AutoAnnotate

Finds clusters and visually annotates them with labels and groups.
Categories: annotation, automation, clustering, enrichment analysis

This App is part of the EnrichmentMap Collection.

Finds clusters and visually annotates them with labels and groups. These visualizations provide a concise visual summary which is helpful for network analysis and interpretation.

Features:

  • Automates running clusterMaker2 to generate clusters. (Or provide your own clusters by selecting any node attribute.)
  • Automatically generates cluster labels based on word frequencies of selected attributes.
  • Manages multiple “Annotation Sets” and easily switches between them.
  • Change the look of the annotations using several display options.
  • Cluster-aware layouts.
  • Automatically group and collapse clusters. Creates a simplified view by collapsing each cluster into a “meta-node” and collapsing edges between clusters into a single “meta-edge”.
  • Allows to manually create and update clusters.
  • Originally designed and used to annotate Enrichment Maps but applicable to any type of network including PPI, pathways, or Social networks.

Warning

Versions of AutoAnnotate prior to version 1.3.3 are not fully compatibile with Cytoscape 3.8. If you are having issues please upgrade to the latest version.

Warning

Versions of AutoAnnotate prior to version 1.3.0 are incompatible with the latest version of clusterMaker2. If you are having issues running AutoAnnotate please upgrade to the latest version.

Links:

DOI

Authors:

1.5.2 3 months ago

Works with Cytoscape 3.9

Release Notes

  • Add action to create column containing cluster labels.

1.5.1 10 months ago

Works with Cytoscape 3.9

Release Notes

  • bug fixes

1.5.0 11 months ago

Works with Cytoscape 3.9

Release Notes

  • UI updates to the AutoAnotate creation dialog.
    • Option to label clusters using the name of the most significant node in the cluster.
    • New slider that alows to choose the granularity of the clusters.
    • Support for using the MCODE app to find clusters in the network.
  • Thumbnail view at the bottom of the cluster panel.
  • Slider at bottom of cluster panel that allows to show/hide nodes according to their significance.
  • Better integration with EnrichmentMap.
  • Advanced options section in the Display Options panel.
  • Bug fixes.

1.4.1 2 years ago

Works with Cytoscape 3.9

Release Notes

  • Fix for issue where annotations created in 1.3 would not load correctly in 1.4

1.4.0 2 years ago

Works with Cytoscape 3.9

Release Notes

  • Support for color palettes.
  • New display option for cluster padding.
  • Summary networks have improved attribute aggregation.
    • Attribute aggregation now works for edges as well as nodes.
    • There is a new settings dialog that shows when creating a summary network. There is no longer a need to go into the group settings.
    • Aggregation settings can be specified for each individual column.
    • New aggregators for EnrichmentMap attributes.
  • Improved support for hidden nodes and edges.
    • Hiding nodes causes the clusters to resize to the visible nodes.
    • Hidden nodes and edges are ignored by clustering algorithms.
  • Bug Fixes

1.3.5 3 years ago

Works with Cytoscape 3.8

Release Notes

  • Creating a summary network is much faster.
  • Bug fixes.

1.3.4 4 years ago

Works with Cytoscape 3.8

Release Notes

  • Add "minimum word occurrence" option when creating labels.
  • Display panel: add "min font size" slider when "scale font by cluster size" is on.
  • Allow CoSE layout to run on selected nodes.
  • Update to Java 11.
  • Bug fixes.

1.3.3 5 years ago

Works with Cytoscape 3.8

Release Notes

Bugfix release to fix incompatibility with Cytoscape 3.8.

1.3.2 6 years ago

Works with Cytoscape 3.7

Release Notes

  • Adds buttons and menu items to access the WordCloud excluded words and delimiters dialogs.
  • Add argument to layout command.

1.3 6 years ago

Works with Cytoscape 3.7

Release Notes

Requires Cytoscape 3.7

  • Drawing annotations is much faster
  • Word wrap feature for cluster labels
  • New cluster-aware layouts
  • New feature: copy annotations to another network
  • Support for column namespaces
  • New “reset defaults” button in creation dialog
  • The “annotate” command now returns JSON
  • Cleaner “quick start” panel
  • Cleaner “display options” panel
  • Cleaner menu layouts
  • Several bug fixes

1.2 8 years ago

Works with Cytoscape 3.4

Release Notes

  • Quick start for new users.
  • Streamlined display options panel.
  • Ability to change annotation colors.
  • Support for hidden nodes.
  • Option to create clusters for singleton nodes.
  • New commands for automating AutoAnnotate from CyREST.
  • Fixes for flickering annotations and performance issues.

1.1.0 9 years ago

Works with Cytoscape 3.3

Release Notes

  • Added "Create Summary Network" feature because it is much faster than "Collapse All".
  • Added status bar to cluster panel.
  • Added "Display Creation Paramters..." feature.
  • Changed the look of the checkmarks in the "collapsed" column.
  • Bug fixes.

1.0.1 9 years ago

Works with Cytoscape 3.3

Release Notes

Bug-fix release that allows AutoAnnotate to work properly with Cytoscape 3.4.

1.0.0 9 years ago

Works with Cytoscape 3.3

Apps that depend on this release

CYTOSCAPE 3

Version 1.5.2

License Click here

Released 6 Jan 2025

Works with Cytoscape 3.9

Download Stats Click here

cytoscapenot running