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Commit e8296319 authored by Michiel Cottaar's avatar Michiel Cottaar Committed by Michiel Cottaar
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Fix the link to the anatomy of a plot figure

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%% Cell type:markdown id:ignored-think tags:
%% Cell type:markdown id:christian-smart tags:
# Matplotlib tutorial
The main plotting library in python is `matplotlib`.
It provides a simple interface to just explore the data,
while also having a lot of flexibility to create publication-worthy plots.
In fact, the vast majority of python-produced plots in papers will be either produced
directly using matplotlib or by one of the many plotting libraries built on top of
matplotlib (such as [seaborn](https://seaborn.pydata.org/) or [nilearn](https://nilearn.github.io/)).
Like everything in python, there is a lot of help available online (just google it or ask your local pythonista).
A particularly useful resource for matplotlib is the [gallery](https://matplotlib.org/gallery/index.html).
Here you can find a wide range of plots.
Just find one that looks like what you want to do and click on it to see (and copy) the code used to generate the plot.
## Contents
- [Basic plotting commands](#basic-plotting-commands)
- [Line plots](#line)
- [Scatter plots](#scatter)
- [Histograms and bar plots](#histograms)
- [Adding error bars](#error)
- [Shading regions](#shade)
- [Displaying images](#image)
- [Adding lines, arrows, text](#annotations)
- [Using the object-oriented interface](#OO)
- [Multiple plots (i.e., subplots)](#subplots)
- [Adjusting plot layouts](#layout)
- [Advanced grid configurations (GridSpec)](#grid-spec)
- [Styling your plot](#styling)
- [Setting title and labels](#labels)
- [Editing the x- and y-axis](#axis)
- [FAQ](#faq)
- [Why am I getting two images?](#double-image)
- [I produced a plot in my python script, but it does not show up](#show)
- [Changing where the image appears: backends](#backends)
<a class="anchor" id="basic-plotting-commands"></a>
## Basic plotting commands
Let's start with the basic imports:
%% Cell type:code id:material-fundamentals tags:
%% Cell type:code id:quick-postage tags:
``` python
import matplotlib.pyplot as plt
import numpy as np
```
%% Cell type:markdown id:dying-savings tags:
%% Cell type:markdown id:prescribed-writing tags:
<a class="anchor" id="line"></a>
### Line plots
A basic lineplot can be made just by calling `plt.plot`:
%% Cell type:code id:determined-melissa tags:
%% Cell type:code id:turkish-marsh tags:
``` python
plt.plot([1, 2, 3], [1.3, 4.2, 3.1])
```
%% Cell type:markdown id:optional-bloom tags:
%% Cell type:markdown id:compact-modeling tags:
To adjust how the line is plotted, check the documentation:
%% Cell type:code id:electric-purpose tags:
%% Cell type:code id:distinct-coordinate tags:
``` python
plt.plot?
```
%% Cell type:markdown id:offshore-narrative tags:
%% Cell type:markdown id:green-dutch tags:
As you can see there are a lot of options.
The ones you will probably use most often are:
- `linestyle`: how the line is plotted (set to '' to omit the line)
- `marker`: how the points are plotted (these are not plotted by default)
- `color`: what color to use (defaults to cycling through a set of 7 colors)
%% Cell type:code id:younger-recall tags:
%% Cell type:code id:adjacent-satellite tags:
``` python
theta = np.linspace(0, 2 * np.pi, 101)
plt.plot(np.sin(theta), np.cos(theta))
plt.plot([-0.3, 0.3], [0.3, 0.3], marker='o', linestyle='', markersize=20)
plt.plot(0, -0.1, marker='s', color='black')
x = np.linspace(-0.5, 0.5, 5)
plt.plot(x, x ** 2 - 0.5, linestyle='--', marker='+', color='red')
```
%% Cell type:markdown id:fewer-wednesday tags:
%% Cell type:markdown id:external-meaning tags:
Because these keywords are so common, you can actually set one or more of them by passing in a string as the third argument.
