updated documentation with analysis report guide

docs/build/_sources/analysis_report.rst.txt

@@ -0,0 +1,52 @@
+###########################################
+How to use the *RNAlysis* analysis reports
+###########################################
+
+
+Understanding the Graph
+=======================
+Each node represents a data table, gene set, or function call. Arrows show the analysis workflow direction.
+
+.. image:: ../../rnalysis/gui/videos/report_overview.webp
+
+Node Details at a Glance
+========================
+Hover over a node to see a preview and list of parameters associated with that step in the analysis.
+
+.. image:: ../../rnalysis/gui/videos/report_view_node.webp
+
+Accessing Associated Files
+==========================
+Click on the link in the hover popup to open the file associated with that node.
+
+.. image:: ../../rnalysis/gui/videos/report_access_files.webp
+
+Navigating the Graph: Panning
+=============================
+To move around the graph, click and drag the screen, or use the arrow buttons on the bottom-left side of your screen.
+
+.. image:: ../../rnalysis/gui/videos/report_pan.webp
+
+Navigating the Graph: Zooming
+=============================
+Use the '+' and '-' buttons on the bottom-right of the screen to zoom in and out of the graph.
+
+.. image:: ../../rnalysis/gui/videos/report_zoom.webp
+
+Fitting the Graph to View
+=========================
+Click the box-shaped button on the bottom-right to fit the entire graph into your current view.
+
+.. image:: ../../rnalysis/gui/videos/report_fit_to_view.webp
+
+Tracing Analysis Paths
+======================
+Click on a node to highlight the path of analysis that led to it. Click again anywhere on the graph to reset the view.
+
+.. image:: ../../rnalysis/gui/videos/report_trace_path.webp
+
+Filtering by Node Type
+======================
+Click on a node type in the legend to highlight all nodes of that type across the graph. Click again to reset the view.
+
+.. image:: ../../rnalysis/gui/videos/report_filter_nodes.webp

docs/build/_sources/index.rst.txt

@@ -34,6 +34,7 @@ RNAlysis |release| documentation
    installation
    quick_start
    tutorial
+   analysis_report
    faq
    user_guide_gui
    user_guide

docs/build/_sources/quick_start.rst.txt

@@ -3,139 +3,135 @@
 ###################################
 
 
-Open the program
-=================
-If you installed *RNAlysis* from PyPi, you can open the graphical user interface by either executing the command `rnalysis-gui` from your terminal, or by typing the following code into a Python console::
+Launching *RNAlysis*
+====================
+Open the graphical user interface by running `rnalysis-gui` in your terminal or executing `gui.run_gui()` in a Python console.
 
-    >>> from rnalysis import gui
-    >>> gui.run_gui()
+.. image:: ../../rnalysis/gui/videos/load_table.webp
 
-Load a table
-============
-Choose a file from your computer, and click 'start' to load it into *RNAlysis*.
+Importing Data
+==============
+Select a file from your computer and click 'Start' to import it into *RNAlysis*.
 
 .. image:: ../../rnalysis/gui/videos/load_table.webp
 
-Examine your table
-==================
-You will now be able to see an overview of your data, including the table's name, type, and dimensions. Click the 'View full table' button to see your table in its entirety.
+Exploring Your Dataset
+======================
+View an overview of your data, including table name, type, and dimensions. Use the 'View full table' button for a comprehensive look.
 
 .. image:: ../../rnalysis/gui/videos/view_table.webp
 
-Filter your table
-=================
-Choose a filtering function, set your desired parameters, and click 'Apply' to filter your table. The changes you make will not affect your original file until you save them.
+Applying Filters
+================
+Select a filtering function, adjust parameters, and click 'Apply' to modify your table. Changes won't affect the original file until saved.
 
 .. image:: ../../rnalysis/gui/videos/filter_table.webp
 
-Undo the operations you applied to your table
-=============================================
-At any moment, you can use the 'Command history' window to undo or redo an operation you applied to your table.
+Undo the operations you applied to your data
+===============================================
+Use the 'Command history' window to undo or redo operations applied to your table at any time.
 
 .. image:: ../../rnalysis/gui/videos/undo_actions.webp
 
-Apply your operations 'in-place' or apply on a new table
+Apply your operations 'in-place' or make a copy
 ========================================================
-Instead of applying operations 'in-place', you can choose to apply the operation to a copy of your table in a new tab. The table in the original tab won't be modified.
+Apply operations 'in-place' or to a copy of your table in a new tab, leaving the original unmodified.
 
 .. image:: ../../rnalysis/gui/videos/apply_inplace.webp
 
-Save the changes you made to your table
-=======================================
-To save result of your filtering operations, click the 'Save table' button and choose where to save the modified table.
-
-.. image:: ../../rnalysis/gui/videos/save_table.webp
-
-Work on multiple tables at the same time
-========================================
-You can work on multiple tables at the same time by opening a new tab and loading another table.
-
-.. image:: ../../rnalysis/gui/videos/new_tab.webp
-
-Different types of tables offer different ways to filter and analyze your data
-==============================================================================
-When loading a table, you can specify its type. Different types of tables support different types of functions: for example, count matrices support clustering analysis.
-
-.. image:: ../../rnalysis/gui/videos/table_types.webp
-
-Create and save graphs
-======================
-Some functions can generate graphs of your data. You can resize those graphs, and save them to your computer in multiple file formats.
+Generating and Saving Visualizations
+====================================
+Create graphs of your data, resize them, and save in various file formats for further use or presentation.
 
