New features in the NG-CHM Galaxy Tool

Version 2.3

This release includes a re-engineered system for processing parameters specified in the Galaxy build tool that is a lot more flexible than the previous method. Consequently, we have extended the Advanced NG-CHM Generator tool to include several new capabilities in the NG-CHM that were not possible previously.

  • You can add multiple data matrices to a heat map. All matrices should have the same rows and columns. Each matrix is shown as a separate data layer in the viewer. For each layer you can specify:
    • custom colors and breakpoints,
    • the selection box color,
    • the color for gaps in the heat map,
    • whether or not to show a grid on the detail map, and if so
    • the color to use for the detail map grid.
  • The initial proportion of the display to use for the summary panel.
  • Whether to display row and/or column dendrograms on the summary heat map only, on both the summary and detail heat maps, or not at all.
  • The relative size of the dendrograms, if displayed.
  • The thickness of covariate bars.
  • The foreground and background colors for continuous covariate bars that are displayed as scatter or bar plots.

The included NG-CHM viewer also includes several significant enhancements:

  • The heat map preferences panel now displays the builder (NG-CHM GUI, Shaidy, Galaxy) and version used to create the heat map.
  • The viewer’s About dialog now includes details for citing the NG-CHM system.
  • The About and Help dialogs are now available in file mode viewer before an NG-CHM is selected, or if a map cannot be loaded.
  • You can search covariate values (e.g. “ovarian” to find ovarian samples in a big heatmap).
  • All modal pop-up panels are now moveable.
  • The appearance of context “bubble help” has been improved.
  • The color to use for heat map gaps can now be edited.