Battery Park City	Two Bridges/Seward Park	Manhattan	Manhattan
7	2019-03-22 12:47:13	2019-03-22 12:58:17	0	1.40	8.5	0.00	11.80	yellow	NaN	Murray Hill	Flatiron	Manhattan	Manhattan
8	2019-03-23 11:48:50	2019-03-23 12:06:14	1	3.63	15.0	1.00	19.30	yellow	credit card	East Harlem South	Midtown Center	Manhattan	Manhattan
9	2019-03-08 16:18:37	2019-03-08 16:26:57	1	1.52	8.0	1.00	13.30	yellow	credit card	Lincoln Square East	Central Park	Manhattan	Manhattan

In the code below, we use an independent t-test to compare the means of two independent groups.

x = 'pickup_borough'
y = 'total'
order = ['Manhattan', 'Brooklyn', 'Bronx', 'Queens']
ax = sns.boxplot(data=df, x=x, y=y, order=order)
pairs = [('Manhattan', 'Queens'), ('Manhattan', 'Bronx'), ('Manhattan', 'Brooklyn')]

annotator = Annotator(ax, pairs, data=df, x=x, y=y, order=order)
annotator.configure(test='t-test_ind')
annotator.apply_and_annotate()
plt.show()

p-value annotation legend:
      ns: p <= 1.00e+00
       *: 1.00e-02 < p <= 5.00e-02
      **: 1.00e-03 < p <= 1.00e-02
     ***: 1.00e-04 < p <= 1.00e-03
    ****: p <= 1.00e-04

Manhattan vs. Brooklyn: t-test independent samples, P_val:3.507e-06 t=-4.643e+00
Manhattan vs. Bronx: t-test independent samples, P_val:4.508e-09 t=-5.874e+00
Manhattan vs. Queens: t-test independent samples, P_val:7.643e-171 t=-2.880e+01

../_images/39fdfd1b347d1fa6d2500a56a553c654c5742ffc2a2987b01702be2d402d70b4.png

From the plot above, we can see that there is statistical evidence that the mean taxi fare in Manhattan is significantly different from the mean taxi fare in Brooklyn or Bronx, or Queens.

Link to statannotations.

6.10.21. Automatically Adjust Annotations in Matplotlib for Readability#

If you want to automatically adjust annotations in a matplotlib plot for readability, use the library adjustText.

import numpy as np

def plot_text(x, y):
    fig, ax = plt.subplots()
    plt.plot(x, y, 'bo')
    texts = [plt.text(x[i], y[i], 'Text%s' %i, ha='center', va='center') for i in range(len(x))]
    return texts

np.random.seed(1)
x, y = np.random.random((2,40))
plot_text(x, y)

../_images/c32c41002571710a004732f36f5dc4c8e4fc7e4c1dc5576672a9d566b3f3f29b.png

from adjustText import adjust_text

texts = plot_text(x, y)
adjust_text(texts)

../_images/24bda356a6e295387833884f877fa3a2b2e5fb7d601e97da29b0564cb6425259.png

Link to adjustText.

6.10.22. Bloxs: Create an Attractive Display in Your Jupyter Notebook#

If you want to create an attractive display for specific information in your notebook, try bloxs. bloxs is a Python library that is ideal for building dashboards, reports, and apps in the notebook.

from bloxs import B
B(22, "Chickens 🐥 in the backyard.")

22 Chickens 🐥 in the backyard.

B("Growth", "on July", points=[1,4,2,3,5,6])

Growth on July

B("Growth", "on July", points=[1,4,2,3,5,6], chart_type="bar")

Growth on July

B("68%", "Loading progress", progress=68)

68% Loading progress

B([
    B(22, "Chickens 🐥 in the backyard."),
    B("68%", "Loading progress", progress=68),
    B("Growth", "on July", points=[1,4,2,3,5,6])
])

22 Chickens 🐥 in the backyard.

68% Loading progress

Growth on July

Link to bloxs.

6.10.23. LovelyPlots: Create Nice Matplotlib Figures for Presentations#

If you want to transform your matplotlib plots into nice figures for scientific papers or presentations, try LovelyPlots. To use LovelyPlots, simply add plt.style.use(ipynb) to your code.

To see how a figure created by LovelyPlots looks like, let’s generate a plotting function, which takes style as its argument

import lovelyplots
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd


def plot(style: list):
    plt.style.use(style)

    np.random.seed(1)
    # Data
    df = pd.DataFrame(
        {
            "x_values": range(1, 11),
            "y1_values": np.random.randn(10),
            "y2_values": np.random.randn(10) + range(1, 11),
            "y3_values": np.random.randn(10) + range(11, 21),
        }
    )

    plt.plot(
        "x_values",
        "y1_values",
        data=df,
    )
    plt.plot(
        "x_values",
        "y2_values",
        data=df,
    )
    plt.plot(
        "x_values",
        "y3_values",
        data=df,
    )

    # show graph
    plt.show()

Create a figure using the default style of matplotlib.

plot(["default"])

../_images/022ac28cb023c57baf7a24f88c8ab73714b96f758c760e391afff644a0380435.png

Create the figures using styles from LovelyPlots.

