VorteX 26-Apr-2018

-Bugfix in the automatic K boundary suggestion function

VorteX 14-Mar-2018

-Upgraded to HSQLDB 2.3.4
-Added the auto-suggestion of the clustering parameter range

VorteX 29-Jun-2017-rev2

• Bug fixes: Euclidean distance is now displayed correctly in the clustering result
• Force-Directed Layout: clusters can be selected by clicking on the graph nodes.
• MST/DMT: can export the snapshot as PDF now.
• X-shift Standalone is now integrated into the same VorteX.jar. For the details on how to run it, please refer to X-shift_standalone_README.txt.
• X-shift Standalone now writes FCS files using DATATYPE/F, which makes FCS files more compatible with the standard FCS reader libraries.
• Changes to standalone version:
  • the data import configuration is now specified in the file 'importConfig.txt' instead of 'config.txt'
  • the algorithm doesn't do elbow-finding by default, rather it runs K=20 for the sake of speed. This is expected
    to give a favourable result on most datasets with >10 dimensions. This can be overturned by passing 'auto'
    command line argument (refer to X-shift_standalone_README.txt for details).

VorteX 21-Apr-2017

Improvements:

*Moved to Maven, single JAR build
*Improved compact database format and simplified database connection interface.
*Database compaction
*Improved FDL rendering and blending of color expression values
*Switch between linear and quantile scales in MST/DMT/FDL graphs
*Switch between black background in FDL

VorteX 3-Mar-2017

Bug fixes:
*FCS export used to write files in DATATYPE/D format, which is not compatible with FlowJo or FlowCore. This has been changed to DATATYPE/F, which is compatible with aforementioned applications.
*Image and FCS export wasn't always working on Mac due to non-existing intermediate directories. This has been addressed.

Features:
*Export of XY coordinates from the Force-Directed Layout, which you can use for downstream analysis and visualization

VorteX 14-Dec-2016

Changes:

Data structures:
*Events in clusters are now displayed showing full info in separate columns (EventID, File Name, Index in File, Name). Names of events are taken from the first column of CSV files or left empty if events were imported from FCS.
*Annotation and clustering import now require EventID to be the first identifier column. EventID is simply a number that indicates the order of a given event in the dataset. EventIDs can be obtained by exporting any clustering into a CSV file, but are lost during FCS export.

Bugfixes:
*Fixes the authorization problem when trying to re-connect to an older database
*Fixed CSV export and import
*Fixed FCS export

Force-Directed Layout:
*FDL rendering improved: colors are brighter, overlapping dots blend their colors
*FDL appears in a tab instead of a separate window

GUI:
*Switched to Native Look-and-feel (better responsiveness, more compact GUI elements)
*Added Filename column in the Cluster Contents Browser

DMT/MST:
*Switched to Gephi Toolkit 0.9.1

Cluster Hierarchy Plot:
*ClusterIDs are shown on the cluster box elements

VorteX Oct4-2016

What's new:

*Data export as FCS
*ModulMap - a force-directed map of clusters where edges represent correlations of cell numbers across samples or any other annotations
*Command line X-shift with automated parameter selection (see X-shift.Standalone)

VorteX 9-Nov-2016

Changes:

*Proportional sampling in FDL (number of datapoints sampled from each cluster can be varied with cluster size)
*Number of edges can be varied w.r.t. to local datapoint density around the given datapoint: points with higher density get more edges, which might improve the look of the FDL layout plot.
*Cluster IDs are shown next to the nodes in MST, DMT and ModuleMap. This can be disabled by toggling 'Show cluster labels' checkbox in the right panel.

VorteX 31-Oct-2016

New features;

Force-Directed Layout:
*Variable node size in visualisation
*Choice between Angular and Euclidean distance
*Restricting the connections between nodes to a user-defined range of a variable. This is useful for constraining the FDL connections between consecutive timepoints etc.

Bug fixes in CSV import