dev-3388-g6c7bf9c0b (May 07 2024)

Bug Fixes

Fix crashing enrichment analysis

dev-3381-gec04ee00f (Apr 22 2024)

Features

Add Softmax data normalisation method to correlation loader

Bug Fixes

Tutorial now works on WebAssembly
Fix locked transforms displaying 'nan' for drop down list parameters

Other

Workaround for crash on NVidia based Windows systems
Update to Qt 6.7.0

dev-3331-g53e7eef9d (Mar 28 2024)

Features

Adjacency matrix loaders can now be cancelled
General improvement to operation on high DPI displays, particularly with fractional scaling factors

Bug Fixes

Fix last row of attribute table being obscured by horizontal scroll bar
Workaround QTBUG-120352; invisible scroll bars
Fix crash in Type Cast transform
Fix Show Edge Direction option not being immediately applied
Fix crash when trying to load single column correlation data tables
Fix row height of some list displays
Fix re-enabling a visualisation with a lost attribute causing errors
Fix operation of context sensitive menu items on macOS

Other

Experimental WebAssembly support
Update to Qt 6.6.3

dev-3148-gd201c1cfb (Nov 15 2023)

Features

Improve file content identity algorithm
Add functionality to import column annotations onto an existing correlation plot
Improve UI feedback for selecting data rectangle, in correlation loader
Better handling of operating system UI theming, including Dark Mode on platforms that support it
High resolution rendering of the correlation plot on high DPI displays
Add antilog functionality to correlation plot
Enable log and antilog correlation scaling methods in situations where they were previously unavailable
Add Shared Text visualisation channel, enabling the textual annotation of groups of nodes

Bug Fixes

Fix crash involving attribute selection UI component
Fix rendering of fonts with overlapping strokes (most obvious on MacOS)
Fix font selection not operating correctly in some circumstances

Other

Update some library based dependencies
Update to Qt 6.6

dev-2936-g186e50f60 (Aug 07 2023)

Features

Add Attribute Value Heatmap option, which displays a correlation heatmap based on some attribute's values
Double clicking the background in overview mode now resets the view
Ease restrictions on zooming in overview mode
Auto zoom now operates in overview mode
Add Focus Selection option to Table menu, which will focus the nodes corresponding to the current table row selection
Add Auto Focus option, which does the same as the above, except automatically whenever the row selection is changed

Bug Fixes

Fix crash on exit with particular versions of MacOS
Fix various subtle renderer transition bugs, particularly when several transitions are started/interrupted in rapid succession
Fix handling of some load failure modes

dev-2883-g437dbfa31 (Jun 09 2023)

Features

Add ability to fix correlation plot sort order when Data Value sort is in force
Add Save As Images By… → Row option to output an image for each selected table row
Add facility to forcibly change the type and description of user defined attributes
Text size can now be altered on-the-fly in the Layout Settings panel
Text size and colour can now be used as a visualisation output in the normal way

Bug Fixes

Fix keyboard interaction with attribute list UI
Fix correlation plot context menu state inconsistencies
Fix display not immediately updating following some preference changes
Fix Save As Images By… misbehaving with respect to file names with multiple dots in them

dev-2819-ga840ce03d (May 16 2023)

Features

Add Find Rows of Interest functionality
Add Type Cast transform, to convert attribute types

Bug Fixes

Fix crash when removing an attribute

dev-2801-g7e7190f5a (May 12 2023)

Features

Allow for loading adjacency matrices from .txt files
Improve error message when loading inconsistent tabular data files
Improve mouse wheel behaviour in correlation plot

Bug Fixes

Fix crash involving favourite transforms
Fix crash when a load is cancelled in a particular phase
Reset UI state when switching from Find By Attribute Value to normal Find
Fix Copy Column To Clipboard copying the wrong data after a sequence of selection changes
Hide Save As Images By when there are no attributes with shared values

Other

Improve node attribute table performance when node selection changes
Selection outlines of transparent graph elements are now rendered transparent too

dev-2781-g6de5393a0 (May 02 2023)

Bug Fixes

Fix various funky UI bugs that resulted from a (now reverted) change intended to work better (in future) with Qt 6.5

dev-2779-g560b4fd3d (Apr 25 2023)

Bug Fixes

Fix clustering algorithms sorting clusters of the same size in an arbitrary order

dev-2777-g9bf98540a (Apr 24 2023)

Features

Add option to load an external node layout using the same file format as produced by the export option
A command line headless mode is now available that enables the creation of .graphia files without manually needing to select parameters in the UI; potentially useful for batch processing on servers
Add Crop To Selection option to the attribute data table, which synchronises the node selection with the current table row selection
Add View → Show Edges option, which allows for disabling the rendering of edges entirely

Bug Fixes

Fix crash when deleting nodes
When exporting node positions, export the non-scaled values
Fix various table row selection issues
Fix URL handler registration on Windows user installations

Other

Improve Windows installer behaviour when dealing with user accounts with admin privileges
Windows installer now employs existing install's uninstaller when updating
Capture updater debug output in order to aid future debugging
Default sort order for Find By Attribute Value is now lexographical

dev-2655-g9ed9bacd1 (Jan 23 2023)

Features

Add ability to save correlation plot images on a per attribute value basis, e.g. saving one image per cluster

Other

Improve video driver crash detection
Improve installer error message on macOS when target directory is not writeable
Update to Qt 6.4.2
Improve scrolling behaviour in various places to be more desktop idiomatic

dev-2604-ge4882047d (Dec 07 2022)

Features

Replace the Initial Transforms section of the correlation loader with Template, allowing for a more flexible and customisable means of appending additional transforms and visualisations

In the k-NN filtering case, add a field that allows selection of a minimum correlation value, so that weak relationships between rows can be discarded

Bug Fixes

Fix crash that occurs when attempting to creat a k-NN graph with zero edges
Fix crash when reloading certain save files where nodes have been manually deleted
Improve macOS update script to deal with the case where the target .app has been renamed

Other

Generate debug information for arm64 platform (Apple M1), making crash diagnosis easier
Make various load failure modes report more specific reasons to the user

dev-2548-gde7e14812 (Nov 23 2022)

Features

Add a Filtering option to correlation parameters, more specifically enabling the ability to filter edges using the k-Nearest Neighbours strategy; this is particularly useful with datasets that are extremely correlated, where traditional thresholding cannot adequately differentiate between rows

dev-2485-ga43f5a4df (Oct 28 2022)

