Fetch neuprint metadata for MANC neurons
Usage
manc_neuprint_meta(
ids = NULL,
conn = manc_neuprint(),
cache = NA,
roiInfo = FALSE,
fields.regex.exclude = NULL,
fields.regex.include = NULL,
...
)Arguments
- ids
A set of body ids in any form understandable to
manc_ids- conn
Optional, a
neuprint_connectionobject, which also specifies the neuPrint server. Defaults tomanc_neuprint()to ensure that query is against the VNC dataset.- cache
whether to cache the query. When
cache=NA(the default) queries are cached for neuprint snapshot versions (but not production datasets). See details.- roiInfo
whether to include the
roiInfofield detailing synapse numbers in different locations. This is omitted by default as it is returned as a character vector of unprocessed JSON.- fields.regex.exclude, fields.regex.include
Optional regular expressions to define fields to include or exclude from the returned metadata.
- ...
Additional arguments passed to
neuprint_get_meta
Value
A data.frame with one row for each (unique) id and NAs for all columns except bodyid when neuprint holds no metadata.
Details
When ids = NULL then a default set of bodies is selected
using the manc_dvid_annotations function. Since April 2025
this uses the node='neuprint'. This should correspond to all neurons
with an annotation. You can also use other searches e.g. to fetch all
neurons, see examples.
This function will now cache neuprint queries when using a snapshot release
(which is assumed not to change). Snapshot releases are identified by
containing the string ":v" as in manc:v1.2.3. The cache
currently lasts for 24h.
Examples
# \donttest{
manc_neuprint_meta("DNp01")
