respond to alessio

Author: chrishalcrow

doc/how_to/customize_a_plot.rst

@@ -3,11 +3,12 @@ Customize a plot
 
 The ``SpikeInterface`` widgets are designed to have reasonable default
 plotting options, but sometimes you’ll want to make adjustments to the
-plots. For doing this, we expose the underlying ``matplotlib`` objects for you to
-edit. Let’s see how to do this in an example. First, let’s make some synthetic
-data and compute some extensions which can be used for plotting.
+plots. For doing this, we expose the underlying ``matplotlib`` objects
+for you to edit. Let’s see how to do this in an example. First, let’s
+make some synthetic data and compute some extensions which can be used
+for plotting.
 
-.. code:: ipython3
+.. code::
 
     import spikeinterface.full as si
     import matplotlib.pyplot as plt
@@ -37,7 +38,7 @@ widgets <https://spikeinterface.readthedocs.io/en/stable/modules/widgets.html#av
 for more!). These functions output a ``widget``. We’ll assign the unit
 locations widget to ``fig_units``.
 
-.. code:: ipython3
+.. code::
 
     fig_units = si.plot_unit_locations(sorting_analyzer)
 
@@ -56,17 +57,18 @@ locations widget to ``fig_units``.
 .. image:: customize_a_plot_files/customize_a_plot_4_1.png
 
 
-By playing with the matplotlib objects, we gain access to the full matplotlib
-machinery: adding custom titles, axis labels, ticks, more plots etc.
-Let’s cusomtise our unit locations plot (Note: the
-``SpikeInterface`` Team does not endorse the following style conventions):
+By getting with the matplotlib objects, we gain access to the full
+``matplotlib`` machinery: adding custom titles, axis labels, ticks, more
+plots etc. Let’s cusomtise our unit locations plot. (Note: the
+``SpikeInterface`` Team does not endorse the following style
+conventions):
 
-.. code:: ipython3
+.. code::
 
     # Get the widget
     fig_units = si.plot_unit_locations(sorting_analyzer)
 
-    # Modify the widget's `axis`` to set the title and xes labels
+    # Modify the widget's `axis`` to set the title and axes labels
     fig_units.ax.set_title("My favorite units", fontname = "Comic Sans MS")
     fig_units.ax.set_xlabel("x probe location (um)")
     fig_units.ax.set_xlabel("y probe location (um)")
@@ -89,10 +91,9 @@ Let’s cusomtise our unit locations plot (Note: the
 
 
 
-
 .. parsed-literal::
 
-    <spikeinterface.widgets.unit_locations.UnitLocationsWidget at 0x17f719cd0>
+    <spikeinterface.widgets.unit_locations.UnitLocationsWidget at 0x147bda550>
 
 
 
@@ -107,7 +108,7 @@ to do this is to set up your figure and axes first, then tell
 ``SpikeInterface`` which axes it should attach the widget plot to.
 Here’s an example of making a unit summary plot.
 
-.. code:: ipython3
+.. code::
 
     import matplotlib.pyplot as plt
     fig, axs = plt.subplots(ncols=2, nrows=1)

examples/how_to/README.md

@@ -14,7 +14,7 @@ with `nbconvert`. Here are the steps (in this example for the `get_started`):
 
 ```
 >>>  jupytext --to notebook get_started.py
->>>  jupytext --set-formats ipynb,py get_started.ipynb
+>>>  jupytext --set-formats ipynb.py get_started.ipynb
 ```
 