Bug Fixes

Fix Copy Column To Clipboard not respecting the current node selection

dev-2478-g5cce5609e (Oct 17 2022)

Bug Fixes

Fix mouse clicks being out of sync with display when a large quantity of column annotations are visible
Fix \"ghost\" node selection box appearing after an unusual combination of mouse drags and key presses
Fix temporary lock-up at the end of a transform application
Fix macOS menu hiding
Fix visually overlapping components when nodes move from one component to another
Fix Copy Column To Clipboard copying the wrong column when the columns have been reordered

Other

Capture more debug output on Windows

dev-2435-gaa85b8180 (Sep 30 2022)

Changes

Clicking on the correlation plot's Y axis no longer sorts by data value
Clicking on a column annotation body no longer sorts by that column annotation

Bug Fixes

Fix Add Template menu option being disabled when no visualisations are employed
Fix plugin window being created as MDI on Windows
Fix Select Source/Targets/Neighbours being generally broken
Fix initial clipping constant having excessive figures after the decimal point
Fix WebSearch plugin operation on Windows
Fix display acuity on Windows when a non-integral scaling factor is being used (e.g. when a using a high DPI monitor)

dev-2414-g93c0bffbe (Sep 21 2022)

Features

Make Winsorization operate on a per-row basis

dev-2409-g6a16356b8 (Sep 20 2022)

Bug Fixes

Fix various instances of the busy indicator being invisible
Fix crash involving the selection of attributes
Fix the appearance of the background of help tool tips on macOS
Improve layout of correlation parameters dialog on macOS
Improve appearance of column annotation sort indicators on Windows
Relax criteria for acceptable input data on correlation files

dev-2395-gad4677c5b (Sep 14 2022)

Features

Source, target and neighbour rows can now be selected in the data table via the context menu
In the correlation loader, input data can now be clipped against a constant, or by Winsorization
Correlation plot columns can now be sorted by hierarachical clustering, using the SLINK method with a Euclidean distance measure

Bug Fixes

Fix directional edges being visible
Fix plugin/extension preferences getting forgotten
Fix graph size estimate plot inappropriately showing \"Empty Graph\" in some circumstances
Fix poor behaviour when loading correlation data with anonymous columns
Fix various assorted problems with menu state, many of which manifested most obviously on macOS

Other

macOS builds now take advantage of Apple M1 hardware

dev-2326-g4979e37f (Aug 11 2022)

Features

Add mechanism to save sets of transforms and visualisations for later recall
Add option to interpret trackpad pan gestures as zooming; this is primarily useful for users of the Apple Magic Mouse, where it's more intuitive for scrolling vertically to map to zooming

Bug Fixes

Fix bookmark hotkeys being inoperative

dev-2301-ga763230a (Jul 11 2022)

Features

Move code base to Qt 6.3 🥳 (Please report bugs/regressions)

dev-2002-g5cf925ef (Jun 23 2022)

Bug Fixes

Fix Remember This Choice not working when the file being opened contained more than one period
Fix potential crash that might occur when changing the find attribute multiple times
Fix crash when plotting an IQR with zero outliers

dev-1997-g830e75cd (Jun 10 2022)

Bug Fixes

Fix keyboard selection in the main data table

dev-1990-g471a74cc (May 25 2022)

Bug Fixes

Fix key detection during attribute import where keys are large integers

dev-1986-ge5cd4532 (May 12 2022)

Bug Fixes

Fix crash that occurred if the application was closed during a particular phase of a load
Fix blank graph rendering in some rare circumstances

dev-1984-gd69a9124 (Apr 29 2022)

Features

Graph metrics display now reflects the visible component, when in component mode

Bug Fixes

Fix GML saver creating key names that start with a digit
Fix various problems with the GraphML saver

dev-1971-g9360a966 (Apr 07 2022)

Features

Make the correlation plot vertically scrollable when it's too large for its container - i.e. when there are many column annotations

Bug Fixes

Fix correlation plot data value sorting occasionally behaving oddly when node selection changes
Fix group by annotation button being inappropriately enabled
Fix changes to transform flags (locked, pinned) not being properly undoable

dev-1957-g6707ab8c (Apr 04 2022)

Features

Add facility to select favourite transforms, which are displayed at the top of the transform list
Improved detection of video driver crashes

Bug Fixes

Bring MCL inline with the reference implementation by not skipping single node clusters
Fix pairwise exporter introducing extra quotes into its output

dev-1923-g31015c13 (Mar 22 2022)

Bug Fixes

Fix crash that occurred when changing the graph with the Find interface active
Prevent showing the main context menu over the Find interface
Fix delay in showing Find By Attribute interface when an attribute has a large quantity of values
Collect more information when a std::exception based crash occurs
Fix force directed layout getting stuck on some contracted graphs
Fix deadlock/crash when cancelling a command

dev-1912-g9be583af (Mar 09 2022)

Features

When there is a choice of file type or plugin to use, said choice can be set as a default, avoiding future prompts
The file type selector of the file open dialog is now used to guide file type and plugin selection
There is now an option (on the Misc tab of the Options dialog) to change the way Find By Attribute Value sorts the list of possible attribute values; it can now be done alphanumerically, in addition to the normal behaviour of sorting from the large to small set size
The correlation plot columns can now be sorted by data value
The pairwise file loader now has a front end that allows for the configuration of columns within the source data table, so it's no longer necessary for pairwise files to be strictly 2 or 3 columns

Bug Fixes

Fix text style options not taking effect immediately
Fix enrichment results export being initially disabled
Fix initial dimensions on screenshot capture preset often being wrong
Fix renderer not updating when focused labelling enabled
Fix adjacency matrix parser not setting the node names
Use the correct file extension when saving a non-native format

dev-1811-g0ab9cf22 (Jan 12 2022)

Features

Add option to clone any attribute into a new user defined attribute
Add option to edit user defined attributes
Add various options to node attribute table context menu
Add a few toolbar buttons for controlling the correlation plot

Bug Fixes

Fix visualisation attribute list not updating following attribute changes
Fix crash on correlation plot when moving the mouse along a particular path
Fix empty graph warning being displayed before estimate completes
Fix crash on loading certain adjacency matrix files

dev-1760-gf6d1d5d3-debug (Sep 30 2021)