plot(["ipynb", "colors10-markers"])

../_images/12080c66f8f82c520f89125b9b2056972f2a272ef9dbddd4eb604318ab2e9d90.png

plot(["ipynb", "colors5-light"])

../_images/c3cc64ba752dd6500a2376ed344e7a208f08fa4cec232fb4578ebc8d0d4f1d98.png

plot(["ipynb", "colors10-ls"])

../_images/a6a145a6b336663158326b1c560ec75642bd776f3d6066e0090ddf591b36be3c.png

Link to LovelyPlots

6.10.24. gif: The Easiest Way to Animate Your matplotlib Plot#

If you want to effortlessly animate your matplotlib plot in Python, use gif.

import pandas as pd
from matplotlib import pyplot as plt
import random

import gif


START = pd.Timestamp("2019-04-20")
END = pd.Timestamp("2020-05-01")


data = [random.uniform(0.5, 10) for _ in range(378)]

df = pd.DataFrame({"date": pd.date_range(start=START, end=END), "time": data})


@gif.frame
def plot(date):
    d = df[df["date"] <= date]
    fig, ax = plt.subplots(figsize=(5, 3), dpi=100)
    plt.plot(d["date"], d["time"])
    ax.set_xlim([START, END])
    ax.set_ylim([0, 10])
    ax.set_xticks([date])
    ax.set_yticks([0, 2, 4, 6, 8, 10])
    ax.set_xticklabels([date.strftime("%b '%y")])
    ax.set_yticklabels([0, 2, 4, 6, 8, "\n10\nhours"])


frames = []
for date in df["date"]:
    frame = plot(date)
    frames.append(frame)

gif.save(frames, "phone.gif", duration=35)

Link to gif.

6.10.25. Visualize the Frequency Tokens in a Text Corpora#

If you want to quickly visualize the frequency of tokens in a collection of text documents, use the combination of scikit-learn’s CountVectorizer and Yellowbrick’s FreqDistVisualizer.

from sklearn.datasets import fetch_20newsgroups

newsgroups_train = fetch_20newsgroups(subset='train')

from sklearn.feature_extraction.text import CountVectorizer
from yellowbrick.text import FreqDistVisualizer


import matplotlib.pyplot as plt

plt.figure(figsize=(8,4))

# Convert corpora to a matrix of token counts
# and remove stop words
vectorizer = CountVectorizer(stop_words='english') 
docs       = vectorizer.fit_transform(newsgroups_train['data'])
features   = vectorizer.get_feature_names()

# Plot a token frequency distribution 
visualizer = FreqDistVisualizer(features=features, n=10)
visualizer.fit(docs)
visualizer.show()

../_images/e6cca66d41d1dc57d663ef6b1e19713f5523174d629ecd0ed89963d6b06e3540.png

<AxesSubplot: title={'center': 'Frequency Distribution of Top 10 tokens'}>

Link to Yellowbrick

6.10.26. prettymaps: Generate Pretty Painting of a Location in Python#

If you want to generate a pretty painting of a location from OpenStreetMap in Python, use prettymaps.

import prettymaps

plot = prettymaps.plot('Stad van de Zon, Heerhugowaard, Netherlands')

Link to prettymaps.

6.10.27. Vizro: Create Modular Data Visualization Applications in Python#

If you want to use modular and simple Python code to create beautiful dashboards, try Vizro.

import vizro.plotly.express as px
from vizro import Vizro
import vizro.models as vm

df = px.data.iris()

page = vm.Page(
    title="My first dashboard",
    components=[
        vm.Graph(id="scatter_chart", figure=px.scatter(df, x="sepal_length", y="petal_width", color="species")),
        vm.Graph(id="hist_chart", figure=px.histogram(df, x="sepal_width", color="species")),
    ],
    controls=[
        vm.Filter(column="species", selector=vm.Dropdown(value=["ALL"])),
    ],
)

dashboard = vm.Dashboard(pages=[page])

Vizro().build(dashboard).run()

Link to vizro.

6.10.28. Drag-and-Drop Visualizations with PyGWalker#

EDA is a crucial step in any Data Science project. For large datasets, EDA can be time-consuming.

PyGWalker simplifies the process of creating visualizations by allowing users to drag and drop variables to create charts without writing much code.

You can use PyGWalker without changing your existing workflow. For example, you can call up PyGWalker with the Dataframe loaded in this way:

import pygwalker as pyg
import pandas as pd

df = pd.read_csv("https://kanaries-app.s3.ap-northeast-1.amazonaws.com/public-datasets/bike_sharing_dc.csv", parse_dates=['date'])
df.head(10)