%% Cell type:code id:romance-payment tags:
%% Cell type:code id:simple-korean tags:
``` python
x = np.linspace(0, 1, 11)
plt.plot(x, x)
plt.plot(x, x ** 2, '--') # sets the linestyle to dashed
plt.plot(x, x ** 3, 's') # sets the marker to square (and turns off the line)
plt.plot(x, x ** 4, '^y:') # sets the marker to triangles (i.e., '^'), linestyle to dotted (i.e., ':'), and the color to yellow (i.e., 'y')
```
%% Cell type:markdown id:democratic-setting tags:
%% Cell type:markdown id:pediatric-sullivan tags:
<a class="anchor" id="scatter"></a>
### Scatter plots
The main extra feature of `plt.scatter` over `plt.plot` is that you can vary the color and size of the points based on some other variable array:
%% Cell type:code id:homeless-opening tags:
%% Cell type:code id:bright-preparation tags:
``` python
x = np.random.rand(30)
y = np.random.rand(30)
plt.scatter(x, y, x * 30, y)
plt.colorbar() # adds a colorbar
```
%% Cell type:markdown id:sitting-scheme tags:
%% Cell type:markdown id:asian-mailing tags:
The third argument is the variable determining the size, while the fourth argument is the variable setting the color.
<a class="anchor" id="histograms"></a>
### Histograms and bar plots
For a simple histogram you can do this:
%% Cell type:code id:trained-mechanism tags:
%% Cell type:code id:massive-relative tags:
``` python
r = np.random.rand(1000)
n,bins,_ = plt.hist((r-0.5)**2, bins=30)
```
%% Cell type:markdown id:convinced-framework tags:
%% Cell type:markdown id:positive-insight tags:
where it also returns the number of elements in each bin, as `n`, and
the bin centres, as `bins`.
> The `_` in the third part on the left
> hand side is a shorthand for just throwing away the corresponding part
> of the return structure.
There is also a call for doing bar plots:
%% Cell type:code id:convinced-cricket tags:
%% Cell type:code id:intensive-taste tags:
``` python
samp1 = r[0:10]
samp2 = r[10:20]
bwidth = 0.3
xcoord = np.arange(10)
plt.bar(xcoord-bwidth, samp1, width=bwidth, color='red', label='Sample 1')
plt.bar(xcoord, samp2, width=bwidth, color='blue', label='Sample 2')
plt.legend(loc='upper left')
```
%% Cell type:markdown id:historical-content tags:
%% Cell type:markdown id:boolean-metropolitan tags:
> If you want more advanced distribution plots beyond a simple histogram, have a look at the seaborn [gallery](https://seaborn.pydata.org/examples/index.html) for (too?) many options.
<a class="anchor" id="error"></a>
### Adding error bars
If your data is not completely perfect and has for some obscure reason some uncertainty associated with it,
you can plot these using `plt.error`:
%% Cell type:code id:broken-deviation tags:
%% Cell type:code id:basic-cambridge tags:
``` python
x = np.arange(5)
y1 = [0.3, 0.5, 0.7, 0.1, 0.3]
yerr = [0.12, 0.28, 0.1, 0.25, 0.6]
xerr = 0.3
plt.errorbar(x, y1, yerr, xerr, marker='s', linestyle='')
```
%% Cell type:markdown id:shared-afghanistan tags:
%% Cell type:markdown id:twelve-assist tags:
<a class="anchor" id="shade"></a>
### Shading regions
An area below a plot can be shaded using `plt.fill`
%% Cell type:code id:changed-dressing tags:
%% Cell type:code id:stuck-teaching tags:
``` python
x = np.linspace(0, 2, 100)
plt.fill(x, np.sin(x * np.pi))
```
%% Cell type:markdown id:infrared-chinese tags:
%% Cell type:markdown id:metric-chemical tags:
This can be nicely combined with a polar projection, to create 2D orientation distribution functions:
%% Cell type:code id:alternative-johnson tags:
%% Cell type:code id:democratic-israel tags:
``` python
plt.subplot(projection='polar')
theta = np.linspace(0, 2 * np.pi, 100)
plt.fill(theta, np.exp(-2 * np.cos(theta) ** 2))
```
%% Cell type:markdown id:primary-momentum tags:
%% Cell type:markdown id:connected-consideration tags:
The area between two lines can be shaded using `fill_between`:
%% Cell type:code id:naughty-colors tags:
