Add 3D section and rename gridspec refs

_episodes/03-plotting.md

@@ -463,9 +463,9 @@ Notice that sharing both axis automatically hid the axis on the inner subplots.
 > ## GridSpec
 >
 > If you need a finer control over the placement and arrangement of subplots,
-> `matplotlib` also provides the [`GridSpec`][gridspec] interface
+> `matplotlib` also provides the [`GridSpec`][matplotlib-gridspec] interface
 > which can be used together with `fig.add_subplot()`.
-> You can find a [gridspec example](girdspec-example) in the `matplotlib` gallery.
+> You can find a [gridspec example](matplotlib-gridspec-example) in the `matplotlib` gallery.
 >
 > ![subplots with gridspec](../fig/subplot-gridspec.png)
 {: .callout }
@@ -671,8 +671,6 @@ plt.title(f"Normal distribution - mean={mean}, stdev={stdev}, samples={samples},
 ## Radial axis
 
 # Changing style
-## Setting colors
-## Setting line style and point style
 ## Color maps
 
 ## Widgets in jupyter
@@ -940,6 +938,14 @@ Other useful resources can be found in popular online learning platforms such as
 [edX](https://www.edx.org/search?q=data%20visualization%20python),
 [Coursera](https://www.coursera.org/search?query=data%20visualization%20python) and many others.
 
+## Plotting in 3D
+
+Matplotlib ships with [`mplot3d`](matplotlib-mplot3d), a 3D plotting interface.
+This interface is still under development and is considered by the authors to be functional,
+but not complete.
+
+If you need advanced 3D capabilities, you might want to look into [VTK][vtk-py], [Blender3D][blender3d-py] or if visualizing 3D proteins, the well known [pymol][pymol-py].
+
 ```
 # Covered above - delete when done
 

_includes/links.md

@@ -13,6 +13,7 @@
 [biopython]: https://biopython.org/
 [black-still-beta]: https://github.com/psf/black#note-this-is-a-beta-product
 [black-used-by]: https://github.com/psf/black#used-by
+[blender3d-py]: https://docs.blender.org/api/current/
 [bokeh-home]: https://bokeh.org/
 [cc-by-human]: https://creativecommons.org/licenses/by/4.0/
 [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
@@ -56,8 +57,6 @@
 [github-importer]: https://import.github.com/
 [gooey]: https://pypi.org/project/Gooey/
 [graphical-abstract]: https://en.wikipedia.org/wiki/Graphical_abstract
-[gridspec]: https://matplotlib.org/tutorials/intermediate/gridspec.html
-[gridspec-example]: https://matplotlib.org/3.1.1/gallery/subplots_axes_and_figures/gridspec_multicolumn.html
 [grus-dont-like-notebooks]: https://www.youtube.com/watch?v=7jiPeIFXb6U
 [if-name-main]: https://stackoverflow.com/a/419185
 [image-analysis-course]: https://git.embl.de/grp-bio-it/image-analysis-with-python
@@ -88,18 +87,21 @@
 [matlab-home]: https://www.mathworks.com/products/matlab.html
 [matplotlib-backends]: https://matplotlib.org/tutorials/introductory/usage.html#the-builtin-backends
 [matplotlib-books]: https://matplotlib.org/resources/index.html
-[matplotlib-colors]: https://matplotlib.org/3.2.2/api/colors_api.html
-[matplotlib-color-names]: https://matplotlib.org/3.2.2/gallery/color/named_colors.html
 [matplotlib-color-codes]: https://matplotlib.org/3.2.2/tutorials/colors/colors.html
+[matplotlib-color-names]: https://matplotlib.org/3.2.2/gallery/color/named_colors.html
+[matplotlib-colors]: https://matplotlib.org/3.2.2/api/colors_api.html
 [matplotlib-gallery]: https://matplotlib.org/gallery/index.html
+[matplotlib-gridspec-example]: https://matplotlib.org/3.1.1/gallery/subplots_axes_and_figures/gridspec_multicolumn.html
+[matplotlib-gridspec]: https://matplotlib.org/tutorials/intermediate/gridspec.html
 [matplotlib-hinton]: https://matplotlib.org/examples/specialty_plots/hinton_demo.html
+[matplotlib-hist]: https://matplotlib.org/3.2.2/api/_as_gen/matplotlib.pyplot.hist.html
 [matplotlib-home]: https://matplotlib.org/
 [matplotlib-linestyle]: https://matplotlib.org/3.2.2/gallery/lines_bars_and_markers/linestyles.html
 [matplotlib-markerstyle]: https://matplotlib.org/3.2.2/api/markers_api.html
-[matplotlib-hist]: https://matplotlib.org/3.2.2/api/_as_gen/matplotlib.pyplot.hist.html
+[matplotlib-mplot3d]: https://matplotlib.org/api/toolkits/mplot3d.html
 [matplotlib-plot]: https://matplotlib.org/3.2.2/api/_as_gen/matplotlib.pyplot.plot.html
-[matplotlib-scatter]: https://matplotlib.org/3.2.2/api/_as_gen/matplotlib.pyplot.scatter.html
 [matplotlib-scatter-examples]: https://matplotlib.org/3.2.2/api/_as_gen/matplotlib.pyplot.scatter.html#examples-using-matplotlib-pyplot-scatter
+[matplotlib-scatter]: https://matplotlib.org/3.2.2/api/_as_gen/matplotlib.pyplot.scatter.html
 [mit-license]: https://opensource.org/licenses/mit-license.html
 [modulo-operator]: https://python-reference.readthedocs.io/en/latest/docs/operators/modulus.html
 [morea]: https://morea-framework.github.io/
@@ -141,6 +143,7 @@
 [pyflakes]: https://pypi.org/project/pyflakes/
 [pyformat.info]: https://pyformat.info/
 [pylint]: https://pypi.org/project/pylint/
+[pymol-py]: https://pymolwiki.org/index.php/Launching_From_a_Script
 [python-escaping]: https://www.w3schools.com/python/gloss_python_escape_characters.asp
 [python-gapminder]: https://swcarpentry.github.io/python-novice-gapminder/
 [python-raw-string]: https://www.askpython.com/python/string/python-raw-strings
@@ -173,6 +176,7 @@
 [typing-module]: https://docs.python.org/3/library/typing.html
 [vega-lite]: https://vega.github.io/vega-lite/
 [vscode-docstring]: https://marketplace.visualstudio.com/items?itemName=njpwerner.autodocstring
+[vtk-py]: https://pypi.org/project/vtk/
 [w3c-py-classes]: https://www.w3schools.com/python/python_classes.asp
 [walrus]: https://www.geeksforgeeks.org/walrus-operator-in-python-3-8/
 [wikipedia-latex]: https://en.wikipedia.org/wiki/LaTeX