 2. Run the notebook

examples/how_to/customize_a_plot.py

@@ -0,0 +1,97 @@
+# ---
+# jupyter:
+#   jupytext:
+#     cell_metadata_filter: -all
+#     formats: py:light,ipynb
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.5'
+#       jupytext_version: 1.17.0
+#   kernelspec:
+#     display_name: .venv
+#     language: python
+#     name: python3
+# ---
+
+# # Customize a plot
+
+# The `SpikeInterface` widgets are designed to have reasonable default plotting options, but
+# sometimes you'll want to make adjustments to the plots. For doing this, we expose the underlying
+# `matplotlib` objects for you to edit. Let's see how to do this in an example. First,
+# let's make some synthetic data and compute some extensions which can be used for plotting.
+
+# +
+import spikeinterface.full as si
+import matplotlib.pyplot as plt
+
+recording, sorting = si.generate_ground_truth_recording(seed=1205)
+sorting_analyzer = si.create_sorting_analyzer(sorting=sorting, recording=recording)
+sorting_analyzer.compute({"random_spikes": {'seed': 1205}, "templates": {}, "unit_locations": {}})
+
+unit_locations = sorting_analyzer.get_extension("unit_locations").get_data()
+# -
+
+# Now we can plot the `unit_locations` and `unit_templates` using the approperiate widgets
+# (see the  [full list of widgets](https://spikeinterface.readthedocs.io/en/stable/modules/widgets.html#available-plotting-functions)
+# for more!). These functions output a `widget`.  We'll assign the unit locations widget to `fig_units`.
+
+# +
+fig_units = si.plot_unit_locations(sorting_analyzer)
+
+# Each widget contains a `matplotlib` figure and axis:
+print(type(fig_units.figure))
+print(type(fig_units.ax))
+# -
+
+# By getting with the matplotlib objects, we gain access to the full `matplotlib` machinery: adding custom
+#  titles, axis labels, ticks, more plots etc. Let's cusomtise our unit locations plot. (Note: the
+# `SpikeInterface` Team does not endorse the following style conventions):
+
+# +
+# Get the widget
+fig_units = si.plot_unit_locations(sorting_analyzer)
+
+# Modify the widget's `axis`` to set the title and axes labels
+fig_units.ax.set_title("My favorite units", fontname = "Comic Sans MS")
+fig_units.ax.set_xlabel("x probe location (um)")
+fig_units.ax.set_xlabel("y probe location (um)")
+
+# You can also set custom ticks
+fig_units.ax.set_xticks([-60,-30,unit_locations[0,0],30,60])
+fig_units.ax.set_xticklabels([-60,-30,"unit_0_x",30,60])
+fig_units.ax.set_yticks([-40,-20,0,unit_locations[0,1],40])
+fig_units.ax.set_yticklabels([-40,-20,0,"unit_0_y",40])
+
+# Change the limits of the plot
+fig_units.ax.set_xlim((-30,50))
+fig_units.ax.set_ylim((-50,50))
+
+# And add extra information on the plot
+fig_units.ax.text(unit_locations[6,0], unit_locations[6,1]+5, s="UNIT 6!!!", fontname="Courier")
+
+fig_units
+# -
+
+# Beautiful!!!
+#
+# You can also combine figures into a multi-figure plot. The easiest way to do this is to set up your figure and axes first, then tell `SpikeInterface` which axes it should attach the widget plot to. Here's an example of making a unit summary plot.
+
+# +
+import matplotlib.pyplot as plt
+fig, axs = plt.subplots(ncols=2, nrows=1)
+
+unit_id=8
+si.plot_unit_locations(sorting_analyzer=sorting_analyzer, ax=axs[0])
+si.plot_unit_templates(sorting_analyzer, axes=[axs[1]], unit_ids=[f'{unit_id}'])
+
+axs[0].plot([unit_locations[8,0], unit_locations[8,0]+50], [unit_locations[8,1], unit_locations[8,1]+50])
+axs[0].text(unit_locations[8,0]+52, unit_locations[8,1]+52, s=f"Unit {unit_id}")
+axs[0].set_title("Unit location", fontsize=10)
+
+fig.suptitle(f"Unit {unit_id} summary", fontfamily="Comic Sans MS", fontsize=20)
+
+fig.tight_layout()
+# -
+
+# For more details on what you can do using matplotlib, check out their [extensive documentation](https://matplotlib.org/stable/)