%% Cell type:code id:engaged-lottery tags:
``` python
x = np.linspace(0, 10, 1000)
y = 5 * np.sin(5 * x) + x - 0.1 * x ** 2
yl = x - 0.1 * x ** 2 - 5
yu = yl + 10
plt.plot(x, y, 'r')
plt.fill_between(x, yl, yu)
```
%% Cell type:markdown id:acknowledged-illustration tags:
%% Cell type:markdown id:paperback-stylus tags:
<a class="anchor" id="image"></a>
### Displaying images
The main command for displaying images is `plt.imshow` (use `plt.pcolor` for cases where you do not have a regular grid)
%% Cell type:code id:protected-toolbox tags:
%% Cell type:code id:acoustic-kitchen tags:
``` python
import nibabel as nib
import os.path as op
nim = nib.load(op.expandvars('${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz'), mmap=False)
imdat = nim.get_data().astype(float)
imslc = imdat[:,:,70]
plt.imshow(imslc, cmap=plt.cm.gray)
plt.colorbar()
plt.grid('off')
```
%% Cell type:markdown id:short-turkey tags:
%% Cell type:markdown id:frank-master tags:
Note that matplotlib will use the **voxel data orientation**, and that
configuring the plot orientation is **your responsibility**. To rotate a
slice, simply transpose the data (`.T`). To invert the data along along an
axis, you don't need to modify the data - simply swap the axis limits around:
%% Cell type:code id:vulnerable-vegetation tags:
%% Cell type:code id:initial-passing tags:
``` python
plt.imshow(imslc.T, cmap=plt.cm.gray)
plt.xlim(reversed(plt.xlim()))
plt.ylim(reversed(plt.ylim()))
plt.colorbar()
plt.grid('off')
```
%% Cell type:markdown id:danish-sandwich tags:
%% Cell type:markdown id:specialized-maintenance tags:
> It is easier to produce informative brain images using nilearn or fsleyes
<a class="anchor" id="annotations"></a>
### Adding lines, arrows, and text
Adding horizontal/vertical lines, arrows, and text:
%% Cell type:code id:checked-helping tags:
%% Cell type:code id:weighted-publicity tags:
``` python
plt.axhline(-1) # horizontal line
plt.axvline(1) # vertical line
plt.arrow(0.2, -0.2, 0.2, -0.8, length_includes_head=True, width=0.01)
plt.text(0.5, 0.5, 'middle of the plot', transform=plt.gca().transAxes, ha='center', va='center')
plt.annotate("line crossing", (1, -1), (0.8, -0.8), arrowprops={}) # adds both text and arrow; need to set the arrowprops keyword for the arrow to be plotted
```
%% Cell type:markdown id:finished-canon tags:
%% Cell type:markdown id:manual-bacon tags:
By default the locations of the arrows and text will be in data coordinates (i.e., whatever is on the axes),
however you can change that. For example to find the middle of the plot in the last example we use
axes coordinates, which are always (0, 0) in the lower left and (1, 1) in the upper right.
See the matplotlib [transformations tutorial](https://matplotlib.org/stable/tutorials/advanced/transforms_tutorial.html)
for more detail.
<a class="anchor" id="OO"></a>
## Using the object-oriented interface
In the examples above we simply added multiple lines/points/bars/images
(collectively called artists in matplotlib) to a single plot.
To prettify this plots, we first need to know what all the features are called:
[[https://matplotlib.org/stable/_images/anatomy.png]]
Based on this plot let's figure out what our first command of `plt.plot([1, 2, 3], [1.3, 4.2, 3.1])`
![anatomy of a plot](https://matplotlib.org/stable/_images/anatomy.png)
Using the terms in this plot let's see what our first command of `plt.plot([1, 2, 3], [1.3, 4.2, 3.1])`
actually does:
1. First it creates a figure and makes this the active figure. Being the active figure means that any subsequent commands will affect figure. You can find the active figure at any point by calling `plt.gcf()`.
2. Then it creates an Axes or Subplot in the figure and makes this the active axes. Any subsequent commands will reuse this active axes. You can find the active axes at any point by calling `plt.gca()`.
