Description Usage Arguments Value Examples
NBLAST a single flycircuit neuron against database and return scores
flycircuit_gmr_topn
finds the top GMR Gal4 lines matching
a FlyCircuit neuron query.
1 2 3 | flycircuit_topn(query, n = 50, ...)
flycircuit_gmr_topn(query, n = 50)
|
query |
A flycircuit identifier |
n |
The number of scores to return (if |
... |
Additional arguments passed to |
a data.frame in descending score order with columns
id Flycircuit Neuron name (or GMR id for flycircuit_gmr_topn
)
score NBLAST score (normalised -1 (bad) to +1 (perfect)). Scores above 0 are potentially interesting, scores above about 0.4 seriously interesing.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 | ## Not run:
## example of remote call via curl
## simple version collecting json results directly (RECOMMENDED)
curl http://vfbdev.inf.ed.ac.uk/ocpu/library/flynblastscores/R/flycircuit_topn/json \
-d 'query="FruMARCM-M002262_seg001"'
# top 3 hits only
curl http://vfbdev.inf.ed.ac.uk/ocpu/library/flynblastscores/R/flycircuit_topn/json \
-d 'query="FruMARCM-M002262_seg001"&n=3'
## more flexible version
curl http://vfbdev.inf.ed.ac.uk/ocpu/library/flynblastscores/R/flycircuit_topn \
-d 'query="FruMARCM-M002262_seg001"'
# (return value looks like this and includes sesion key)
/ocpu/tmp/x05f62b2975/R/.val
/ocpu/tmp/x05f62b2975/messages
/ocpu/tmp/x05f62b2975/stdout
/ocpu/tmp/x05f62b2975/source
/ocpu/tmp/x05f62b2975/console
/ocpu/tmp/x05f62b2975/info
/ocpu/tmp/x05f62b2975/files/DESCRIPTION
# now collect results
curl http://vfbdev.inf.ed.ac.uk/ocpu/tmp/x05f62b2975/R/.val/json
curl http://vfbdev.inf.ed.ac.uk/ocpu/tmp/x05f62b2975/R/.val/csv
# specify number of hits, use "neuron" identifier
curl http://vfbdev.inf.ed.ac.uk/ocpu/library/flynblastscores/R/flycircuit_topn \
-d 'query="fru-M-200266"&n=10'
## End(Not run)
# NBLAST a flycircuit neuron
qid="VGlut-F-100184"
res=flycircuit_gmr_topn(qid)
res
# return all results
resall=flycircuit_gmr_topn(qid, n=0)
nrow(resall)
# look at co-registered top hits on VFB
if(require('vfbr')){
# find vfb ids for hits
vfbids=vfbr::gmr_vfbid(res$id)
# find vfb id for query
qvfbid=vfb_tovfbids(qid)
# stack browser URL for query neuron and top 10 hits
u=vfb_stack_url(rev(c(qvfbid, vfbids[1:10])), clear = TRUE)
## Not run:
browseURL(u)
## End(Not run)
}
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