Question: Java TreeView like tools
0
gravatar for krushnach80
2.8 years ago by
krushnach80740
krushnach80740 wrote:

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

rna-seq • 1.4k views
ADD COMMENTlink modified 2.8 years ago by Hugo280 • written 2.8 years ago by krushnach80740
3

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.

ADD REPLYlink written 2.8 years ago by Jean-Karim Heriche22k
1

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.

ADD REPLYlink written 2.1 years ago by rleach120

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

ADD REPLYlink written 2.1 years ago by geek_y11k

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

ADD REPLYlink written 2.1 years ago by krushnach80740

rleach : Please make an official announcement when ready.

ADD REPLYlink written 2.1 years ago by genomax83k

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

ADD REPLYlink written 2.1 years ago by krushnach80740
3
gravatar for geek_y
2.8 years ago by
geek_y11k
Barcelona
geek_y11k wrote:

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.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by geek_y11k

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

ADD REPLYlink written 2.8 years ago by krushnach80740
1

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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by geek_y11k
1
gravatar for Hugo
2.8 years ago by
Hugo280
Universidade de Vigo, Ourense (Spain)
Hugo280 wrote:

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.

ADD COMMENTlink written 2.8 years ago by Hugo280
0
gravatar for Jean-Karim Heriche
2.8 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

Many of the R heatmap packages provide similar functions.

ADD COMMENTlink written 2.8 years ago by Jean-Karim Heriche22k
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