Features

In the correlation plot, when Group By Annotation is enabled there is now another option to colour the IQR boxes with a user selected annotation
The correlation plot can now be panned and zoomed using the mouse wheel
When displaying IQR plots, outliers can now be disabled by toggling the Show Outliers menu option
Add facility to configure network proxy

Bug Fixes

Fix a crash that occurred when removing attributes
Fix graphia:// style links not working reliably where there is a chain of web server redirects
The epsilon used when log scaling data is now computed to use an appropriately sized value rather than a fixed constant
Fix numeric column annotations with empty values being treated as categorical ones
Hopefully at least reduce the occurence of the macOS pthreads crash
Fix inoperative slider when a transform parameter has a large range
Fix potential crash when importing attributes when there is no key match
(Hopefully) workaround a crash in Qt that occurs when interacting with the graph size estimate plot on macOS

dev-1653-g942d9d6a (Aug 13 2021)

Features

In the correlation plot, data can now be combined into IQR boxplots based on one or more annotations, enabled by selecting Group By Annotation in the Plot menu
In the correlation plot, data can now be log scaled when rendering IQR boxplots
Improved IQR rendering performance
Added Biweight Midcorrelation (Bicor) correlation algorithm

Bug Fixes

Fix plot grid lines getting incorrectly enabled in some circumstances
Fix redundant plot redraws

dev-1547-g3beebadd (Jul 21 2021)

Features

Downloadable files can now be opened directly, either by using the Open Url option in the File menu, or by dragging and dropping hyperlinks onto the main window
A Graphia specific URL scheme is now registered so that the application may now be opened by clicking special hyperlinks; these can be created using the Link Generator
Loading pairwise CSV, TSV, SSV and XLSX tables is now possible
Loading Cytoscape eXchange files is now possible, as used on NDex
Added Forward Attribute transform; for contracted edges, this will forward a selected attribute's values to all 'child' multi-elements
Added Average Attribute transform; create a new attribute whose values are determined by averaging the values of a numerical attribute, using a categorical attribute
Layout settings are now accesible via a toolbar button
Node and edge sizes are now saved in the .graphia file and are adjustable via Layout Settings
Layout settings can now be saved as named presets, for quick access to frequently used settings
Erroring visualisations can now have their source attribute changed, i.e. so they can be 'repaired'
Attributes can now be imported using integral keys

Bug Fixes

Fix loading GML files where the edges precede the nodes
Fix missing column annotations where there were a large number of unique values
Fix various issues involving attributes that change values and/or type during transforms
Fix loading of some older .graphia file versions
Fix malformed tab titles when the source file name contains periods
Fix wrong initial save file name
Fix possibility of dismissing the correlation parameters dialog before the data rect had been found
When loading correlation data with duplicate attribute column names, these are now considered separately rather than overwriting each other

Linux

An XDG desktop item is now automatically created, so Graphia will appear in system menus

dev-1350-g04d8368a (May 03 2021)

Features

Correlating tables of discrete values is now possible, using the Jaccard Index or Simple Matching Coefficient algorithms
For continuous correlation, the Euclidean Distance and Cosine Similarity algorithms are now available
When loading from an adjacency matrix, it is now possible to choose to discard edges based on edge weight, and to skip double edges where the matrix is symmetric
When importing attributes, there is now an option to replace existing attributes (if they share the same name)
User attributes can now be removed if desired, accessible via Tools → Remove Attributes…
Column annotation colours are now assigned by palette rather than by hashing the string value
Numerical column annotations are now displayed using a gradient
Hyperlinks in table cells are now clickable and some basic HTML 3.2 can be displayed
Generally improved performance when there are a large number of components
Clustering algorithms now create node attributes reflecting the size of the clusters in which the respective nodes belong, effectively allowing filtering operations on the size of clusters
Graphviz dot files may now be loaded
A log is now made of the steps taken in the graph's creation, accessible via Tools → Show Provenance Log…
In the correlation plot, values can now be scaled by an attribute value
When viewing enrichment results, the chosen attribute names are now used for the column headers

Bug Fixes

Fix crash involving search and selection
Fix crash when sorting column annotations
Fix crash caused by graph visuals being altered during a graph change
Fix crash when loading from empty files
Fix palette editor behaviour when there are few assignable values
Fix Matlab loader not handling some forms of adjacency matrix
Fix attribute ranges and shared values not getting updated under some circumstances
Fix transforms and visualisations not being refreshed when referenced attribute values change
Improve installer/uninstaller behaviour when the user chooses to install to a pre-existing and non-empty directory (on Windows)

dev-955-g9c051144 (Jan 04 2021)

Features

Add attribute import functionality, accessible via Tools → Import Attributes From Table…
Add option to disable multisampling, for a performance improvment, particularly on old hardware
Add text to the Options dialog on macOS, suggesting opening the application in Low Resolution Mode for a further performance improvement
Add option to stay in component mode when finding, by default off
Format the enrichment results table in such a way improves Microsoft Excel's interpretation of it, when exported

Bug Fixes

Fix empty values being included in enrichment results

dev-838-g41f75ac1 (Nov 11 2020)

Features

Add search functionality in all the places where attributes are chosen; this is most useful when selecting a Data Value attribute in the case where there are many
Add ability copy the contents of a column from the node attribute table to the clipboard, accessible by right clicking the column header
Add options to the node attribute table header context menu to explicitly sort ascending or descending
Add Apply buttons to the gradient, palette and numeric mapping visualisation dialogs, for immediate preview of settings
Add Latest Changes option to Help menu, which shows any new changes present in the running version

Bug Fixes

Fix broken correlation plot interaction
Fix double clicking a transform name in the transform creation dialog disabling subsequent initial mouse click
Fix occasionally ambiguous Esc key shortcut
Fix help tool tips being badly sized on macOS
Fix flickering of windows when adjusting the correlation plot on macOS
Fix node selection not working after a specific sequence of transforms
Fix crash that occurred when an attribute was destroyed and recreated with the same name, but a different element type
Fix crash that occurred after selecting some nodes, then cycling a transform a number of times
Fix 'Remove Leaves' transform behaving inconsistently with respect to singletons

