Java TreeView like tools

Question

[1769mkc]

I have tried javaTreeview tools its really handy to view heatmap along with the clustering it forms .But this seem to be quite old not being updated .Are there any other tool similar to JavaTreeview ?Do suggest

[Jean-Karim Heriche]

A software being old and not updated is not necessarily a bad thing especially if it is still being used. It could mean the tool is stable, no new bugs are found and there are no need for new functionality. It's often a pain when tools are updated too often.

[rleach]

It is being updated, in fact: http://treeview.princeton.edu. We're on the cusp of the first beta release. Final code review in process. Prepping publication too.

[GouthamAtla]

Honestly, I liked the previous version. It looks very complicated now.

[1769mkc]

wow...after 9 months of my query i see the new one..cool will give it a try

[GenoMax]

rleach : Please make an official announcement when ready.

[1769mkc]

@rleach I guess i can give it a try it won;t be an issue i suppose..

Answer 1

[GouthamAtla]

Never saw a better alternative GUI to JavaTreeview in terms of searching and selecting subset of genes and playing around.

For plotting, I use ComplexHeatmap which allows many customisations.

[1769mkc]

in complex heatmap i can take out gene clusters ...with gene name but not unlike JavaTree view...

[GouthamAtla]

Yes. There is no easy tool to search the genes like in javaTreeView. But complex heatmap provides lot of customizations to make nice heatmaps and to annotate them. It takes a while to get used to it.

Answer 2

[Hugo]

If you are interested in a Java library only for heatmap visualization, then you can have a look at GC4S (https://github.com/hlfernandez/GC4S/), which includes a JHeatMap component to create interactive, customizable heatmaps. For heatmap and dendogram visualization, I also think that JavaTreeview is a very good option.

Answer 3

[Jean-Karim Heriche]

Many of the R heatmap packages provide similar functions.