This tutorial covers the basic pyplot interface of matplotlib. You will use the interface to produce quickly efficient visualizations of your data.
Basic plotting
Generate two data arrays of equal lengths (X and Y variable). This could look like this:
import numpy as np t = np.arange(0.1, 9.2, 0.15) #add some noise to dependent variable y = t+np.random.rand(len(t))
Import matplotlib.pyplot and plot the data as an XY graph:
import matplotlib.pyplot as plt plt.plot(t,y) plt.show()
The plot apears only after you call plt.show() (unless you are in interactive mode activated by plt.ion()). I will omit the line in the following examples.
Label the axes by calling plt.xlabel and plt.ylabel functions.
You can select line and point style passing a third format argument to plt.plot function. For example, to plot only points:
plt.plot(t,y,'.')
Find out from the plt.plot docstring about other formats. Plot the data with red stars and dashed line.
Importing data.
Import the supplied CSV file crabs.csv. The easiest way to do it is to use numpy.recfromcsv function:
data = np.recfromcsv(``crabs.csv``)
which returns a NumPy record array with the fields as descibed in Pt. 2 of Advanded matplotlib exercise.
Plot 4th (FL) and 5th (RW) columns against each other.
Escaping the flatland.
In this exercise you will try to represent 3 different variables on the 2D screen using different visualization techniques.
Plot columns CL and RW each against FL on different sub-panels:
plt.subplot(211) #plotting command 1 plt.subplot(212) #plotting command 2
Plot the same panels, but arranged vertically.
Plot both variables on the same panel, but using two different Y axes. You may add another Y axis using plt.twinx function. Don't forget to add labels.
Plot one of the variables (CL) as position along the Y axis and the other (RW) as a size of the circle. To this end, you may use the plt.scatter command.
Which of these different representations are better in showing the relations between these variables? Choose the one you find the most efficient.
Grouping.
The crab data contains measurement on crabs of different species and sex (categorical variables). Group the data points belonging to the same species or sex using different techniques:
Final figure.
Congratulations, you have just learnt the basics of matplotlib and you are ready to create your own data visualizations. I hope you enjoyed the exercise.
Additional resources:
http://matplotlib.sourceforge.net/users/pyplot_tutorial.html
The goal of this exercise is to get accustomed to object-oriented interface to matplotlib and go through entire process of figure preparation - from design to the final figure ready for submission.
Open the supplied example of mpl_template.py.
Import CSV file crabs.csv into Python. These data have 200 rows and 8 columns, describing 5 morphological measurements on 50 crabs each of two colour forms and both sexes, of the species Leptograpsus variegatus collected at Fremantle, W. Australia (From Venables & Ripley,Modern Applied Statistics with S, Springer, 2002).
The file contain following columns:
Recommend way of doing it is with numpy.recfromcsv function (returns a numpy record array introduced during the numpy lecture), but other alternatives are allowed (such as csv module or standard IO).
Modify the plot template to plot two of the above measurements against each other. Do not forget to update labels!
Add a third dimension to the plot using different methods (choose two):
Which of the data representation is the most accurate?
Group variables belonging to the same crab group (blue male, blue female, etc., choose one method):
Repeat exercise 4 and 5, but represent different dependent variables/groups in different (non-overlapping) axes.
Does use of multiple panels increase readability?
Preparing publication-quality figure file. Let us assume that you want to prepare the final figure for submission by combining panels each of which contains one of the figures presented above. Although it is possible (and straigthforward) to do that by creating independent axes in the figure, often such approach poses several problems (for example, if the panel itself contains several axes, we would have to shift all of them to new positions). Therefore, here we will do that as a post processing step:
choose two of above figures and export them to SVG file.
modify the combine_svg.py example to read in the figures and move them to their final positions.
use inkscape from command line to export the generated SVG file to a format of choice, such as PDF:
inkscape final_figure1.svg --export-pdf=final_figure1.pdf
(Optional) You may easily automate the entire process using a simple Makefile similar to this one (available in exercises directory):
mpl_figure1.svg : mpl_figure1.py
python mpl_figure1.py mpl_figure1.svg
mpl_figure2.svg : mpl_figure2.py
python mpl_figure2.py mpl_figure2.svg
final_figure1.svg : final_figure1.py mpl_figure1.svg mpl_figure2.svg
python combine_svg.py
%.pdf : %.svg
inkscape $< --export-pdf=$@
"Test drive" your figure. Use the "Visualization Checklist" (presented during the lecture and available together with handouts) to test whether your figure is optimally designed. What could be improved?
The goal of this exercise is to create a simple website that will present geographic data on popularity of different research topics over the world. To this end, you will download the list of publications fulfilling your search criteria from the Pubmed, group them according to countries (based on affiliations), count them, and present the results on a world map.
Required modules: Biopython, CherryPy, gviz_api
Required files (supplied): pubmed.py, map_world.py, page_template.html, iso_contries.csv
At the end of this exercises, you should be able to:
Use the supllied pubmed.py module to download data from pubmed and store the results in a CSV file. You will need to use the following functions:
Don't forget to change the email address to your email (see at the top of pubmed.py)
Present the results of the Pubmed search on a map rendered in the browser.
Add dynamic content to the map.
So far the map shows the results of the search stored in CSV file on whichever topic you chose. However, it would be nice to allow the web-app user to specify his own search term and visualize the results. To this end, you will combine the pubmed.py module with the web framework map_world.py.
Add a simple form to the body of page_template.html. It may look like this (if you know HTML the code should look familiar):
<form action="search" name="SearchForm" method="get"> <input type="text" name="keyword" id="search_field" size="55"> <input type="submit" id="updateButton" value="Search"> </form>
Run the web application. See what happens when you type in the term and click search (look at the requested URL). In order to handle the request you will only need to add a search method (or whatever you specified as an action in the above form) to HelloWorld, which takes a keyword parameter called keyword. For the time being, let the return value of the method be the value of the parameter. Perform the search again an see what happens... Simple, isn't it? That's CherryPy!
Implement the search method to run the Pubmed search with the term given in keyword (compare with Point 1 above), store the results in DataTable, generate a JavaScript code for this table and pass it to the page template. Decorate the function woith cherrypy.expose decorator to expose it to the external world. Test your implementation. Pubmed searches are quite slow, so you may need to wait a while (in the meantime think how to cache the results of search, so that next time you run the same search it is faster).
I hope you enjoyed this exercise!
Additional Resources: