We’d like to communicate two things: We have released a new version of Gitools which brings new capabilities. With these the new Gitools 2.1.0 in the suitcase, Nuria and myself are traveling to Heidelberg, to give a tutorial session at the Vizualizing Biological data conference (VIZBI).
Hierarchical Clustering in Gitools
The new version of Gitools (2.1) contains many internal changes and improvements for usability and analyses. Below we list the new main features which we will try to explain in more detail in upcoming posts.
- File import: Any flat text file containing values may now be imported to Gitools.
- Data integration: Via file import it is possible to load new data layers on an existing heatmap. You have a heatmap with methylation values and now the mutations have come in? Just load them as an additional value for each cell.
- Group Comparisons may now be done much more easily and for a series of groups at once. Group by annotations, values or without constraints and check for differences between two groups of samples.
- Bookmarks: Gitools heatmaps can now be bookmarked. Save a constellation of visible rows and columns in their order and the value being viewed.
- Clustering: The clustering code has been improved. We tackled in particular the difficulty of combining hierarchical clustering and interactive heatmaps. Besides that a classical newick tree is being generated, the heatmap is annotated with colored clusters representing the tree and its splits. Thus the order of the heatmap may be changed without invalidating the hierarchical tree.
There are many more things to discover in the details, especially within contextual menus.
If you want to try it yourself you can follow the step-by-step Tutorial we have prepared for VIZBI at http://www.gitools.org/vizbi
Let us know if you have questions.