3. Finally it creates a Line2D artist containing the x-coordinates `[1, 2, 3]` and `[1.3, 4.2, 3.1]` ands adds this to the active axes.
4. At some later time, when actually creating the plot, matplotlib will also automatically determine for you a default range for the x-axis and y-axis and where the ticks should be.
This concept of an "active" figure and "active" axes can be very helpful with a single plot, it can quickly get very confusing when you have multiple sub-plots within a figure or even multiple figures.
In that case we want to be more explicit about what sub-plot we want to add the artist to.
We can do this by switching from the "procedural" interface used above to the "object-oriented" interface.
The commands are very similar, we just have to do a little more setup.
For example, the equivalent of `plt.plot([1, 2, 3], [1.3, 4.2, 3.1])` is:
%% Cell type:code id:original-melissa tags:
%% Cell type:code id:earned-anaheim tags:
``` python
fig = plt.figure()
ax = fig.add_subplot()
ax.plot([1, 2, 3], [1.3, 4.2, 3.1])
```
%% Cell type:markdown id:handy-anniversary tags:
%% Cell type:markdown id:valued-hungary tags:
Note that here we explicitly create the figure and add a single sub-plot to the figure.
We then call the `plot` function explicitly on this figure.
The "Axes" object has all of the same plotting command as we used above,
although the commands to adjust the properties of things like the title, x-axis, and y-axis are slighly different.
<a class="anchor" id="subplots"></a>
## Multiple plots (i.e., subplots)
As stated one of the strengths of the object-oriented interface is that it is easier to work with multiple plots.
While we could do this in the procedural interface:
%% Cell type:code id:occupied-enforcement tags:
%% Cell type:code id:intensive-bruce tags:
``` python
plt.subplot(221)
plt.title("Upper left")
plt.subplot(222)
plt.title("Upper right")
plt.subplot(223)
plt.title("Lower left")
plt.subplot(224)
plt.title("Lower right")
```
%% Cell type:markdown id:encouraging-poultry tags:
%% Cell type:markdown id:upset-stanley tags:
For such a simple example, this works fine. But for longer examples you would find yourself constantly looking back through the
code to figure out which of the subplots this specific `plt.title` command is affecting.
The recommended way to this instead is:
%% Cell type:code id:elect-printer tags:
%% Cell type:code id:frank-treatment tags:
``` python
fig, axes = plt.subplots(nrows=2, ncols=2)
axes[0, 0].set_title("Upper left")
axes[0, 1].set_title("Upper right")
axes[1, 0].set_title("Lower left")
axes[1, 1].set_title("Lower right")
```
%% Cell type:markdown id:brief-auction tags:
%% Cell type:markdown id:occupational-astronomy tags:
Here we use `plt.subplots`, which creates both a new figure for us and a grid of sub-plots.
The returned `axes` object is in this case a 2x2 array of `Axes` objects, to which we set the title using the normal numpy indexing.
> Seaborn is great for creating grids of closely related plots. Before you spent a lot of time implementing your own have a look if seaborn already has what you want on their [gallery](https://seaborn.pydata.org/examples/index.html)
<a class="anchor" id="layout"></a>
### Adjusting plot layout
The default layout of sub-plots often leads to overlap between the labels/titles of the various subplots (as above) or to excessive amounts of whitespace in between. We can often fix this by just adding `fig.tight_layout` (or `plt.tight_layout`) after making the plot:
%% Cell type:code id:binding-tobacco tags:
%% Cell type:code id:joint-chick tags:
``` python
fig, axes = plt.subplots(nrows=2, ncols=2)
axes[0, 0].set_title("Upper left")
axes[0, 1].set_title("Upper right")
axes[1, 0].set_title("Lower left")
axes[1, 1].set_title("Lower right")
fig.tight_layout()
```
%% Cell type:markdown id:canadian-africa tags:
%% Cell type:markdown id:illegal-spanish tags:
Uncomment `fig.tight_layout` and see how it adjusts the spacings between the plots automatically to reduce the whitespace.
If you want more explicit control, you can use `fig.subplots_adjust` (or `plt.subplots_adjust` to do this for the active figure).
