search

robertaboukhalil / ginkgo

Cloud-based single-cell copy-number variation analysis tool
qb.cshl.edu/ginkgo
BSD 2-Clause "Simplified" License
47 stars 28 forks source link

Phylogenetic Tree output? #5

Closed jmfa closed 7 years ago

jmfa commented 7 years ago

Dear Robert,

I'm currently using the standalone version of ginkgo and am wondering how can I build a phylogenetic tree from the data? In the web-based platform, there's a tree in the results (which according to the paper is estimated by "first computing the Pearson correlation between all samples and using these dissimilarity values to cluster the samples"). However, in the standalone version, I don't get such tree. Instead, I just get the different dendrograms derived from the heatmaps.

jherrero commented 7 years ago

The dendrograms are the different trees that Ginkgo pre-computes. You get all the trees in JPEG, in PDF, in XML (phyloXML) and in Newick format. If you want to read the tree in R, have a look at the ape package. If you are after the interactive tree, I am afraid the standalone version does not offer that functionality.

I hope this helps

jmfa commented 7 years ago

Right, yes. I was looking for the interactive tree. Thanks for the quick and helpful reply, @jherrero.

robertaboukhalil commented 7 years ago

Thanks @jherrero!