Fetch neuprint metadata for MANC neurons
Usage
manc_neuprint_meta(
ids = NULL,
conn = manc_neuprint(),
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.- 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.
Examples
# \donttest{
manc_neuprint_meta("DNp01")
#> bodyid post pre downstream upstream synweight totalNtPredictions
#> 1 10000 2002 1027 4318 2002 6320 1027
#> 2 10002 1902 933 3826 1902 5728 933
#> predictedNt celltypeTotalNtPredictions celltypePredictedNt voxels
#> 1 acetylcholine 1960 acetylcholine 38743961712
#> 2 acetylcholine 1960 acetylcholine 39414880927
#> class entryNerve name ntAcetylcholineProb ntGabaProb
#> 1 descending neuron CvC DNlt002_CvC_R 0.5142119 0.1707151
#> 2 descending neuron CvC DNlt002_CvC_L 0.4596285 0.1434814
#> ntGlutamateProb ntUnknownProb origin location locationType
#> 1 0.2175471 0.09752578 brain 24481,36044,67070 neck
#> 2 0.2562304 0.14065966 brain 23217,35252,67070 neck
#> predictedNtProb prefix rootLocation rootSide statusLabel subclass
#> 1 0.5142119 DN 24481,36044,67070 RHS Roughly traced lt
#> 2 0.4596285 DN 23217,35252,67070 LHS Roughly traced lt
#> synonyms systematicType target type vfbId modality tag
#> 1 GF, Giant Fiber DNlt002 LTct_RL DNp01 VFB_jrcv07ps <NA> <NA>
#> 2 GF, Giant Fiber DNlt002 LTct_RL DNp01 VFB_jrcv07pu <NA> <NA>
#> cluster subcluster receptorType status group somaSide birthtime hemilineage
#> 1 NA NA <NA> Traced 10000 <NA> <NA> <NA>
#> 2 NA NA <NA> Traced 10000 <NA> <NA> <NA>
#> serial serialMotif somaNeuromere somaLocation description avgLocation
#> 1 NA <NA> <NA> <NA> Giant fiber <NA>
#> 2 NA <NA> <NA> <NA> Giant fiber <NA>
#> exitNerve subclassabbr transmission tosomaLocation longTract source soma
#> 1 None <NA> electrical <NA> none <NA> FALSE
#> 2 None <NA> electrical <NA> none <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 totalNtPredictions
#> 1 28027 437 456 4868 437 5305 456
#> 2 19177 411 569 4629 411 5040 569
#> 3 20240 594 601 4447 594 5041 601
#> 4 13967 912 644 4252 912 5164 644
#> 5 17446 724 655 4455 724 5179 655
#> 6 171382 746 541 4320 746 5066 541
#> predictedNt celltypeTotalNtPredictions celltypePredictedNt voxels
#> 1 acetylcholine 45044 glutamate 225825889
#> 2 acetylcholine 18960 acetylcholine 589533979
#> 3 acetylcholine 9470 acetylcholine 566489384
#> 4 acetylcholine 11136 acetylcholine 1243780740
#> 5 acetylcholine 18960 acetylcholine 750977826
#> 6 acetylcholine 16834 acetylcholine 465918537
#> class entryNerve name ntAcetylcholineProb ntGabaProb
#> 1 sensory neuron MesoLN_R SNppxx_MesoLN_R 0.5811309 0.03783341
#> 2 sensory neuron AbNT_R SNxx23_AbNT_R 0.9122434 0.03305553
#> 3 sensory neuron MetaLN_R SNxx29_MetaLN_R 0.7210513 0.22840150
#> 4 sensory neuron AbNT_L SNxx10_AbNT_L 0.8687301 0.05167811
#> 5 sensory neuron AbNT_R SNxx23_AbNT_R 0.8022338 0.07676595
#> 6 sensory neuron AbNT_R SNxx07_AbNT_R 0.8937346 0.03987283
#> ntGlutamateProb ntUnknownProb origin location locationType
#> 1 0.36905804 0.011977710 mesothoracic leg 25981,36162,29442 auto
#> 2 0.04326012 0.011440937 abdomen 25729,12900,7969 auto
#> 3 0.03870988 0.011837316 metathoracic leg 23896,22133,19804 auto
#> 4 0.06977999 0.009811865 abdomen 22095,14384,8847 auto
#> 5 0.09062613 0.030374180 abdomen 25555,14853,7796 auto
#> 6 0.05699900 0.009393622 abdomen 27032,12900,7461 user
#> predictedNtProb prefix rootLocation rootSide statusLabel
#> 1 0.5811309 SN 27866,36885,22115 RHS Prelim Roughly traced
#> 2 0.9122434 SN 26421,8062,16 RHS Prelim Roughly traced
#> 3 0.7210513 SN 32867,17818,7495 RHS Prelim Roughly traced
#> 4 0.8687301 SN 25947,7375,16 LHS Prelim Roughly traced
#> 5 0.8022338 SN 26876,7774,15 RHS Prelim Roughly traced
#> 6 0.8937346 <NA> 26665,8341,29 RHS Prelim Roughly traced
#> subclass synonyms systematicType target type
#> 1 <NA> <NA> SNppxx LegNpT2_R SNppxx
#> 2 <NA> <NA> SNxx23 ANm SNxx23
#> 3 <NA> ppk heat nociceptive SNxx29 LegNpT3_R.ANm SNxx29
#> 4 <NA> <NA> SNxx10 ANm SNxx10
#> 5 <NA> <NA> SNxx23 ANm SNxx23
#> 6 <NA> <NA> SNxx07 ANm SNxx07
#> vfbId modality tag cluster subcluster receptorType status
#> 1 VFB_jrcv0lmj proprioceptive 15.08.h3 NA NA <NA> Traced
#> 2 VFB_jrcv0esp unknown <NA> 38 75 <NA> Traced
#> 3 VFB_jrcv0fm8 unknown <NA> 43 33 <NA> Traced
#> 4 VFB_jrcv0arz unknown <NA> 25 68 <NA> Traced
#> 5 VFB_jrcv0dgm unknown <NA> 38 75 <NA> Traced
#> 6 VFB_jrcv3o8m unknown <NA> 22 67 <NA> Traced
#> group somaSide birthtime hemilineage serial serialMotif somaNeuromere
#> 1 NA <NA> <NA> <NA> NA <NA> <NA>
#> 2 NA <NA> <NA> <NA> NA <NA> <NA>
#> 3 NA <NA> <NA> <NA> 20453 <NA> <NA>
#> 4 NA <NA> <NA> <NA> NA <NA> <NA>
#> 5 NA <NA> <NA> <NA> NA <NA> <NA>
#> 6 NA <NA> <NA> <NA> NA <NA> <NA>
#> somaLocation description avgLocation exitNerve subclassabbr transmission
#> 1 <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 <NA> unusual <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>
#> tosomaLocation longTract source soma
#> 1 <NA> <NA> <NA> FALSE
#> 2 <NA> <NA> <NA> FALSE
#> 3 <NA> <NA> <NA> FALSE
#> 4 <NA> <NA> <NA> FALSE
#> 5 <NA> <NA> <NA> FALSE
#> 6 <NA> <NA> <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)
} # }