Final Up to date on March 28, 2022

Information visualization is a crucial side of all AI and machine studying purposes. You’ll be able to achieve key insights of your knowledge by way of completely different graphical representations. On this tutorial, we’ll speak about a couple of choices for knowledge visualization in Python. We’ll use the MNIST dataset and the Tensorflow library for quantity crunching and knowledge manipulation. As an instance numerous strategies for creating several types of graphs, we’ll use the Python’s graphing libraries particularly matplotlib, Seaborn and Bokeh.

After finishing this tutorial, you’ll know:

  • Tips on how to visualize photos in matplotlib
  • Tips on how to make scatter plots in matplotlib, Seaborn and Bokeh
  • Tips on how to make multiline plots in matplotlib, Seaborn and Bokeh

Let’s get began.

Picture of Istanbul taken from airplane

Information Visualization in Python With matplotlib, Seaborn and Bokeh
Picture by Mehreen Saeed, some rights reserved.

Tutorial Overview

This tutorial is split into 7 components; they’re:

  • Preparation of scatter knowledge
  • Figures in matplotlib
  • Scatter plots in matplotlib and Seaborn
  • Scatter plots in Bokeh
  • Preparation of line plot knowledge
  • Line plots in matplotlib, Seaborn, and Bokeh
  • Extra on visualization

Preparation of scatter knowledge

On this publish, we’ll use matplotlib, seaborn, and bokeh. They’re all exterior libraries have to be put in. To put in them utilizing pip, run the next command:

For demonstration functions, we may even use the MNIST handwritten digits dataset. We are going to load it from Tensorflow and run PCA algorithm on it. Therefore we may even want to put in Tensorflow and pandas:

The code afterwards will assume the next imports are executed:

We load the MNIST dataset from keras.datasets library. To maintain issues easy, we’ll retain solely the subset of information containing the primary three digits. We’ll additionally ignore the take a look at set for now.

Figures in matplotlib

Seaborn is certainly an add-on to matplotlib. Due to this fact you’ll want to perceive how matplotlib handles plots even in case you’re utilizing Seaborn.

Matplotlib calls its canvas the determine. You’ll be able to divide the determine into a number of sections referred to as subplots, so you possibly can put two visualizations side-by-side.

For instance, let’s visualize the primary 16 photos of our MNIST dataset utilizing matplotlib. We’ll create 2 rows and eight columns utilizing the subplots() operate. The subplots() operate will create the axes objects for every unit. Then we’ll show every picture on every axes object utilizing the imshow() methodology. Lastly, the determine shall be proven utilizing the present() operate.

First 16 images of the training dataset displayed in 2 rows and 8 columns

First 16 photos of the coaching dataset displayed in 2 rows and eight columns

Right here we are able to see a couple of properties of matplotlib. There’s a default determine and default axes in matplotlib. There are a variety of capabilities outlined in matplotlib below the pyplot submodule for plotting on the default axes. If we need to plot on a selected axes, we are able to use the plotting operate below the axes objects. The operations to control a determine is procedural. That means, there’s a knowledge construction remembered internally by matplotlib and our operations will mutate it. The present() operate merely show the results of a sequence of operations. Due to that, we are able to step by step fine-tune numerous particulars on the determine. Within the instance above, we hid the “ticks” (i.e., the markers on axes) by setting xticks and yticks to empty lists.

Scatter plots in matplotlib and Seaborn

One of many widespread visualizations we use in machine studying initiatives is the scatter plot.

For instance, we apply PCA to the MNIST dataset and extract the primary three elements of every picture. Within the code under, we compute the eigenvectors and eigenvalues from the dataset, then initiatives the info of every picture alongside the path of the eigenvectors, and retailer the end in x_pca. For simplicity, we didn’t normalize the info to zero imply and unit variance earlier than computing the eigenvectors. This omission doesn’t have an effect on our function of visualization.

The eigenvalues printed are as follows:

The array x_pca is in form 18623 x 784. Let’s contemplate the final two columns because the x- and y-coordinates and make the purpose of every row within the plot. We will additional colour the purpose in response to which digit it corresponds to.

The next code generates a scatter plot utilizing matplotlib. The plot is created utilizing the axes object’s scatter() operate, which takes the x- and y-coordinates as the primary two argument. The c argument to scatter() methodology specifies a price that can turn into its colour. The s argument specifies its dimension. The code additionally creates a legend and provides a title to the plot.

