Update api documentation

Author: Andrew Ramirez

docs/api.rst

@@ -1,26 +1,79 @@
 API Reference
 =============
 
-.. automodule:: RISE
-   :members:
-   :undoc-members:
-   :show-inheritance:
+Core Functions
+--------------
+
+Factorization
+~~~~~~~~~~~~~
 
 .. automodule:: RISE.factorization
-   :members:
+   :members: pf2, rise_pca_r2x, correct_conditions
    :undoc-members:
    :show-inheritance:
 
+Data Import
+~~~~~~~~~~~
+
 .. automodule:: RISE.imports
-   :members:
+   :members: import_thomson, import_lupus
    :undoc-members:
    :show-inheritance:
 
+Preprocessing
+~~~~~~~~~~~~~
+
+.. autofunction:: parafac2.normalize.prepare_dataset
+
+Visualization Functions
+-----------------------
+
+General Plotting
+~~~~~~~~~~~~~~~~
+
+.. automodule:: RISE.figures.commonFuncs.plotGeneral
+   :members: plot_r2x
+   :undoc-members:
+   :show-inheritance:
+
+Factor Plotting
+~~~~~~~~~~~~~~~
+
+.. automodule:: RISE.figures.commonFuncs.plotFactors
+   :members: plot_condition_factors, plot_eigenstate_factors, plot_gene_factors
+   :undoc-members:
+   :show-inheritance:
+
+PaCMAP Visualization
+~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: RISE.figures.commonFuncs.plotPaCMAP
+   :members: plot_labels_pacmap, plot_gene_pacmap, plot_wp_pacmap
+   :undoc-members:
+   :show-inheritance:
+
+Factor Stability
+~~~~~~~~~~~~~~~~
+
+.. automodule:: RISE.figures.figureS4
+   :members: plot_fms_diff_ranks, calculateFMS
+   :undoc-members:
+   :show-inheritance:
+
+Additional Modules
+------------------
+
+Logistic Regression
+~~~~~~~~~~~~~~~~~~~
+
 .. automodule:: RISE.logisticReg
    :members:
    :undoc-members:
    :show-inheritance:
 
+Cell Gating
+~~~~~~~~~~~
+
 .. automodule:: RISE.gating
    :members:
    :undoc-members: