Merge from master

CMakeLists.txt

@@ -1,9 +1,9 @@
 cmake_minimum_required(VERSION 3.22)
 
 # -----------------------------------------------------------------------------
-# CrossSpeciesComparisonGeneDetectPlugin
+# XSCGeneDetectPlugin
 # -----------------------------------------------------------------------------
-PROJECT("CrossSpeciesComparisonGeneDetectPlugin")
+PROJECT("XSCGeneDetectPlugin")
 
 # -----------------------------------------------------------------------------
 # CMake Options
@@ -36,11 +36,16 @@ find_package(ManiVault COMPONENTS Core PointData ClusterData CONFIG QUIET)
 # -----------------------------------------------------------------------------
 # Define the plugin sources
 set(PLUGIN_SOURCES
-    src/CrossSpeciesComparisonGeneDetectPlugin.h
-    src/CrossSpeciesComparisonGeneDetectPlugin.cpp
+    src/XSCGeneDetectPlugin.h
+    src/XSCGeneDetectPlugin.cpp
     src/SettingsAction.h
     src/SettingsAction.cpp
-    src/CrossSpeciesComparisonGeneDetectPlugin.json
+    src/SettingsAction.Ui.inl
+    src/SettingsAction.Analysis.inl
+    src/SettingsAction.Data.inl
+    src/SettingsAction.Tree.inl
+    src/SettingsAction.Serialization.inl
+    src/XSCGeneDetectPlugin.json
 )
 set(LIBS
     src/lib/Clustering/fastcluster.cpp
@@ -56,13 +61,13 @@ set(LIBS
 )
 
 set(PLUGIN_MOC_HEADERS
-    src/CrossSpeciesComparisonGeneDetectPlugin.h
+    src/XSCGeneDetectPlugin.h
 )
 set(AUX
-    res/CrossSpeciesComparisonGeneDetect_chart.qrc
+    res/XSCGeneDetect_chart.qrc
 )
 
-qt6_add_resources(RESOURCE_FILES res/CrossSpeciesComparisonGeneDetect_chart.qrc)
+qt6_add_resources(RESOURCE_FILES res/XSCGeneDetect_chart.qrc)
 
 source_group(Plugin FILES ${PLUGIN_SOURCES})
 source_group(LibFiles FILES ${LIBS})
@@ -102,19 +107,19 @@ target_link_libraries(${PROJECT_NAME} PRIVATE Qt6::Concurrent )
 
 
 # Allow override of plugin library path from the build system
-set(CROSSSPECIESCOMPARISONTREEDATA_LINK_LIBRARY "${CROSSSPECIESCOMPARISONTREEDATA_LINK_LIBRARY}" CACHE STRING "Path to CrossSpeciesComparisonTreeData library")
-if(NOT CROSSSPECIESCOMPARISONTREEDATA_LINK_LIBRARY)
+set(XSCTREEDATA_LINK_LIBRARY "${XSCTREEDATA_LINK_LIBRARY}" CACHE STRING "Path to XSCTreeData library")
+if(NOT XSCTREEDATA_LINK_LIBRARY)
     set(CSCTDPLUGIN_LINK_PATH "${MV_CSCTD_INSTALL_DIR}/$<CONFIGURATION>/$<IF:$<CXX_COMPILER_ID:MSVC>,lib,Plugins>")
     set(MV_LINK_SUFFIX $<IF:$<CXX_COMPILER_ID:MSVC>,${CMAKE_LINK_LIBRARY_SUFFIX},${CMAKE_SHARED_LIBRARY_SUFFIX}>)
-    set(CROSSSPECIESCOMPARISONTREEDATA_LINK_LIBRARY "${CSCTDPLUGIN_LINK_PATH}/${CMAKE_SHARED_LIBRARY_PREFIX}CrossSpeciesComparisonTreeData${MV_LINK_SUFFIX}")
+    set(XSCTREEDATA_LINK_LIBRARY "${CSCTDPLUGIN_LINK_PATH}/${CMAKE_SHARED_LIBRARY_PREFIX}XSCTreeData${MV_LINK_SUFFIX}")
 endif()
 
 # Link to ManiVault and data plugins
 target_link_libraries(${PROJECT_NAME} PRIVATE ManiVault::Core)
 target_link_libraries(${PROJECT_NAME} PRIVATE ManiVault::PointData)
 target_link_libraries(${PROJECT_NAME} PRIVATE ManiVault::ClusterData)
 
-target_link_libraries(${PROJECT_NAME} PRIVATE "${CROSSSPECIESCOMPARISONTREEDATA_LINK_LIBRARY}")
+target_link_libraries(${PROJECT_NAME} PRIVATE "${XSCTREEDATA_LINK_LIBRARY}")
 
 # -----------------------------------------------------------------------------
 # Target installation

LICENSE.txt

@@ -0,0 +1,167 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
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+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
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+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
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+
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+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
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+  2. Conveying Modified Versions.
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+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
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+   function or data, the facility still operates, and performs
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+   b) under the GNU GPL, with none of the additional permissions of
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+
+                     END OF TERMS AND CONDITIONS