2D scatter plot generated using Matplotlib

2D scatter plot generated utilizing matplotlib

Placing the above altogether, the next is the whole code to generate the 2D scatter plot utilizing matplotlib:

Matplotlib additionally permits a 3D scatter plot to be produced. To take action, you’ll want to create an axes object with 3D projection first. Then the 3D scatter plot is created with the scatter3D() operate, with the x-, y-, and z-coordinates as the primary three arguments. The code under makes use of the info projected alongside the eigenvectors akin to the three largest eigenvalues. As an alternative of making a legend, this code creates a colorbar.

3D scatter plot generated using Matplotlib

3D scatter plot generated utilizing matplotlib

The scatter3D() operate simply places the factors onto the 3D area. Afterwards, we are able to nonetheless modify how the determine shows such because the label of every axis and the background colour. However in 3D plots, one widespread tweak is the viewport, particularly, the angle we take a look at the 3D area. Viewport is managed by the view_init() operate within the axes object:

The viewport is managed by the elevation angle (i.e., angle to the horizon airplane) and the azimuthal angle (i.e., rotation on the horizon airplane). By default, matplotlib makes use of 30 diploma elevation and -60 diploma azimuthal, as proven above.

Placing all the things collectively, the next is the whole code to create the 3D scatter plot in matplotlib:

Creating scatter plots in Seaborn is equally simple. The scatterplot() methodology mechanically creates a legend and makes use of completely different symbols for various courses when plotting the factors. By default, the plot is created on the “present axes” from matplotlib, until the axes object is specified by the ax argument.

2D scatter plot generated using Seaborn

2D scatter plot generated utilizing Seaborn

The good thing about Seaborn over matplotlib is 2 fold: First now we have a elegant default type. For instance, if we examine the purpose type within the two scatter plots above, the Seaborn one has a border across the dot to stop the numerous factors smurged collectively. Certainly, if we run the next line earlier than calling any matplotlib capabilities:

we are able to nonetheless use the matplotlib capabilities however get a greater wanting determine by utilizing Seaborn’s type. Secondly, it’s extra handy to make use of Seaborn if we’re utilizing pandas DataFrame to carry our knowledge. For instance, let’s convert our MNIST knowledge from a tensor right into a pandas DataFrame:

which the DataFrame seems to be like the next:

Then, we are able to reproduce the Seaborn’s scatter plot with the next:

which we don’t cross in arrays as coordinates to the scatterplot() operate, however column names to the knowledge argument as a substitute.

The next is the whole code to generate a scatter plot utilizing Seaborn with the info saved in pandas:

Seaborn as a wrapper to some matplotlib capabilities, shouldn’t be changing matplotlib fully. Plotting in 3D, for instance, aren’t supported by Seaborn and we nonetheless have to resort to matplotlib capabilities for such functions.

Scatter plots in Bokeh

The plots created by matplotlib and Seaborn are static photos. If you’ll want to zoom in, pan, or toggle the show of some a part of the plot, you must use Bokeh as a substitute.

Creating scatter plots in Bokeh can be simple. The next code generates a scatter plot and provides a legend. The present() methodology from Bokeh library opens a brand new browser window to show the picture. You’ll be able to work together with the plot by scaling, zooming, scrolling and extra choices which might be proven within the toolbar subsequent to the rendered plot. You may also cover a part of the scatter by clicking on the legend.

Bokeh will produce the plot in HTML with Javascript. All of your actions to regulate the plot are dealt with by some Javascript capabilities. Its output would seems to be like the next:

2D scatter plot generated using Bokeh in a new browser window. Note the various options on the right for interacting with the plot.

2D scatter plot generated utilizing Bokeh in a brand new browser window. Be aware the assorted choices on the best for interacting with the plot.

The next is the whole code to generate the above scatter plot utilizing Bokeh:

In case you are rendering the Bokeh plot in Jupyter pocket book, you may even see the plot is produced in a brand new browser window. To place the plot within the Jupyter pocket book, you’ll want to inform Bokeh that you’re below the pocket book surroundings by operating the next earlier than the Bokeh capabilities:

Additionally word that we create the scatter plot of the three digit in a loop, one digit at a time. That is required to make the legend interactive, since every time scatter() known as, a brand new object is created. If we use create all scatter factors directly, like the next, clicking on the legend will cover and present all the things as a substitute of solely the factors of one of many digits.

