Include neuron list of superclusters and clusters from nblast online?

natverse / nat.nblast

R package implementing the NBLAST neuron search algorithm, as an add-on for the NeuroAnatomy Toolbox (nat) R package.

http://natverse.org/nat.nblast/

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Include neuron list of superclusters and clusters from nblast online? #33

Closed jennyl617 closed 8 years ago

jennyl617 commented 8 years ago

I was wondering if you had a dataset listing all the neurons belonging to each cluster/supercluster from online in your nblast R package, or whether this information is only accessible on the website. Thanks very much!

edit: Just found https://github.com/jefferislab/NBLAST_clusters_online --thanks!

jefferis commented 8 years ago

Thanks for your interest. You can access this information using the https://github.com/jefferis/flycircuit package.

library(flycircuit)
apres16k.p0=load_si_data('apres16k.p0.rds')
apdf=as.data.frame(apres16k.p0)
str(apdf)

You can take a look at the source code for the figures at http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/www/paper/ and https://github.com/jefferislab/NBLAST_figures. If you need more help, please contact us via https://groups.google.com/forum/embed/?place=forum/nat-user#!forum/nat-user.

jennyl617 commented 8 years ago

Just a quick question: I noticed I get different flycircuit ids when I do the following: fc_idid(apdf$item[(apdf$cluster == 1)]) versus apdf$idx[(apdf$cluster == 1)]

Did I perhaps miss something? Looks like the ids for the first half of the list are correct, but begin to diverge afterward. Thanks so much for your help!

jefferis commented 8 years ago

The first form using fcidid is correct. The other id is not a flycircuit id but a sequential number generated in the clustering. In general I recommend referring to neurons using the character identifiers to avoid such ambiguities.