For example, we can remove any whitespace between the plots using:
%% Cell type:code id:hollow-metadata tags:
%% Cell type:code id:accomplished-watershed tags:
``` python
np.random.seed(1)
fig, axes = plt.subplots(nrows=2, ncols=2, sharex=True, sharey=True)
for ax in axes.flat:
offset = np.random.rand(2) * 5
ax.scatter(np.random.randn(10) + offset[0], np.random.randn(10) + offset[1])
fig.suptitle("group of plots, sharing x- and y-axes")
fig.subplots_adjust(wspace=0, hspace=0, top=0.9)
```
%% Cell type:markdown id:willing-grade tags:
%% Cell type:markdown id:standing-course tags:
<a class="anchor" id="grid-spec"></a>
### Advanced grid configurations (GridSpec)
You can create more advanced grid layouts using [GridSpec](https://matplotlib.org/stable/tutorials/intermediate/gridspec.html).
An example taken from that website is:
%% Cell type:code id:loved-munich tags:
%% Cell type:code id:silent-voluntary tags:
``` python
fig = plt.figure(constrained_layout=True)
gs = fig.add_gridspec(3, 3)
f3_ax1 = fig.add_subplot(gs[0, :])
f3_ax1.set_title('gs[0, :]')
f3_ax2 = fig.add_subplot(gs[1, :-1])
f3_ax2.set_title('gs[1, :-1]')
f3_ax3 = fig.add_subplot(gs[1:, -1])
f3_ax3.set_title('gs[1:, -1]')
f3_ax4 = fig.add_subplot(gs[-1, 0])
f3_ax4.set_title('gs[-1, 0]')
f3_ax5 = fig.add_subplot(gs[-1, -2])
f3_ax5.set_title('gs[-1, -2]')
```
%% Cell type:markdown id:invalid-roads tags:
%% Cell type:markdown id:roman-discharge tags:
<a class="anchor" id="styling"></a>
## Styling your plot
<a class="anchor" id="labels"></a>
### Setting title and labels
You can edit a large number of plot properties by using the `Axes.set_*` interface.
We have already seen several examples of this above, but here is one more:
%% Cell type:code id:roman-nicaragua tags:
%% Cell type:code id:english-yahoo tags:
``` python
fig, axes = plt.subplots()
axes.plot([1, 2, 3], [2.3, 4.1, 0.8])
axes.set_xlabel('xlabel')
axes.set_ylabel('ylabel')
axes.set_title('title')
```
%% Cell type:markdown id:appropriate-affairs tags:
%% Cell type:markdown id:constant-evolution tags:
You can also set any of these properties by calling `Axes.set` directly:
%% Cell type:code id:afraid-fields tags:
%% Cell type:code id:suspended-biography tags:
``` python
fig, axes = plt.subplots()
axes.plot([1, 2, 3], [2.3, 4.1, 0.8])
axes.set(
xlabel='xlabel',
ylabel='ylabel',
title='title',
)
```
%% Cell type:markdown id:hired-journey tags:
%% Cell type:markdown id:annual-hundred tags:
> To match the matlab API and save some typing the equivalent commands in the procedural interface do not have the `set_` preset. So, they are `plt.xlabel`, `plt.ylabel`, `plt.title`. This is also true for many of the `set_` commands we will see below.
You can edit the font of the text when setting the label:
%% Cell type:code id:legislative-parallel tags:
%% Cell type:code id:trained-mouse tags:
``` python
fig, axes = plt.subplots()
axes.plot([1, 2, 3], [2.3, 4.1, 0.8])
axes.set_xlabel("xlabel", color='red')
axes.set_ylabel("ylabel", fontsize='larger')
```
%% Cell type:markdown id:possible-sacramento tags:
%% Cell type:markdown id:elementary-mentor tags:
<a class="anchor" id="axis"></a>
### Editing the x- and y-axis
We can change many of the properties of the x- and y-axis by using `set_` commands.