Other

Improve robustness of transform creation
Minor performance improvements to AvailableAttributesModel

dev-745-gafb88628 (Oct 09 2020)

Bug Fixes

Fix crash when clicking off axis on correlation plot
Fix crash when sorting column annotations during a tooltip update
Prevent the possibility of creating invalid transforms, in some circumstances

Other

Improve column annotation rendering performance
Improve column annotation sort performance
Improve performance of AvailableAttributesModel

dev-730-gbf240c7a (Oct 01 2020)

Bug Fixes

Fix dead lock that could occur when a command completes very quickly

dev-628-g95ac4d0e-open-source (Apr 20 2020)

Bug Fixes

Fix crash on Windows

4.2 (Sep 12 2023)

4.2

Bug Fixes

Fix node selection not being reflected in correlation plot

4.1

Bug Fixes

Fix clustering algorithms labelling clusters in an arbitrary order when they happened to be the same size
Fix crashes and data corruption related to favourite transforms
Fix crash that occurred when cancelling a load at a particular point
Fix crash that occurred when removing a table column
Restore attribute selection keyboard based interface from 3.x
Fix instances where the context menus on some UI elements would get out of sync with respect to their main menu equivalents
Fix visualisation descriptions not appearing in the visualisation creation dialog
Fix various issues with filenames when saving plot images
Fix crash that occurred on MacOS when exiting
Fix various assorted issues with the data table

4.0

Loading

When there is a choice of file type or plugin to use, said choice can be set as a default, avoiding future prompts
The file type selector of the file open dialog is now used to guide file type and plugin selection
The pairwise file loader now has a front end that allows for the configuration of columns within the source data table, so it's no longer necessary for pairwise files to be strictly 2 or 3 columns

Transforms and Visualisations

Add facility to select favourite transforms, which are displayed at the top of the transform list
Add mechanism to save sets of transforms and visualisations for later recall

Attributes

There is now an option (on the Misc tab of the Options dialog) to change the way Find By Attribute Value sorts the list of possible attribute values; it can now be done alphanumerically, in addition to the normal behaviour of sorting from the large to small set size

Correlation

The correlation plot columns can now be sorted by data value
The correlation plot is now vertically scrollable when it's too large for its container - i.e. when there are many column annotations
In the correlation loader, input data can now be clipped against a constant, or by Winsorization
Correlation plot columns can now be sorted by hierarchical clustering, using the SLINK method with a Euclidean distance measure
Add a Filtering option to correlation parameters, more specifically enabling the ability to filter edges using the k-Nearest Neighbours strategy; this is particularly useful with datasets that are extremely correlated, where traditional thresholding cannot adequately differentiate between rows
Replace the Initial Transforms section of the correlation loader with Template, allowing for a more flexible and customisable means of appending additional transforms and visualisations
Add ability to save correlation plot images on a per attribute value basis, e.g. saving one image per cluster

Miscellaneous

In plugins that have a data table, the source, target and neighbour rows can now be selected
Graph metrics display now reflects the visible component, when in component mode
Add option to interpret trackpad pan gestures as zooming; this is primarily useful for users of the Apple Magic Mouse, where it's more intuitive for scrolling vertically to map to zooming

Bug Fixes

Bring MCL inline with the reference implementation by not skipping single node clusters
Fix pairwise exporter introducing extra quotes into its output
Fix crash that occurred when changing the graph with the Find interface active
Prevent showing the main context menu over the Find interface
Fix delay in showing Find By Attribute interface when an attribute has a large quantity of values
Fix deadlock/crash when cancelling a command
Fix initial dimensions on screenshot capture preset often being wrong
Fix renderer not updating when focused labelling enabled
Use the correct file extension when saving a non-native format
Fix correlation plot data value sorting occasionally behaving oddly when node selection changes
Fix changes to transform flags (locked, pinned) not being properly undoable
Fix blank graph rendering in some rare circumstances
Fix potential crash that might occur when changing the find attribute multiple times
Fix graph size estimate plot inappropriately showing \"Empty Graph\" in some circumstances
Fix poor behaviour when loading correlation data with anonymous columns
Fix \"ghost\" node selection box appearing after an unusual combination of mouse drags and key presses
Fix temporary lock-up at the end of a transform application
Fix visually overlapping components when nodes move from one component to another
Fix crash when reloading certain save files where nodes have been manually deleted

Other

Move code base to Qt 6/Qt Quick 2 (Please report bugs/regressions)
macOS builds now take advantage of Apple M1 hardware
Capture more debug output on Windows
Improve video driver crash detection
Collect more information when a std::exception based crash occurs
Improve macOS update script to deal with the case where the target .app has been renamed
Improve installer error message on macOS when target directory is not writeable
Allow selection of alternative UI themes where available

4.1 (Aug 28 2023)

4.1

Bug Fixes

Fix clustering algorithms labelling clusters in an arbitrary order when they happened to be the same size
Fix crashes and data corruption related to favourite transforms
Fix crash that occurred when cancelling a load at a particular point
Fix crash that occurred when removing a table column
Restore attribute selection keyboard based interface from 3.x
Fix instances where the context menus on some UI elements would get out of sync with respect to their main menu equivalents
Fix visualisation descriptions not appearing in the visualisation creation dialog
Fix various issues with filenames when saving plot images
Fix crash that occurred on MacOS when exiting
Fix various assorted issues with the data table

4.0

Loading

When there is a choice of file type or plugin to use, said choice can be set as a default, avoiding future prompts
The file type selector of the file open dialog is now used to guide file type and plugin selection
The pairwise file loader now has a front end that allows for the configuration of columns within the source data table, so it's no longer necessary for pairwise files to be strictly 2 or 3 columns

Transforms and Visualisations

Add facility to select favourite transforms, which are displayed at the top of the transform list
Add mechanism to save sets of transforms and visualisations for later recall

Attributes

There is now an option (on the Misc tab of the Options dialog) to change the way Find By Attribute Value sorts the list of possible attribute values; it can now be done alphanumerically, in addition to the normal behaviour of sorting from the large to small set size

