add gui.rst to docs

docs/source/gui.rst

@@ -0,0 +1,77 @@
+
+Using the interface
+-------------------
+
+Start SNUB from the command line::
+
+    conda activate snub
+    snub
+
+Open a project
+~~~~~~~~~~~~~~
+
+Open your project by going to ``File > Open Project``, navigate to the project directory, and hitting ``Choose`` with the directory selected. Multiple projects can be opened at once as different tabs. Projects can also be opened by including their paths as command line argument(s)::
+
+   snub /path/to/project1 /path/to/project2
+
+.. image:: ../media/use_case0.gif
+   :align: center
+
+|
+
+Navigate the timeline
+~~~~~~~~~~~~~~~~~~~~~
+
+The brower is divided into two sections. The track-stack (on the right below) contains data-views that have time as a dimension, such as heatmaps, trace plots and spike plots. The tracks are always synchronized so that the same horizontal coordinate represents the same point in time. 
+
+* Click/drag to change the current time.
+* Use scrolls/gestures to change the visible time window.  
+* Use the play button and speed slider at the bottom to watch in real time
+* Toggle "center playhead" to keep the current time centered
+* Toggle the timeline unit between minutes:seconds and "timestemps". Timesteps are multiples of the ``min_step`` parameters in the projects config file, and can be useful for accessing specific timepoinmts (e.g. video frames) outside of SNUB.
+
+.. image:: ../media/use_case1.gif
+   :align: center
+
+|
+
+Plot activity traces
+~~~~~~~~~~~~~~~~~~~~
+
+By default, all heatmaps and spike plots are paired with a trace plot (set ``add_traceplot=False`` to override). 
+
+* Right click on any row of the heatmap/spike-plot to view it in the trace plot. 
+* View groups of rows in more detail using the vertical zoom and shift buttons in the right-click menu. 
+
+.. image:: ../media/use_case3.gif
+   :align: center
+
+|
+
+Use selections
+~~~~~~~~~~~~~~
+
+The panel-stack (on the left below) contains data-views such as videos, scatter plots and 3D mesh views. The video panel always displays the current frame and the scatter plot highlights any nodes that represent the current time. A useful way to relate the scatter plot and timeline views is through selections.
+
+* Use shift+drag to select points in the scatter view or intervals in the timeline.
+* Use command/control+drag to deselect points and intervals.
+* Selections are synchronized across all views.
+* Selections can also be used to re-order the rows of a heatmap based on the total activity within the selected interval(s).
+
+.. image:: ../media/use_case2.gif
+   :align: center
+
+|
+
+Color the scatter plot
+~~~~~~~~~~~~~~~~~~~~~~
+
+Another way to probe the scatter plot is through node coloring.
+
+* Use right-click -> "Color by ..." to view variables of interest in the scatter plot.
+* Include variables using ``variables`` and ``variable_labels`` in :py:func:`snub.io.add_scatter`.
+* Bring nodes with high values to the top using right-click -> "Sort by color value".
+
+.. image:: ../media/use_case4.gif
+   :align: center
+