dev-3444-g930223aca (Jun 06 2024)

Features

• Command line arguments can now be passed to the application via the URL of the WebAssembly version
• Warnings are now shown regarding duplicate values when importing attributes or column annotations

Bug Fixes

• Fix potential crash in correlation annotation rendering
• Fix editing of attributes not undoing correctly
• Fix custom visualisation mapping controls being available when attribute has no range

Other

• Reduce probability of subwindows getting hidden in the background on open
• Adjust source code to use modern Qt QML build system
• Improve performance of Find By Attribute Value
• Disable code signing on Windows build

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

5.1 (Aug 08 2024)

5.1

Bug Fixes

• Fix operation of WebSearch plugin under Windows

5.0

Loading

• Allow for loading adjacency matrices from .txt files
• Improve error message when loading inconsistent tabular data files
• Improve file content identity algorithm
• Adjacency matrix loaders can now be cancelled

Transforms and Visualisations

• Add Type Cast transform, to convert attribute types

• Text Size can now be used as a visualisation channel

  

• Text Colour can now be used as a visualisation channel

  

• Add Shared Text visualisation channel, enabling the textual annotation of groups of nodes

  

Attributes

• Add facility to edit the type and description of user defined attributes

  

• Warnings are now shown regarding duplicate values when importing attributes

Correlation

• Add Find Rows of Interest functionality, identifying rows that correlate with selected columns

  

• 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 functionality to import column annotations onto an existing correlation plot

• 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 Softmax data normalisation method to correlation loader

• Warnings are now shown regarding duplicate values when importing column annotations

Miscellaneous

• WebAssembly support

  

• 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; 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

• Text size can now be altered on-the-fly in the Layout Settings panel

• Double clicking the background in overview mode now resets the view

• Ease restrictions on zooming 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

• Better handling of operating system UI theming, including Dark Mode on platforms that support it

• Default sort order for Find By Attribute Value is now lexographical

Bug Fixes

• When exporting node positions, export the non-scaled values
• Fix various table row selection issues
• 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
• Fix crash when removing an attribute
• Fix keyboard interaction with attribute list UI
• Fix correlation plot context menu state inconsistencies
• Fix Save As Images By… misbehaving with respect to file names with multiple dots in them
• Fix various subtle renderer transition bugs, particularly when several transitions are started/interrupted in rapid succession
• Fix handling of some load failure modes
• 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
• Fix last row of attribute table being obscured by horizontal scroll bar
• Fix some visual options not being immediately applied
• Fix crash when trying to load single column correlation data tables
• Fix re-enabling a visualisation with a lost attribute causing errors
• Fix operation of context sensitive menu items on MacOS
• Fix locked transforms displaying 'nan' for drop down list parameters
• Fix potential crash in correlation annotation rendering
• Fix editing of attributes not undoing correctly
• Fix custom visualisation mapping controls being available when attribute has no range

Other

• General improvement to operation on high DPI displays, particularly with fractional scaling factors as seen on Windows
• Improve node attribute table performance when node selection changes
• Selection outlines of transparent graph elements are now rendered transparent too
• Update to Qt 6.7.0

5.0 (Jul 30 2024)

5.0

Loading

• Allow for loading adjacency matrices from .txt files
• Improve error message when loading inconsistent tabular data files
• Improve file content identity algorithm
• Adjacency matrix loaders can now be cancelled

Transforms and Visualisations

• Add Type Cast transform, to convert attribute types

• Text Size can now be used as a visualisation channel

  

• Text Colour can now be used as a visualisation channel

  

• Add Shared Text visualisation channel, enabling the textual annotation of groups of nodes

  

Attributes

• Add facility to edit the type and description of user defined attributes

  

• Warnings are now shown regarding duplicate values when importing attributes

Correlation

• Add Find Rows of Interest functionality, identifying rows that correlate with selected columns

  

• 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 functionality to import column annotations onto an existing correlation plot

• 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 Softmax data normalisation method to correlation loader

• Warnings are now shown regarding duplicate values when importing column annotations

Miscellaneous

• WebAssembly support

  

• 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; 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

• Text size can now be altered on-the-fly in the Layout Settings panel

• Double clicking the background in overview mode now resets the view

• Ease restrictions on zooming 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

• Better handling of operating system UI theming, including Dark Mode on platforms that support it

• Default sort order for Find By Attribute Value is now lexographical

Bug Fixes

• When exporting node positions, export the non-scaled values
• Fix various table row selection issues
• 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
• Fix crash when removing an attribute
• Fix keyboard interaction with attribute list UI
• Fix correlation plot context menu state inconsistencies
• Fix Save As Images By… misbehaving with respect to file names with multiple dots in them
• Fix various subtle renderer transition bugs, particularly when several transitions are started/interrupted in rapid succession
• Fix handling of some load failure modes
• 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
• Fix last row of attribute table being obscured by horizontal scroll bar
• Fix some visual options not being immediately applied
• Fix crash when trying to load single column correlation data tables
• Fix re-enabling a visualisation with a lost attribute causing errors
• Fix operation of context sensitive menu items on MacOS
• Fix locked transforms displaying 'nan' for drop down list parameters
• Fix potential crash in correlation annotation rendering
• Fix editing of attributes not undoing correctly
• Fix custom visualisation mapping controls being available when attribute has no range

Other

• General improvement to operation on high DPI displays, particularly with fractional scaling factors as seen on Windows
• Improve node attribute table performance when node selection changes
• Selection outlines of transparent graph elements are now rendered transparent too
• Update to Qt 6.7.0

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

2.0 (May 22 2020)

2.0 Final Release