- The range shown on an axis can be set using `ax.set_xlim` (or `plt.xlim`)
- You can switch to a logarithmic (or other) axis using `ax.set_xscale('log')`
- The location of the ticks can be set using `ax.set_xticks` (or `plt.xticks`)
- The text shown for the ticks can be set using `ax.set_xticklabels` (or as a second argument to `plt.xticks`)
- The style of the ticks can be adjusted by looping through the ticks (obtained through `ax.get_xticks` or calling `plt.xticks` without arguments).
For example:
%% Cell type:code id:executed-space tags:
%% Cell type:code id:capital-surgeon tags:
``` python
fig, axes = plt.subplots()
axes.errorbar([0, 1, 2], [0.8, 0.4, -0.2], 0.1, linestyle='-', marker='s')
axes.set_xticks((0, 1, 2))
axes.set_xticklabels(('start', 'middle', 'end'))
for tick in axes.get_xticklabels():
tick.set(
rotation=45,
size='larger'
)
axes.set_xlabel("Progression through practical")
axes.set_yticks((0, 0.5, 1))
axes.set_yticklabels(('0', '50%', '100%'))
fig.tight_layout()
```
%% Cell type:markdown id:administrative-acquisition tags:
%% Cell type:markdown id:discrete-hartford tags:
<a class="anchor" id="faq"></a>
## FAQ
<a class="anchor" id="double-image"></a>
### Why am I getting two images?
Any figure you produce in the notebook will be shown by default once a cell successfully finishes (i.e., without error).
If the code in a notebook cell crashes after creating the figure, this figure will still be in memory.
It will be shown after another cell successfully finishes.
You can remove this additional plot simply by rerunning the cell, after which you should only see the plot produced by the cell in question.
<a class="anchor" id="show"></a>
### I produced a plot in my python script, but it does not show up?
Add `plt.show()` to the end of your script (or save the figure to a file using `plt.savefig` or `fig.savefig`).
`plt.show` will show the image to you and will block the script to allow you to take in and adjust the figure before saving or discarding it.
<a class="anchor" id="backends"></a>
### Changing where the image appears: backends
Matplotlib works across a wide range of environments: Linux, Mac OS, Windows, in the browser, and more.
The exact detail of how to show you your plot will be different across all of these environments.
This procedure used to translate your `Figure`/`Axes` objects into an actual visualisation is called the backend.
In this notebook we were using the `inline` backend, which is the default when running in a notebook.
While very robust, this backend has the disadvantage that it only produces static plots.
We could have had interactive plots if only we had changed backends to `nbagg`.
You can change backends in the IPython terminal/notebook using:
%% Cell type:code id:directed-trouble tags:
%% Cell type:code id:fifty-relaxation tags:
``` python
%matplotlib nbagg
```
%% Cell type:markdown id:indian-integrity tags:
%% Cell type:markdown id:fifty-sunglasses tags:
> If you are using Jupyterlab (new version of the jupyter notebook) the `nbagg` backend will not work. Instead you will have to install `ipympl` and then use the `widgets` backend to get an interactive backend (this also works in the old notebooks).
In python scripts, this will give you a syntax error and you should instead use:
%% Cell type:code id:pregnant-raising tags:
%% Cell type:code id:underlying-dealer tags:
``` python
import matplotlib
matplotlib.use("osx")
```
%% Cell type:markdown id:ceramic-liquid tags:
%% Cell type:markdown id:general-subscriber tags:
Usually, the default backend will be fine, so you will not have to set it.
Note that setting it explicitly will make your script less portable.
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......@@ -198,8 +198,10 @@ for more detail.
In the examples above we simply added multiple lines/points/bars/images
(collectively called artists in matplotlib) to a single plot.
To prettify this plots, we first need to know what all the features are called:
[[https://matplotlib.org/stable/_images/anatomy.png]]
Based on this plot let's figure out what our first command of `plt.plot([1, 2, 3], [1.3, 4.2, 3.1])`
![anatomy of a plot](https://matplotlib.org/stable/_images/anatomy.png)
Using the terms in this plot let's see what our first command of `plt.plot([1, 2, 3], [1.3, 4.2, 3.1])`
actually does:
1. First it creates a figure and makes this the active figure. Being the active figure means that any subsequent commands will affect figure. You can find the active figure at any point by calling `plt.gcf()`.
......
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