	date	month	season	hour	year	holiday	temperature	feeling_temp	humidity	winspeed	casual	registered	count	am or pm	Day of the week
0	2011-01-01	1	winter	0	2011	no	3.28	3.0014	81.0	0.0000	3	13	16	am	6
1	2011-01-01	1	winter	1	2011	no	2.34	1.9982	80.0	0.0000	8	32	40	am	6
2	2011-01-01	1	winter	2	2011	no	2.34	1.9982	80.0	0.0000	5	27	32	am	6
3	2011-01-01	1	winter	3	2011	no	3.28	3.0014	75.0	0.0000	3	10	13	am	6
4	2011-01-01	1	winter	4	2011	no	3.28	3.0014	75.0	0.0000	0	1	1	am	6
5	2011-01-01	1	winter	5	2011	no	3.28	1.0016	75.0	6.0032	0	1	1	am	6
6	2011-01-01	1	winter	6	2011	no	2.34	1.9982	80.0	0.0000	2	0	2	am	6
7	2011-01-01	1	winter	7	2011	no	1.40	1.0016	86.0	0.0000	1	2	3	am	6
8	2011-01-01	1	winter	8	2011	no	3.28	3.0014	75.0	0.0000	1	7	8	am	6
9	2011-01-01	1	winter	9	2011	no	7.04	7.0010	76.0	0.0000	8	6	14	am	6

And then just walk around!

pyg.walk(df)

<pygwalker.api.pygwalker.PygWalker at 0x137d39650>

Link to PygWalker.

6.10.29. hvPlot: One API for Multiple Plotting Libraries#

Switching between plotting libraries lets you leverage their unique strengths. However, learning multiple specific APIs can significantly increase your cognitive load.

hvPlot provides a unified, high-level API that allows using the same syntax for Bokeh, Matplotlib, and Plotly. Here’s an example of how hvPlot can be used with different backends:

Default (Bokeh):

import hvplot.pandas
from bokeh.sampledata.penguins import data as df

hvplot.extension('plotly')

df.hvplot.scatter(x='bill_length_mm', y='bill_depth_mm', by='species')

Matplotlib:

import hvplot.pandas

hvplot.extension('matplotlib')

df.hvplot.scatter(x='bill_length_mm', y='bill_depth_mm', by='species')

Plotly:

import hvplot.pandas
from bokeh.sampledata.penguins import data as df

hvplot.extension('plotly')

df.hvplot.scatter(x='bill_length_mm', y='bill_depth_mm', by='species')

Link to hvPlot.

!pip install cutecharts

If you want to make graphs for a technical presentation more interesting and memorable, use cute charts, a Python visualization library.

from cutecharts.charts import Bar


def bar_base() -> Bar:
    chart = Bar("🍨 Most Popular Ice Cream Flavors")
    labels = ["🍫 Chocolate", "🫐 Blueberry", "🍓 Strawberry"]
    colors = ["#8B4513", "#4169E1", "#FF69B4"]

    chart.set_options(
        labels=labels,
        x_label="Flavor Type",
        y_label="Number of Scoops Sold",
        colors=colors,
    )
    chart.add_series("scoop sold", [856, 423, 774])
    return chart


bar_base().render_notebook()

Link to cute charts.

Visualization

Contents

6.10. Visualization#

6.10.1. Use Seaborn Style on Matplotlib Plots#

6.10.2. Graphviz: Create a Flowchart to Capture Your Ideas in Python#

6.10.3. folium: Create an Interactive Map in Python#

6.10.4. dtreeviz: Visualize and Interpret a Decision Tree Model#

6.10.5. supertree: Interactive Decision Tree Visualization for Python#

6.10.6. HiPlot - High Dimensional Interactive Plotting#

6.10.7. missingno.dendogram: Visualize Correlation Between Missing Data#

6.10.8. matplotlib-venn: Create a Venn Diagram Using Python#

6.10.9. squarify: Plot Treemap in Python#

6.10.10. UMAP: Dimension Reduction in Python#

6.10.11. Evidently: Detect and Visualize Data Drift#

6.10.12. Mermaid: Create Class Diagrams for Your Python Classes Using Text and Code#

6.10.13. Mermaid: Create Flow Chart Using Code#

6.10.14. pretty-confusion-matrix: Plot a Pretty and Comprehensible Confusion Matrix#

6.10.15. matplotx: Useful Extensions for Matplotlib#

6.10.16. ipysankeywidget: IPython Sankey Diagram Widget#

6.10.17. ipyvizzu: Add Animation to Your Charts with Ease#

6.10.18. ipyvizzu-story: Create an Interactive Presentation in Your Jupyter Notebook#

6.10.19. Lux: A Python API for Intelligent Visual Discovery#

6.10.20. Add Statistical Significance Annotations on Seaborn Plots#

6.10.21. Automatically Adjust Annotations in Matplotlib for Readability#

6.10.22. Bloxs: Create an Attractive Display in Your Jupyter Notebook#

6.10.23. LovelyPlots: Create Nice Matplotlib Figures for Presentations#

6.10.24. gif: The Easiest Way to Animate Your matplotlib Plot#

6.10.25. Visualize the Frequency Tokens in a Text Corpora#

6.10.26. prettymaps: Generate Pretty Painting of a Location in Python#

6.10.27. Vizro: Create Modular Data Visualization Applications in Python#

6.10.28. Drag-and-Drop Visualizations with PyGWalker#

6.10.29. hvPlot: One API for Multiple Plotting Libraries#