Correlation

The correlation plot columns can now be sorted by data value
The correlation plot is now vertically scrollable when it's too large for its container - i.e. when there are many column annotations
In the correlation loader, input data can now be clipped against a constant, or by Winsorization
Correlation plot columns can now be sorted by hierarchical clustering, using the SLINK method with a Euclidean distance measure
Add a Filtering option to correlation parameters, more specifically enabling the ability to filter edges using the k-Nearest Neighbours strategy; this is particularly useful with datasets that are extremely correlated, where traditional thresholding cannot adequately differentiate between rows
Replace the Initial Transforms section of the correlation loader with Template, allowing for a more flexible and customisable means of appending additional transforms and visualisations
Add ability to save correlation plot images on a per attribute value basis, e.g. saving one image per cluster

Miscellaneous

In plugins that have a data table, the source, target and neighbour rows can now be selected
Graph metrics display now reflects the visible component, when in component mode
Add option to interpret trackpad pan gestures as zooming; this is primarily useful for users of the Apple Magic Mouse, where it's more intuitive for scrolling vertically to map to zooming

Bug Fixes

Bring MCL inline with the reference implementation by not skipping single node clusters
Fix pairwise exporter introducing extra quotes into its output
Fix crash that occurred when changing the graph with the Find interface active
Prevent showing the main context menu over the Find interface
Fix delay in showing Find By Attribute interface when an attribute has a large quantity of values
Fix deadlock/crash when cancelling a command
Fix initial dimensions on screenshot capture preset often being wrong
Fix renderer not updating when focused labelling enabled
Use the correct file extension when saving a non-native format
Fix correlation plot data value sorting occasionally behaving oddly when node selection changes
Fix changes to transform flags (locked, pinned) not being properly undoable
Fix blank graph rendering in some rare circumstances
Fix potential crash that might occur when changing the find attribute multiple times
Fix graph size estimate plot inappropriately showing \"Empty Graph\" in some circumstances
Fix poor behaviour when loading correlation data with anonymous columns
Fix \"ghost\" node selection box appearing after an unusual combination of mouse drags and key presses
Fix temporary lock-up at the end of a transform application
Fix visually overlapping components when nodes move from one component to another
Fix crash when reloading certain save files where nodes have been manually deleted

Other

Move code base to Qt 6/Qt Quick 2 (Please report bugs/regressions)
macOS builds now take advantage of Apple M1 hardware
Capture more debug output on Windows
Improve video driver crash detection
Collect more information when a std::exception based crash occurs
Improve macOS update script to deal with the case where the target .app has been renamed
Improve installer error message on macOS when target directory is not writeable
Allow selection of alternative UI themes where available

4.0 (Apr 24 2023)

4.0

Loading

When there is a choice of file type or plugin to use, said choice can be set as a default, avoiding future prompts
The file type selector of the file open dialog is now used to guide file type and plugin selection
The pairwise file loader now has a front end that allows for the configuration of columns within the source data table, so it's no longer necessary for pairwise files to be strictly 2 or 3 columns

Transforms and Visualisations

Add facility to select favourite transforms, which are displayed at the top of the transform list
Add mechanism to save sets of transforms and visualisations for later recall

Attributes

There is now an option (on the Misc tab of the Options dialog) to change the way Find By Attribute Value sorts the list of possible attribute values; it can now be done alphanumerically, in addition to the normal behaviour of sorting from the large to small set size

Correlation

The correlation plot columns can now be sorted by data value
The correlation plot is now vertically scrollable when it's too large for its container - i.e. when there are many column annotations
In the correlation loader, input data can now be clipped against a constant, or by Winsorization
Correlation plot columns can now be sorted by hierarchical clustering, using the SLINK method with a Euclidean distance measure
Add a Filtering option to correlation parameters, more specifically enabling the ability to filter edges using the k-Nearest Neighbours strategy; this is particularly useful with datasets that are extremely correlated, where traditional thresholding cannot adequately differentiate between rows
Replace the Initial Transforms section of the correlation loader with Template, allowing for a more flexible and customisable means of appending additional transforms and visualisations
Add ability to save correlation plot images on a per attribute value basis, e.g. saving one image per cluster

Miscellaneous

In plugins that have a data table, the source, target and neighbour rows can now be selected
Graph metrics display now reflects the visible component, when in component mode
Add option to interpret trackpad pan gestures as zooming; this is primarily useful for users of the Apple Magic Mouse, where it's more intuitive for scrolling vertically to map to zooming

Bug Fixes

Bring MCL inline with the reference implementation by not skipping single node clusters
Fix pairwise exporter introducing extra quotes into its output
Fix crash that occurred when changing the graph with the Find interface active
Prevent showing the main context menu over the Find interface
Fix delay in showing Find By Attribute interface when an attribute has a large quantity of values
Fix deadlock/crash when cancelling a command
Fix initial dimensions on screenshot capture preset often being wrong
Fix renderer not updating when focused labelling enabled
Use the correct file extension when saving a non-native format
Fix correlation plot data value sorting occasionally behaving oddly when node selection changes
Fix changes to transform flags (locked, pinned) not being properly undoable
Fix blank graph rendering in some rare circumstances
Fix potential crash that might occur when changing the find attribute multiple times
Fix graph size estimate plot inappropriately showing \"Empty Graph\" in some circumstances
Fix poor behaviour when loading correlation data with anonymous columns
Fix \"ghost\" node selection box appearing after an unusual combination of mouse drags and key presses
Fix temporary lock-up at the end of a transform application
Fix visually overlapping components when nodes move from one component to another
Fix crash when reloading certain save files where nodes have been manually deleted

Other

Move code base to Qt 6/Qt Quick 2 (Please report bugs/regressions)
macOS builds now take advantage of Apple M1 hardware
Capture more debug output on Windows
Improve video driver crash detection
Collect more information when a std::exception based crash occurs
Improve macOS update script to deal with the case where the target .app has been renamed
Improve installer error message on macOS when target directory is not writeable
Allow selection of alternative UI themes where available

3.2 (Nov 23 2022)

3.2

Bug Fixes

Improve stability across all platforms, particularly with respect to the use of enrichment analysis
Fix operation of Copy Column To Clipboard functionality
Linux
Improve compatibility across a greater number of distributions