Preparation of line plot knowledge

Earlier than we transfer on to indicate how we are able to visualize line plot knowledge, let’s generate some knowledge for illustration. Under is a straightforward classifier utilizing the Keras library, which we prepare it to be taught the handwritten digit classification. The historical past object returned by the match() methodology is a dictionary that incorporates all the training historical past of the coaching stage. For simplicity, we’ll prepare the mannequin utilizing solely 10 epochs.

The code above will produce a dictionary with keys loss, accuracy, val_loss, and val_accuracy, as follows:

Line plots in matplotlib, Seaborn, and Bokeh

Let’s take a look at numerous choices for visualizing the training historical past obtained from coaching our classifier.

Making a multi-line plots in matplotlib is as trivial as following. We receive the checklist of values of the coaching and validation accuracies from the historical past, and by default, matplotlib will contemplate that as sequential knowledge (i.e., x-coordinates are integers counting from 0 onwards).

Multi-line plot using Matplotlib

Multi-line plot utilizing Matplotlib

The entire code for creating the multi-line plot is as follows:

Equally, we are able to do the identical in Seaborn. As now we have seen within the case of scatter plot, we are able to cross within the knowledge to Seaborn as a sequence of values explicitly, or by way of a pandas DataFrame. Let’s plot the coaching loss and validation loss within the following utilizing a pandas DataFrame:

It is going to print the next desk, which is the DataFrame we created from the historical past:

And the plot it generated is as follows:

Multi-line plot using Seaborn

Multi-line plot utilizing Seaborn

By default, Seaborn will perceive the column labels from the DataFrame and use it as legend. Within the above, we offer a brand new label for every plot. Furthermore, the x-axis of the road plot is taken from the index of the DataFrame by default, which is integer operating from 0 to 9 in our case as we are able to see above.

The entire code of manufacturing the plot in Seaborn is as follows:

As you possibly can count on, we are able to additionally present arguments x and y along with knowledge to our name to lineplot() as in our instance of Seaborn scatter plot above if we need to management the x- and y-coordinates exactly.

Bokeh also can generate multi-line plots, as illustrated within the code under. As we noticed within the scatter plot instance, we have to present the x- and y-coordinates explicitly and do one line at a time. Once more, the present() methodology opens a brand new browser window to show the plot and you may work together with it.

Multi-line plot using Bokeh. Note the options for user interaction shown on the toolbar on the right.

Multi-line plot utilizing Bokeh. Be aware the choices for person interplay proven on the toolbar on the best.

The entire code for making the Bokeh plot is as follows:

Extra on visualization

Every of the instruments we launched above has much more capabilities for us to regulate the bits and items of the main points within the visualization. It is very important search on their respective documentation to seek out the methods you possibly can polish your plots. It’s equally necessary to take a look at the instance code of their documentation to be taught how one can probably make your visualization higher.

With out offering an excessive amount of element, listed here are some concepts that you could be need to add to your visualization:

  • add auxiliary strains, comparable to to mark the coaching and validation dataset on a time sequence knowledge. The axvline() operate from matplotlib could make a vertical line on plots for this function
  • add annotations, comparable to arrows and textual content labels to determine key factors on the plot. See the annotate() operate in matplotlib axes objects.
  • management the transparency degree in case of overlapping graphic components. All plotting capabilities we launched above permits an alpha argument to supply a price between 0 and 1 for the way a lot we are able to see by way of the graph.
  • if the info is best illustrated this fashion, we might present among the axes in log scale. It’s normally referred to as the log plot or semilog plot.

Earlier than we conclude this publish, the next is an instance that we are able to create a side-by-side visualization in matplotlib, which certainly one of them is created utilizing Seaborn:

Aspect-by-side visualization created utilizing matplotlib and Seaborn

The equal in Bokeh is to create every subplot individually after which specify the format after we present it:

Aspect-by-side plot created in Bokeh

Additional Studying

This part supplies extra assets on the subject in case you are seeking to go deeper.



API Reference


On this tutorial, you found numerous choices for knowledge visualization in Python.

Particularly, you realized:

  • Tips on how to create subplots in several rows and columns
  • Tips on how to render photos utilizing Matplotlib
  • Tips on how to generate 2D and 3D scatter plots utilizing Matplotlib
  • Tips on how to create 2D plots utilizing seaborn and Bokeh
  • Tips on how to create multi-line plots utilizing Matplotlib, Seaborn and Bokeh

Do you may have any questions on knowledge visualization choices mentioned on this publish? Ask your questions within the feedback under and I’ll do my finest to reply.


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