add docs

Author: chrishalcrow

README.md

@@ -222,7 +222,7 @@ sigui --mode=web --root-folder path-to-my-analyzers
 ![launcher_web](docs/source/images/launcher_web.png)
 
 
-## Customizing the layout
+## Customizing layout and settings
 
 You can create your own custom layout by specifying which views you'd like
 to see, and where they go. The basic window layout supports eight "zones",
@@ -248,7 +248,7 @@ E.g. suppose your layout is only non-empty in zones 1, 4, 5, 6 and 7:
 +---------------+--------------+
 ```
 
-Then zone1 will stretch right-wards to make a three-zone view. Zone4 will stretch
+Then zone1 will stretch right-wards to make a two-zone view. Zone4 will stretch
 downwards to make a long two-zone view.
 
 To specify your own layout, put the specification in a `.json` file. This should
@@ -278,6 +278,41 @@ sigui --layout_file=path/to/my_layout.json path/to/sorting_analyzer
 
 Find a list of available views [in this file](https://github.com/SpikeInterface/spikeinterface-gui/blob/main/spikeinterface_gui/viewlist.py).
 
+You can also edit the initial settings for each view. There are two ways to do this.
+First, you can open the gui, edit the settings of any or all views, then press the 
+"Save as default settings" button in the `mainsettings` view. This will save a 
+`settings.json` file in your spikeinterface-gui config (saved in `~/.config/spikeinterface_gui/`).
+The saved settings will automatically load next time you start the gui.
+
+If you want more direct control, you can pass your own setting json file
+to the `settings-file` flag (or by passing a `user_settings` dict to `run_mainwindow`). 
+The settings file should contain a settings dict for each view. The view names are the
+same as used in the layout file, and each setting name can be seen in the settings
+tab of each view. Below is an example settings file:
+
+**my_settings.json**
+
+``` json
+{
+    "probe": {
+        "show_channel_id": true
+    },
+    "waveform": {
+        "overlap": false, 
+        "plot_std": false
+    },
+    "spikeamplitude": {
+        "max_spikes_per_unit": 1000, 
+        "alpha": 0.2
+    }
+}
+```
+
+You can then use this file by running e.g.
+
+```bash
+sigui --settings_file=path/to/my_settings.json path/to/sorting_analyzer
+```
 
 ## Deploy the GUI in web mode
 

docs/source/custom_layout.rst renamed to docs/source/custom_layout_settings.rst

@@ -1,5 +1,5 @@
-Customizing the layout
-======================
+Customizing layout and settings
+===============================
 
 You can create your own custom layout by specifying which views you'd like
 to see, and where they go. The basic window layout supports eight "zones",
@@ -26,7 +26,7 @@ E.g. suppose your layout is only non-empty in zones 1, 4, 5, 6 and 7:
     +---------------+--------------+
 
 
-Then zone1 will stretch right-wards to make a three-zone view. Zone4 will stretch
+Then zone1 will stretch right-wards to make a two-zone view. Zone4 will stretch
 downwards to make a long two-zone view.
 
 To specify your own layout, put the specification in a ``.json`` file. This should
@@ -55,3 +55,40 @@ using the ``--layout_file`` flag:
    sigui --layout_file=path/to/my_layout.json path/to/sorting_analyzer
 
 Find a list of available views `in this file <https://github.com/SpikeInterface/spikeinterface-gui/blob/main/spikeinterface_gui/viewlist.py>`_.
+
+You can also edit the initial settings for each view. There are two ways to do this.
+First, you can open the gui, edit the settings of any or all views, then press the 
+"Save as default settings" button in the ``mainsettings`` view. This will save a 
+``settings.json`` file in your spikeinterface-gui config (saved in ``~/.config/spikeinterface_gui/``).
+The saved settings will automatically load next time you start the gui.
+
+If you want more direct control, you can pass your own setting json file
+to the ``settings-file`` flag (or by passing a ``user_settings`` dict to ``run_mainwindow``). 
+The settings file should contain a settings dict for each view. The view names are the
+same as used in the layout file, and each setting name can be seen in the settings
+tab of each view. Below is an example settings file:
+
+**my_settings.json**
+
+.. code-block:: json
+
+    {
+        "probe": {
+            "show_channel_id": true
+        },
+        "waveform": {
+            "overlap": false, 
+            "plot_std": false
+        },
+        "spikeamplitude": {
+            "max_spikes_per_unit": 1000, 
+            "alpha": 0.2
+        }
+    }
+
+
+You can then use this file by running e.g.
+
+.. code-block:: bash
+
+    sigui --settings_file=path/to/my_settings.json path/to/sorting_analyzer