3.1

Bug Fixes

Fix display not updating when focused labelling option used
Fix occasional incorrect screenshot dimensions
Fix text style options sometimes not taking effect immediately
Fix adjacency matrix loader not setting node names
Fix crash that occurred when the graph changed during a find
Fix layout getting stuck on certain contracted graphs
Fix crash that occurred sometimes when cancelling a command
Fix transform flags (e.g. locked or pinned) not being properly recorded as an undoable step
Fix GML saver creating key names with a leading digit (which is prohibted by the standard)
Fix various issues with the GraphML saver
Fix crash that occurred if the application is closed at a specific point of a load
Fix import of attributes where the keys are large integers
Fix crash when plotting an IQR with zero outliers
Fix crash that occurred when flipping between find types multiple times
Fix blank plugin window when multiple tabs open

3.0

Loading

Downloadable files can now be opened directly, either by using the Open Url option in the File menu, or by dragging and dropping hyperlinks onto the main window
A Graphia specific URL scheme is now registered so that the application may now be opened by clicking special hyperlinks; these can be created using the Link Generator
Tabular lists of node pairs can now be loaded from pairwise CSV, TSV, SSV and XLSX files
Loading Cytoscape eXchange files is now possible, as used on NDex
Graphviz .dot files may now be loaded
When loading from an adjacency matrix, it is now possible to choose to discard edges based on edge weight, and to skip double edges where the matrix is symmetric

Transforms

Added Forward Attribute transform; for graphs with contracted edges, this will copy the selected attribute's values to all elements hidden by the contraction
Added Average Attribute transform; create a new attribute whose values are determined by averaging the values of a numerical attribute on the basis of a categorical attribute - this allows for e.g. finding a cluster's average attribute value
Clustering algorithms now create additional node attributes that reflect the size of the clusters in which the respective nodes belong, effectively allowing filtering operations on the size of clusters

Visualisations

Visualisations that use deleted source attributes can now have their source attributes changed, in contrast to the prior behaviour where a broken visualisation would need to be deleted and recreated
For numerical visualisations, the mapping of input value to output value can now be fine tuned
An Apply button is now present on the gradient, palette and numeric mapping visualisation dialogs, for immediate preview of any changed settings

Attributes

Attributes can now be imported, accessible via Tools → Import Attributes From Table…
User defined attributes can now be removed if desired, accessible via Tools → Remove Attributes…
Attributes can now be cloned, accessible via Tools → Clone Attribute…
User defined attributes can now be edited, accessible via Tools → Edit Attribute…
There is now search functionality in all the places where attributes are chosen; this is most useful when selecting a Data Value attribute in the case where there are many
The node attribute table now has a context sensitive menu that provides options relevant to the clicked attribute
The contents of a column from the node attribute table can now be copied to the clipboard, accessible by the context menu

Layout

Layout settings are now accessible via a toolbar button
Node and edge sizes are now saved in the .graphia file and are adjustable via Layout Settings
Layout settings can now be saved as named presets, for quick access to frequently used settings

Enrichment

When viewing enrichment results, the chosen attribute names are now used for the column headers
The enrichment results table is now formatted in a way that improves Microsoft Excel's interpretation of it, when exported
Enrichment data columns are now correctly named regarding the the metrics actually employed

Correlation

Correlating tables of discrete values is now possible, using the Jaccard Index or Simple Matching Coefficient algorithms
For continuous correlation, the Euclidean Distance, Cosine Similarity and Biweight Midcorrelation (Bicor) algorithms are now available
Column annotation colours are now assigned by palette rather than by hashing the string value
Numerical column annotations are now displayed using a gradient
In the data plot, values can now be scaled by an attribute value
The epsilon used when log scaling data is now computed to use an appropriately sized value rather than a fixed constant
When loading correlation data with duplicate attribute column names, these are now considered separately rather than overwriting each other
The data plot can now be panned by dragging and zoomed using the mouse wheel
In the plot, data can now be combined into IQR boxplots based on one or more annotations, enabled by selecting Group By Annotation in the Plot menu
Furthermore, when Group By Annotation is enabled there is now another option to colour the IQR boxes with a user selected annotation
When displaying IQR plots, outliers can now be disabled by toggling the Show Outliers menu option
Various buttons have been added to the tool bar to control the correlation plot
Data can now be log scaled when rendering IQR boxplots

Miscellaneous

Hyperlinks in table cells are now clickable and some basic HTML 3.2 can be displayed
A log is now made of the steps taken in the graph's creation, accessible via Tools → Show Provenance Log…
There is now an option to stay in component mode when finding, by default off
The Latest Changes option was added to the Help menu, which shows any new changes present in the running version

Bug Fixes

Fix loading GML files where the edges precede the nodes
Fix crash when loading from empty files
Fix Matlab loader not handling some forms of adjacency matrix
Fix empty values being included in enrichment results
Fix plot grid lines getting incorrectly enabled in some circumstances
Fix missing column annotations where there were a large number of unique values
Fix possibility of dismissing the correlation parameters dialog before the data frame had been found
Fix occasionally ambiguous Esc key shortcut
Fix crash involving search and selection
Fix crash caused by graph visuals being altered during a graph change
Fix palette editor behaviour when there are few assignable values
Fix attribute ranges and shared values not getting updated in some circumstances
Fix transforms and visualisations not being refreshed when referenced attribute values change
Fix various issues involving attributes that change values and/or type during transforms
Fix malformed tab titles when the source file name contains periods
Fix wrong initial save file name
Fix empty graph warning being displayed before correlation estimate completes
Fix visualisation attribute list not updating following attribute changes
Fix crash on correlation plot when moving the mouse along a particular path

Performance

Generally improved performance when there are a large number of components
Add option to disable multisampling, yielding a performance improvement
Add text to the Options dialog on macOS, suggesting opening the application in Low Resolution Mode for a further performance improvement
Improve performance of attributes model
Improved correlation data plot IQR rendering performance
Redundant correlation plot redraws have been reduced
Improve correlation column annotation rendering performance
Improve correlation column annotation sort performance

Linux

An XDG desktop item is now automatically created, so Graphia will appear in system menus

3.1 (Jul 18 2022)

3.1

Bug Fixes

Fix display not updating when focused labelling option used
Fix occasional incorrect screenshot dimensions
Fix text style options sometimes not taking effect immediately
Fix adjacency matrix loader not setting node names
Fix crash that occurred when the graph changed during a find
Fix layout getting stuck on certain contracted graphs
Fix crash that occurred sometimes when cancelling a command
Fix transform flags (e.g. locked or pinned) not being properly recorded as an undoable step
Fix GML saver creating key names with a leading digit (which is prohibted by the standard)
Fix various issues with the GraphML saver
Fix crash that occurred if the application is closed at a specific point of a load
Fix import of attributes where the keys are large integers
Fix crash when plotting an IQR with zero outliers
Fix crash that occurred when flipping between find types multiple times
Fix blank plugin window when multiple tabs open