README.md

@@ -1 +1,107 @@
-CrossSpeciesComparisonGeneDetectPlugin
+# XSCGeneDetectPlugin
+
+`XSCGeneDetectPlugin` is a ManiVault view plugin for exploring cross-species gene expression differences from point-based single-cell style datasets.
+
+The plugin is designed for workflows where a user:
+
+- selects a subset of cells in an embedding or scatterplot,
+- compares selected versus non-selected cells across species,
+- ranks genes by differential expression,
+- inspects per-species statistics in tables,
+- and projects those statistics back onto phylogenetic tree and scatterplot views.
+
+## What The Plugin Does
+
+At a high level, the plugin combines five pieces of information:
+
+- a main expression dataset (`Points`),
+- a low-dimensional embedding dataset (`Points`),
+- a species assignment dataset (`Cluster`),
+- one or more hierarchy / cell-type cluster datasets (`Cluster`),
+- and a reference phylogenetic tree dataset (`XSCTree`).
+
+From these inputs, it computes:
+
+- mean expression per gene and species,
+- selected-versus-non-selected expression statistics,
+- top-N ranked genes per species,
+- species-level abundance summaries within selected hierarchy branches,
+- table models for ranked genes and species summaries,
+- optional scatterplot coloring datasets,
+- and optional tree payloads for hierarchy-specific exploration.
+
+## Repository Layout
+
+- [CMakeLists.txt](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/CMakeLists.txt): CMake target definition and ManiVault/Qt integration.
+- [src/XSCGeneDetectPlugin.h](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/src/XSCGeneDetectPlugin.h): plugin class declaration.
+- [src/XSCGeneDetectPlugin.cpp](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/src/XSCGeneDetectPlugin.cpp): plugin wiring, view integration, table rendering, and scatterplot/tree coordination.
+- [src/SettingsAction.h](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/src/SettingsAction.h): main state container and action declarations.
+- [src/SettingsAction.cpp](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/src/SettingsAction.cpp): shared helpers and compilation unit for the split inline implementation.
+- [src/SettingsAction.Ui.inl](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/src/SettingsAction.Ui.inl): UI/action wiring.
+- [src/SettingsAction.Analysis.inl](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/src/SettingsAction.Analysis.inl): main analysis and ranking logic.
+- [src/SettingsAction.Data.inl](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/src/SettingsAction.Data.inl): dataset creation, model generation, and export helpers.
+- [src/SettingsAction.Tree.inl](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/src/SettingsAction.Tree.inl): tree-related logic.
+- [src/SettingsAction.Serialization.inl](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/src/SettingsAction.Serialization.inl): serialization support.
+
+## Build Requirements
+
+The project expects a ManiVault development environment with:
+
+- CMake 3.22 or newer,
+- Qt 6 with `Widgets`, `WebEngineWidgets`, and `Concurrent`,
+- ManiVault packages for `Core`, `PointData`, and `ClusterData`,
+- the `XSCTreeData` plugin/library available at build or install time.
+
+Relevant CMake variables:
+
+- `ManiVault_INSTALL_DIR`: ManiVault installation root.
+- `MV_CSCTD_INSTALL_DIR`: installation root for `XSCTreeData`.
+- `XSCTREEDATA_LINK_LIBRARY`: optional explicit override for the tree data plugin library.
+
+## Building
+
+Typical CMake flow:
+
+```powershell
+cmake -S . -B build -DManiVault_INSTALL_DIR="C:\Path\To\ManiVault"
+cmake --build build --config Release
+```
+
+On successful build, the plugin is installed into the ManiVault `Plugins` directory via the post-build install step defined in [CMakeLists.txt](E:/Coding/DevBundle/GenerateTHESISImages/source/XSCGeneDetectPlugin/CMakeLists.txt).
+
+## Runtime Data Expectations
+
+The plugin assumes:
+
+- the selected species and hierarchy cluster datasets are children of the main points dataset,
+- the embedding dataset is also a child of the main points dataset,
+- point dimension names correspond to gene identifiers,
+- the reference tree contains the same species names as the species cluster dataset.
+
+If these relationships are missing or inconsistent, the plugin will refuse to compute and log diagnostic messages.
+
+## Performance Notes
+
+Recent optimization work focused on reducing full recomputation cost and UI overhead:
+
+- chunked matrix reads are used instead of fetching one gene at a time,
+- selected-cell statistics are aggregated in-memory after a single chunked read over the selected points,
+- repeated linear lookups in selection remapping and hierarchy membership checks were replaced with hashed or linear-time helpers,
+- forced waits around t-SNE stop actions were removed,
+- expensive UI auto-sizing and duplicate signal connections were reduced.
+
+Even with those changes, some operations can still be costly on very large datasets because the plugin may need to:
+
+- rebuild large table models,
+- update multiple derived ManiVault datasets,
+- refresh scatterplot color/selection state,
+- and serialize many tree payloads for hierarchy exploration.
+
+## Maintenance Notes
+
+If you extend the analysis logic, prefer:
+
+- batched point reads over per-gene calls,
+- explicit invalidation/caching boundaries,
+- stable table widths over repeated `resizeColumnsToContents()` calls in hot paths,
+- and avoiding repeated signal connections inside methods that run on every update.