Query VFB's Neo4J graph database
Usage
vfb_neo4j_query(
x,
...,
path = "db/data",
server = getOption("vfbr.server.neo4j")
)Arguments
- x
A character query in Neo4J's cypher language
- ...
Additional arguments passed to
neo2R::cypher()- path
The relative path on the server for the Neo4J endpoint
- server
The server's root URL
Details
Under the hood, this uses the RNeo4j::cypher function to call
a Neo4J service running on the specified VFB server.
See also
RNeo4j::RNeo4j, RNeo4j::cypher and
https://neo4j.com/docs/rest-docs/3.3/
Other query:
vfb_owl_query(),
vfb_solr_query()
Examples
# \donttest{
# ask for all neuronal classes
nclasses=vfb_neo4j_query("MATCH (n:Neuron:Class) RETURN n.label")
nrow(nclasses)
#> [1] 14247
head(nclasses)
#> n.label
#> 1 adult Drosulfakinin neuron
#> 2 adult natalisin small pars intercerebralis neuron
#> 3 labellar taste bristle mechanosensory neuron
#> 4 wedge projection neuron
#> 5 wind sensitive wedge projection neuron
#> 6 interoceptive SEZ neuron
# Find all images with an associated neuronal class
q=paste("MATCH (p:Class:Neuron)<-[:INSTANCEOF]-(i:Individual:has_image)",
"RETURN distinct i.label, p.label, p.symbol;")
nclasses_image=vfb_neo4j_query(q)
nrow(nclasses_image)
#> [1] 98821
head(nclasses_image)
#> i.label p.label p.symbol
#> 1 WEDPN13_R (FlyEM-HB:5812989041) wedge projection neuron WPN
#> 2 WEDPN13_R (FlyEM-HB:5813023929) wedge projection neuron WPN
#> 3 WEDPN14_R (FlyEM-HB:1080886521) wedge projection neuron WPN
#> 4 WEDPN17_c_R (FlyEM-HB:1224069121) wedge projection neuron WPN
#> 5 WEDPN17_a_R (FlyEM-HB:1386858837) wedge projection neuron WPN
#> 6 WEDPN15_R (FlyEM-HB:5813018784) wedge projection neuron WPN
# how many neuronal classes have images?
length(unique(nclasses_image$p.label))
#> [1] 5968
# look at number of images for each neuronal class
# NB some of these are rather generic classes where
# a specific cell type annotation was not available.
table_by_nclass <- table(nclasses_image$p.label)
subset(as.data.frame(table_by_nclass), Freq>200)
#> Var1 Freq
#> 91 adult ALl1 lineage neuron 284
#> 106 adult DM6 lineage neuron 294
#> 114 adult GABAergic neuron 6534
#> 149 adult alpha'/beta' Kenyon cell 264
#> 1041 adult cholinergic neuron 15119
#> 1521 adult dopaminergic neuron 2431
#> 1572 adult fan-shaped body 1 column-crepine neuron 254
#> 1575 adult fan-shaped body 1 column-superior medial protocerebrum neuron 277
#> 1620 adult fan-shaped body vertical delta neuron 354
#> 1624 adult fruitless MB neuron 682
#> 1700 adult gamma Kenyon cell 1040
#> 1701 adult glutamatergic neuron 5666
#> 2573 adult multiglomerular antennal lobe projection neuron 210
#> 2658 adult neuron 18026
#> 5060 alpha/beta Kenyon cell 629
#> 5061 alpha/beta core Kenyon cell 1019
#> 5063 alpha/beta surface Kenyon cell 595
#> 5064 alpha/beta surface/core Kenyon cell 211
#> 5073 antennal lobe projection neuron of ALl1 lineage 281
#> 5217 embryonic/larval neuron 4104
#> 5224 gamma main Kenyon cell 614
#> 5634 larval mushroom body second order output neuron 208
#> 5708 lobula columnar neuron LC10 627
#> 5710 lobula columnar neuron LC12 439
#> 5742 lobula-lobula plate columnar neuron LLPC 328
#> 5764 medial antennal lobe tract projection neuron 248
#> 5769 medulla columnar neuron MC61 347
#> 5792 mushroom body dopaminergic neuron 1933
#> 5835 neuron 7288
# }