3.0

Loading

Downloadable files can now be opened directly, either by using the Open Url option in the File menu, or by dragging and dropping hyperlinks onto the main window
A Graphia specific URL scheme is now registered so that the application may now be opened by clicking special hyperlinks; these can be created using the Link Generator
Tabular lists of node pairs can now be loaded from pairwise CSV, TSV, SSV and XLSX files
Loading Cytoscape eXchange files is now possible, as used on NDex
Graphviz .dot files may now be loaded
When loading from an adjacency matrix, it is now possible to choose to discard edges based on edge weight, and to skip double edges where the matrix is symmetric

Transforms

Added Forward Attribute transform; for graphs with contracted edges, this will copy the selected attribute's values to all elements hidden by the contraction
Added Average Attribute transform; create a new attribute whose values are determined by averaging the values of a numerical attribute on the basis of a categorical attribute - this allows for e.g. finding a cluster's average attribute value
Clustering algorithms now create additional node attributes that reflect the size of the clusters in which the respective nodes belong, effectively allowing filtering operations on the size of clusters

Visualisations

Visualisations that use deleted source attributes can now have their source attributes changed, in contrast to the prior behaviour where a broken visualisation would need to be deleted and recreated
For numerical visualisations, the mapping of input value to output value can now be fine tuned
An Apply button is now present on the gradient, palette and numeric mapping visualisation dialogs, for immediate preview of any changed settings

Attributes

Attributes can now be imported, accessible via Tools → Import Attributes From Table…
User defined attributes can now be removed if desired, accessible via Tools → Remove Attributes…
Attributes can now be cloned, accessible via Tools → Clone Attribute…
User defined attributes can now be edited, accessible via Tools → Edit Attribute…
There is now search functionality in all the places where attributes are chosen; this is most useful when selecting a Data Value attribute in the case where there are many
The node attribute table now has a context sensitive menu that provides options relevant to the clicked attribute
The contents of a column from the node attribute table can now be copied to the clipboard, accessible by the context menu

Layout

Layout settings are now accessible via a toolbar button
Node and edge sizes are now saved in the .graphia file and are adjustable via Layout Settings
Layout settings can now be saved as named presets, for quick access to frequently used settings

Enrichment

When viewing enrichment results, the chosen attribute names are now used for the column headers
The enrichment results table is now formatted in a way that improves Microsoft Excel's interpretation of it, when exported
Enrichment data columns are now correctly named regarding the the metrics actually employed

Correlation

Correlating tables of discrete values is now possible, using the Jaccard Index or Simple Matching Coefficient algorithms
For continuous correlation, the Euclidean Distance, Cosine Similarity and Biweight Midcorrelation (Bicor) algorithms are now available
Column annotation colours are now assigned by palette rather than by hashing the string value
Numerical column annotations are now displayed using a gradient
In the data plot, values can now be scaled by an attribute value
The epsilon used when log scaling data is now computed to use an appropriately sized value rather than a fixed constant
When loading correlation data with duplicate attribute column names, these are now considered separately rather than overwriting each other
The data plot can now be panned by dragging and zoomed using the mouse wheel
In the plot, data can now be combined into IQR boxplots based on one or more annotations, enabled by selecting Group By Annotation in the Plot menu
Furthermore, when Group By Annotation is enabled there is now another option to colour the IQR boxes with a user selected annotation
When displaying IQR plots, outliers can now be disabled by toggling the Show Outliers menu option
Various buttons have been added to the tool bar to control the correlation plot
Data can now be log scaled when rendering IQR boxplots

Miscellaneous

Hyperlinks in table cells are now clickable and some basic HTML 3.2 can be displayed
A log is now made of the steps taken in the graph's creation, accessible via Tools → Show Provenance Log…
There is now an option to stay in component mode when finding, by default off
The Latest Changes option was added to the Help menu, which shows any new changes present in the running version

Bug Fixes

Fix loading GML files where the edges precede the nodes
Fix crash when loading from empty files
Fix Matlab loader not handling some forms of adjacency matrix
Fix empty values being included in enrichment results
Fix plot grid lines getting incorrectly enabled in some circumstances
Fix missing column annotations where there were a large number of unique values
Fix possibility of dismissing the correlation parameters dialog before the data frame had been found
Fix occasionally ambiguous Esc key shortcut
Fix crash involving search and selection
Fix crash caused by graph visuals being altered during a graph change
Fix palette editor behaviour when there are few assignable values
Fix attribute ranges and shared values not getting updated in some circumstances
Fix transforms and visualisations not being refreshed when referenced attribute values change
Fix various issues involving attributes that change values and/or type during transforms
Fix malformed tab titles when the source file name contains periods
Fix wrong initial save file name
Fix empty graph warning being displayed before correlation estimate completes
Fix visualisation attribute list not updating following attribute changes
Fix crash on correlation plot when moving the mouse along a particular path

Performance

Generally improved performance when there are a large number of components
Add option to disable multisampling, yielding a performance improvement
Add text to the Options dialog on macOS, suggesting opening the application in Low Resolution Mode for a further performance improvement
Improve performance of attributes model
Improved correlation data plot IQR rendering performance
Redundant correlation plot redraws have been reduced
Improve correlation column annotation rendering performance
Improve correlation column annotation sort performance

Linux

An XDG desktop item is now automatically created, so Graphia will appear in system menus

3.0 (Feb 07 2022)

Loading

Downloadable files can now be opened directly, either by using the Open Url option in the File menu, or by dragging and dropping hyperlinks onto the main window
A Graphia specific URL scheme is now registered so that the application may now be opened by clicking special hyperlinks; these can be created using the Link Generator
Tabular lists of node pairs can now be loaded from pairwise CSV, TSV, SSV and XLSX files
Loading Cytoscape eXchange files is now possible, as used on NDex
Graphviz .dot files may now be loaded
When loading from an adjacency matrix, it is now possible to choose to discard edges based on edge weight, and to skip double edges where the matrix is symmetric