 .. image:: ../../rnalysis/gui/videos/generate_graphs.webp
 
-Quickly look-up genes in your database of choice
-==================================================
-Easily access information about your genes with a simple right-click.
-Select from a range of biological databases such as GeneCards, NCBI Genes, UniProtKB and others,
-which can be configured in the settings menu to fit your specific needs.
+Analyze Multiple Tables at the Same Time
+=========================================
+Open new tabs to work on multiple tables simultaneously, enhancing your analytical capabilities.
 
-.. image:: ../../rnalysis/gui/videos/quick_search.webp
+.. image:: ../../rnalysis/gui/videos/new_tab.webp
 
-Sort your tabs and change their icons
-=====================================
-To help organize your workspace, you can sort tabs by right-clicking a tab and choosing a sorting method. You can also change specific tabs' colors, to help you differentiate them.
+Organizing Your Workspace
+=========================
+Sort tabs and customize their colors to efficiently manage your analytical workspace.
 
 .. image:: ../../rnalysis/gui/videos/sort_tabs.webp
 
-Restore tabs you closed
-=======================
-If you accidentally closed one of your tabs - don't worry! You can restore closed tabs through the 'Edit' menu.
+Saving Modified Tables
+======================
+Click 'Save table' to store the results of your filtering operations in a location of your choice.
 
-.. image:: ../../rnalysis/gui/videos/restore_tabs.webp
+.. image:: ../../rnalysis/gui/videos/save_table.webp
 
-Import lists of genes as Gene Sets
-==================================
-In addition to tables, *RNAlysis* can also import lists of genes as Gene Sets. We will soon review what we can do with those gene sets.
+Creating Gene Sets
+==================
+Import lists of genes as Gene Sets for specialized analysis within *RNAlysis*.
 
 .. image:: ../../rnalysis/gui/videos/import_gene_sets.webp
 
-Visualize the intersections between your tables and gene sets
-=============================================================
-In the 'Visualize Gene Sets' window you can create Venn diagrams and UpSet plots that will display the various intersections between your tables and gene sets.
+Visualizing Gene Set Intersections
+==================================
+Use the 'Visualize Gene Sets' window to create Venn diagrams and UpSet plots, illustrating intersections between tables and gene sets.
 
 .. image:: ../../rnalysis/gui/videos/visualize_gene_sets.webp
 
-Apply set operations to your tables and gene sets
-=================================================
-In the 'Set Operations' window you can extract specific subsets from your data. Either use predefined set operations, or click on specific subsets in the preview pane to select them.
+Performing Set Operations
+=========================
+Extract specific subsets from your data using predefined set operations or by selecting subsets in the preview pane.
 
 .. image:: ../../rnalysis/gui/videos/set_operations.webp
 
-Perform enrichment analysis on your tables and gene sets
-========================================================
-In the 'Enrichment Analysis' window, you can perform various types of enrichment analysis on the tables and gene sets you filtered.
+Conducting Enrichment Analysis
+==============================
+Perform various types of enrichment analysis on your filtered tables and gene sets to gain biological insights.
 
 .. image:: ../../rnalysis/gui/videos/enrichment_analysis.webp
 
-Create Pipelines to streamline your data analysis
-=================================================
-You can group multiple operations in a specific order and with specific parameters into a Pipeline. Just add those functions to the Pipeline in the order you choose.
+Rapid Gene Information Lookup
+=============================
+Right-click to quickly access gene information from various biological databases, customizable in the settings menu.
+
+.. image:: ../../rnalysis/gui/videos/quick_search.webp
+
+Building Analysis Pipelines
+===========================
+Group multiple operations with specific parameters into a Pipeline to streamline your data analysis workflow.
 
 .. image:: ../../rnalysis/gui/videos/create_pipeline.webp
 
-Apply Pipelines to one or more of your tables
-=============================================
-You can apply a Pipeline to a group of tables through the 'Pipelines' menu. Using Pipelines to analyze multiple datasets can make your workflow faster and less error-prone.
+Executing Pipelines
+===================
+Apply Pipelines to multiple tables simultaneously, enhancing efficiency and reducing errors in your analysis.
 
 .. image:: ../../rnalysis/gui/videos/apply_pipeline.webp
 
-Export and share Pipelines to make your analysis more reproducible
-==================================================================
-Pipelines you export can be imported from any computer, and can be shared with others to help make your analysis easier to understand and more reproducible.
+Sharing and Reproducing Analyses
+================================
+Export and share Pipelines to facilitate reproducibility and collaborative analysis across different computers.
 
 .. image:: ../../rnalysis/gui/videos/export_pipeline.webp
 
-Interface with other bioinformatic tools
-==================================================================
-*RNAlysis* offers a graphic interface for many bioinformatic tools.
-Analyze your data at any stage - adapter trimming, alignment, feature counting, or differential expression.
+Integrating External Bioinformatic Tools
+========================================
+Access a graphical interface for various bioinformatic tools, covering stages from adapter trimming to differential expression analysis.
 
 .. image:: ../../rnalysis/gui/videos/external_windows.webp
 
-Create an interactive analysis report
-==================================================================
-Create an interactive analysis report with the click of a button.
-All tables, gene sets, and graphs you generate will be added to your report automatically.
+Leveraging Table-Specific Functions
+===================================
+Specify table types when loading to access specialized functions, such as clustering analysis for count matrices.
+
+.. image:: ../../rnalysis/gui/videos/table_types.webp
+
+Recovering Closed Tabs
+======================
+Restore accidentally closed tabs through the 'Edit' menu to recover your work.
+
+.. image:: ../../rnalysis/gui/videos/restore_tabs.webp
+
+
+Generating Interactive Analysis Reports
+=======================================
+Create comprehensive, interactive analysis reports with a single click, automatically including all generated tables, gene sets, and graphs.
 
 .. image:: ../../rnalysis/gui/videos/create_report.webp