#> bodyid post pre downstream upstream synweight class description
#> 1 10000 2002 1027 4318 2002 6320 descending neuron Giant fiber
#> 2 10002 1902 933 3826 1902 5728 descending neuron Giant fiber
#> entryNerve exitNerve group name longTract ntAcetylcholineProb
#> 1 CvC None 10000 DNlt002_CvC_R none 0.5142120
#> 2 CvC None 10000 DNlt002_CvC_L none 0.4596285
#> ntGabaProb ntGlutamateProb ntUnknownProb origin location
#> 1 0.1707151 0.2175471 0.09752578 brain 24481,36044,67070
#> 2 0.1434814 0.2562304 0.14065966 brain 23217,35252,67070
#> locationType predictedNtProb prefix rootLocation rootSide statusLabel
#> 1 neck 0.5142120 DN 24481,36044,67070 RHS Roughly traced
#> 2 neck 0.4596285 DN 23217,35252,67070 LHS Roughly traced
#> subclass synonyms systematicType target transmission type
#> 1 lt GF, Giant Fiber DNlt002 LTct_RL electrical DNp01
#> 2 lt GF, Giant Fiber DNlt002 LTct_RL electrical DNp01
#> vfbId modality tag somaSide cluster subcluster avgLocation birthtime
#> 1 VFB_jrcv07ps <NA> <NA> <NA> NA NA <NA> <NA>
#> 2 VFB_jrcv07pu <NA> <NA> <NA> NA NA <NA> <NA>
#> hemilineage serial serialMotif somaNeuromere subclassabbr receptorType
#> 1 <NA> NA <NA> <NA> <NA> <NA>
#> 2 <NA> NA <NA> <NA> <NA> <NA>
#> tosomaLocation source somaLocation status totalNtPredictions predictedNt
#> 1 <NA> <NA> <NA> Traced 1027 acetylcholine
#> 2 <NA> <NA> <NA> Traced 933 acetylcholine
#> celltypeTotalNtPredictions celltypePredictedNt voxels fruDsx soma
#> 1 1960 acetylcholine 38743961712 <NA> FALSE
#> 2 1960 acetylcholine 39414880927 <NA> FALSE
# use of a full CYPHER query. NB Each field relating to the neuron must be
# be preceded by "n."
bignogroup <-
manc_neuprint_meta("where:NOT exists(n.group) AND n.synweight>5000 AND n.class CONTAINS 'neuron'")
head(bignogroup)
#> bodyid post pre downstream upstream synweight class description
#> 1 28027 437 456 4868 437 5305 sensory neuron <NA>
#> 2 19177 411 569 4629 411 5040 sensory neuron <NA>
#> 3 20240 594 601 4447 594 5041 sensory neuron unusual
#> 4 13967 912 644 4252 912 5164 sensory neuron <NA>
#> 5 17446 724 655 4455 724 5179 sensory neuron <NA>
#> 6 171382 746 541 4320 746 5066 sensory neuron <NA>
#> entryNerve exitNerve group name longTract ntAcetylcholineProb
#> 1 MesoLN_R <NA> NA SNppxx_MesoLN_R <NA> 0.5811309
#> 2 AbNT_R <NA> NA SNxx23_AbNT_R <NA> 0.9122434
#> 3 MetaLN_R <NA> NA SNxx29_MetaLN_R <NA> 0.7210513
#> 4 AbNT_L <NA> NA SNxx10_AbNT_L <NA> 0.8687301
#> 5 AbNT_R <NA> NA SNxx23_AbNT_R <NA> 0.8022338
#> 6 AbNT_R <NA> NA SNxx07_AbNT_R <NA> 0.8937346
#> ntGabaProb ntGlutamateProb ntUnknownProb origin location
#> 1 0.03783341 0.36905804 0.011977710 mesothoracic leg 25981,36162,29442
#> 2 0.03305553 0.04326012 0.011440937 abdomen 25729,12900,7969
#> 3 0.22840150 0.03870988 0.011837316 metathoracic leg 23896,22133,19804
#> 4 0.05167811 0.06977998 0.009811865 abdomen 22095,14384,8847
#> 5 0.07676595 0.09062613 0.030374181 abdomen 25555,14853,7796
#> 6 0.03987283 0.05699900 0.009393622 abdomen 27032,12900,7461
#> locationType predictedNtProb prefix rootLocation rootSide
#> 1 auto 0.5811309 SN 27866,36885,22115 RHS
#> 2 auto 0.9122434 SN 26421,8062,16 RHS
#> 3 auto 0.7210513 SN 32867,17818,7495 RHS
#> 4 auto 0.8687301 SN 25947,7375,16 LHS
#> 5 auto 0.8022338 SN 26876,7774,15 RHS
#> 6 user 0.8937346 <NA> 26665,8341,29 RHS
#> statusLabel subclass synonyms systematicType
#> 1 Prelim Roughly traced <NA> <NA> SNppxx
#> 2 Prelim Roughly traced <NA> <NA> SNxx23
#> 3 Prelim Roughly traced <NA> ppk heat nociceptive SNxx29
#> 4 Prelim Roughly traced <NA> <NA> SNxx10
#> 5 Prelim Roughly traced <NA> <NA> SNxx23
#> 6 Prelim Roughly traced <NA> <NA> SNxx07
#> target transmission type vfbId modality tag
#> 1 LegNpT2_R <NA> SNppxx VFB_jrcv0lmj proprioceptive 15.08.h3
#> 2 ANm <NA> SNxx23 VFB_jrcv0esp unknown <NA>
#> 3 LegNpT3_R.ANm <NA> SNxx29 VFB_jrcv0fm8 unknown <NA>
#> 4 ANm <NA> SNxx10 VFB_jrcv0arz unknown <NA>
#> 5 ANm <NA> SNxx23 VFB_jrcv0dgm unknown <NA>
#> 6 ANm <NA> SNxx07 VFB_jrcv3o8m unknown <NA>
#> somaSide cluster subcluster avgLocation birthtime hemilineage serial
#> 1 <NA> NA NA <NA> <NA> <NA> NA
#> 2 <NA> 38 75 <NA> <NA> <NA> NA
#> 3 <NA> 43 33 <NA> <NA> <NA> 20453
#> 4 <NA> 25 68 <NA> <NA> <NA> NA
#> 5 <NA> 38 75 <NA> <NA> <NA> NA
#> 6 <NA> 22 67 <NA> <NA> <NA> NA
#> serialMotif somaNeuromere subclassabbr receptorType tosomaLocation source
#> 1 <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA> <NA> <NA>
#> 4 <NA> <NA> <NA> <NA> <NA> <NA>
#> 5 <NA> <NA> <NA> <NA> <NA> <NA>
#> 6 <NA> <NA> <NA> <NA> <NA> <NA>
#> somaLocation status totalNtPredictions predictedNt
#> 1 <NA> Traced 456 acetylcholine
#> 2 <NA> Traced 569 acetylcholine
#> 3 <NA> Traced 601 acetylcholine
#> 4 <NA> Traced 644 acetylcholine
#> 5 <NA> Traced 655 acetylcholine
#> 6 <NA> Traced 541 acetylcholine
#> celltypeTotalNtPredictions celltypePredictedNt voxels fruDsx soma
#> 1 45044 glutamate 225825889 <NA> FALSE
#> 2 18960 acetylcholine 589533979 <NA> FALSE
#> 3 9470 acetylcholine 566489384 <NA> FALSE
#> 4 11136 acetylcholine 1243780740 <NA> FALSE
#> 5 18960 acetylcholine 750977826 <NA> FALSE
#> 6 16834 acetylcholine 465918537 <NA> FALSE
# }
if (FALSE) { # \dontrun{
# fetch all neurons
allneurons <- manc_neuprint_meta('where:exists(n.bodyId)')
# in theory you could do this, but it often seems to time out:
allsegs=neuprintr::neuprint_ids('where:exists(n.bodyId)', all_segments=TRUE)
} # }