Transforms

Added Forward Attribute transform; for graphs with contracted edges, this will copy the selected attribute's values to all elements hidden by the contraction
Added Average Attribute transform; create a new attribute whose values are determined by averaging the values of a numerical attribute on the basis of a categorical attribute - this allows for e.g. finding a cluster's average attribute value
Clustering algorithms now create additional node attributes that reflect the size of the clusters in which the respective nodes belong, effectively allowing filtering operations on the size of clusters

Visualisations

Visualisations that use deleted source attributes can now have their source attributes changed, in contrast to the prior behaviour where a broken visualisation would need to be deleted and recreated
For numerical visualisations, the mapping of input value to output value can now be fine tuned
An Apply button is now present on the gradient, palette and numeric mapping visualisation dialogs, for immediate preview of any changed settings

Attributes

Attributes can now be imported, accessible via Tools → Import Attributes From Table…
User defined attributes can now be removed if desired, accessible via Tools → Remove Attributes…
Attributes can now be cloned, accessible via Tools → Clone Attribute…
User defined attributes can now be edited, accessible via Tools → Edit Attribute…
There is now search functionality in all the places where attributes are chosen; this is most useful when selecting a Data Value attribute in the case where there are many
The node attribute table now has a context sensitive menu that provides options relevant to the clicked attribute
The contents of a column from the node attribute table can now be copied to the clipboard, accessible by the context menu

Layout

Layout settings are now accessible via a toolbar button
Node and edge sizes are now saved in the .graphia file and are adjustable via Layout Settings
Layout settings can now be saved as named presets, for quick access to frequently used settings

Enrichment

When viewing enrichment results, the chosen attribute names are now used for the column headers
The enrichment results table is now formatted in a way that improves Microsoft Excel's interpretation of it, when exported
Enrichment data columns are now correctly named regarding the the metrics actually employed

Correlation

Correlating tables of discrete values is now possible, using the Jaccard Index or Simple Matching Coefficient algorithms
For continuous correlation, the Euclidean Distance, Cosine Similarity and Biweight Midcorrelation (Bicor) algorithms are now available
Column annotation colours are now assigned by palette rather than by hashing the string value
Numerical column annotations are now displayed using a gradient
In the data plot, values can now be scaled by an attribute value
The epsilon used when log scaling data is now computed to use an appropriately sized value rather than a fixed constant
When loading correlation data with duplicate attribute column names, these are now considered separately rather than overwriting each other
The data plot can now be panned by dragging and zoomed using the mouse wheel
In the plot, data can now be combined into IQR boxplots based on one or more annotations, enabled by selecting Group By Annotation in the Plot menu
Furthermore, when Group By Annotation is enabled there is now another option to colour the IQR boxes with a user selected annotation
When displaying IQR plots, outliers can now be disabled by toggling the Show Outliers menu option
Various buttons have been added to the tool bar to control the correlation plot
Data can now be log scaled when rendering IQR boxplots

Miscellaneous

Hyperlinks in table cells are now clickable and some basic HTML 3.2 can be displayed
A log is now made of the steps taken in the graph's creation, accessible via Tools → Show Provenance Log…
There is now an option to stay in component mode when finding, by default off
The Latest Changes option was added to the Help menu, which shows any new changes present in the running version

Bug Fixes

Fix loading GML files where the edges precede the nodes
Fix crash when loading from empty files
Fix Matlab loader not handling some forms of adjacency matrix
Fix empty values being included in enrichment results
Fix plot grid lines getting incorrectly enabled in some circumstances
Fix missing column annotations where there were a large number of unique values
Fix possibility of dismissing the correlation parameters dialog before the data frame had been found
Fix occasionally ambiguous Esc key shortcut
Fix crash involving search and selection
Fix crash caused by graph visuals being altered during a graph change
Fix palette editor behaviour when there are few assignable values
Fix attribute ranges and shared values not getting updated in some circumstances
Fix transforms and visualisations not being refreshed when referenced attribute values change
Fix various issues involving attributes that change values and/or type during transforms
Fix malformed tab titles when the source file name contains periods
Fix wrong initial save file name
Fix empty graph warning being displayed before correlation estimate completes
Fix visualisation attribute list not updating following attribute changes
Fix crash on correlation plot when moving the mouse along a particular path

Performance

Generally improved performance when there are a large number of components
Add option to disable multisampling, yielding a performance improvement
Add text to the Options dialog on macOS, suggesting opening the application in Low Resolution Mode for a further performance improvement
Improve performance of attributes model
Improved correlation data plot IQR rendering performance
Redundant correlation plot redraws have been reduced
Improve correlation column annotation rendering performance
Improve correlation column annotation sort performance

Linux

An XDG desktop item is now automatically created, so Graphia will appear in system menus

2.2 (Jan 27 2021)

Bug Fixes

Fix Visual Studio runtime not being copied to installation directory on Windows

2.1 (Dec 18 2020)

Bug Fixes

Fix GraphML parser failing on some input files
Fix node selection not working after a specific sequence of transforms
Fix crash that occurred when an attribute was destroyed and recreated with the same name, but a different element type
Fix crash that occurred after selecting some nodes, then cycling a transform a number of times
Fix 'Remove Leaves' transform behaving inconsistently with respect to singletons
Prevent the possibility of creating invalid transforms, in some circumstances
Fix double clicking a transform name in the transform creation dialog disabling subsequent initial mouse click
Fix various renderer crashes
Fix empty values being included in enrichment results
Fix enrichment result table cells being interpreted as dates in Microsoft Excel
macOS amend-existing-head.sh changelog.md CNAME confirm-upload.sh diff.sh generate-changelog.md.sh index.json Fix help tool tips being badly sized amend-existing-head.sh changelog.md CNAME confirm-upload.sh diff.sh generate-changelog.md.sh index.json Fix flickering of windows when adjusting the correlation plot amend-existing-head.sh changelog.md CNAME confirm-upload.sh diff.sh generate-changelog.md.sh index.json Fix the WebSearch plugin being broken
Linux amend-existing-head.sh changelog.md CNAME confirm-upload.sh diff.sh generate-changelog.md.sh index.json Improve distribution compatibility amend-existing-head.sh changelog.md CNAME confirm-upload.sh diff.sh generate-changelog.md.sh index.json Fix crashes with WebSearch plugin on some platforms