4.2

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Bug Fixes

• Fix node selection not being reflected in correlation plot

4.1

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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

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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

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

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

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

Bug Fixes

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