Return clio-store body annotations for set of ids or a flexible query
Source:R/annotations.R
manc_body_annotations.Rdclio_fields returns all the fields currently known to
exist in the clio store for a given dataset. A short description...
Arguments
- ids
A set of body ids in any form understandable to
manc_ids- query
A json query string (see examples or documentation) or an R list with field names as elements.
- json
Whether to return unparsed JSON rather than an R list (default
FALSE).- config
An optional httr::config (expert use only, must include a bearer token)
- cache
Whether to cache the result of this call for 5 minutes.
- update.bodyids
Whether to update the bodyid associated with annotations based on the position field. The default value of this has been switched to
FALSEas of Feb 2022.- test
Whether to unset the clio-store test server (default
FALSE)- show.extra
Extra columns to show with user/timestamp information.
- ...
Additional arguments passed to
pbapply::pblapply- dataset
short name of the dataset (VNC or CNS)
Value
An R data.frame or a character vector containing JSON (when
json=TRUE). Two additional fields will be added
original.bodyid When
update.bodyids=TRUEthis field contains the original bodyid from Clio whereasbodyidcontains the updated value implied by the position.autoTRUEsignals that the record contains only data automatically copied over from DVID without any manual annotation.See slack for details of the position / position type fields.
Details
Missing values in each output column are filled with NA. But if a whole column is missing from the results of a particular query then it will not appear at all.
When neither query and ids are missing then we return all
entries in the clio store database. This currently includes annotations for
all body ids - even the ones that are no longer current.
See also
swagger docs or basic docs from Bill Katz.
Other manc-annotation:
manc_annotate_body(),
manc_meta(),
manc_point_annotations()
Examples
if (FALSE) { # \dontrun{
manc_body_annotations(ids=11442)
manc_body_annotations(ids=11442, show.extra='user')
manc_body_annotations(query='{"hemilineage": "0B"}')
manc_body_annotations(query=list(user="janedoe@gmail.com"))
manc_body_annotations(query=list(soma_side="RHS"))
manc_body_annotations(ids=manc_xyz2bodyid(mancneckseeds))
# use clio node to ensure for bodyid consistency
manc_body_annotations(ids=
manc_xyz2bodyid(mancneckseeds, node="clio"))
# fetch all bodyids
mba=manc_body_annotations()
} # }
clio_fields()
#> [1] "systematic_type_time" "position_type"
#> [3] "long_tract" "root_side_user"
#> [5] "predicted_nt" "typing_notes_time"
#> [7] "source" "systematic_type_user"
#> [9] "subcluster_time" "tag_user"
#> [11] "group_old_user" "type_user"
#> [13] "hemilineage" "soma_side_time"
#> [15] "birthtime_time" "subcluster"
#> [17] "entry_nerve_user" "status"
#> [19] "nt_gaba_prob_user" "nt_acetylcholine_prob_user"
#> [21] "group_time" "serial_motif_time"
#> [23] "tag_time" "source_time"
#> [25] "user" "target_user"
#> [27] "synonyms_time" "description"
#> [29] "typing_notes_user" "subclassabbr"
#> [31] "subclass" "bodyid"
#> [33] "user_user" "soma_position_user"
#> [35] "typing_notes" "soma_position_time"
#> [37] "soma_position" "naming_user"
#> [39] "entry_nerve_time" "predicted_nt_user"
#> [41] "nt_acetylcholine_prob_time" "root_position_user"
#> [43] "prefix_time" "group_old"
#> [45] "class_time" "to_review_time"
#> [47] "soma_neuromere_user" "avg_location_user"
#> [49] "cluster_user" "position_type_user"
#> [51] "confidence_user" "naming_user_user"
#> [53] "tosoma_position_time" "target_time"
#> [55] "group_user" "description_time"
#> [57] "synonyms" "subcluster_user"
#> [59] "hemilineage_time" "position"
#> [61] "subclass_time" "vfb_id"
#> [63] "user_time" "prefix_user"
#> [65] "source_user" "avg_location"
#> [67] "birthtime" "serial_motif"
#> [69] "confidence_time" "cluster"
#> [71] "systematic_type" "group"
#> [73] "receptor_type" "reviewer_user"
#> [75] "neuropils_axonal" "nt_gaba_prob"
#> [77] "transmission_time" "position_user"
#> [79] "neuropils_dendritic_time" "old_bodyids_user"
#> [81] "tosoma_position" "instance_time"
#> [83] "nt_glutamate_prob_time" "transmission"
#> [85] "serial_user" "receptor_type_time"
#> [87] "modality_user" "instance_user"
#> [89] "nt_unknown_prob" "class"
#> [91] "confidence" "modality"
#> [93] "root_position_time" "root_side"
#> [95] "naming_user_time" "old_bodyids"
#> [97] "root_position" "type_time"
#> [99] "neuropils_dendritic" "position_type_time"
#> [101] "vfb_id_time" "class_user"
#> [103] "exit_nerve" "serial_time"
#> [105] "cluster_time" "description_user"
#> [107] "predicted_nt_prob_user" "origin"
#> [109] "synonyms_user" "nt_glutamate_prob_user"
#> [111] "soma_side" "avg_location_time"
#> [113] "neuropils_dendritic_user" "old_bodyids_time"
#> [115] "prefix" "root_side_time"
#> [117] "nt_acetylcholine_prob" "reviewer_time"
#> [119] "subclassabbr_user" "exit_nerve_user"
#> [121] "subclass_user" "vfb_id_user"
#> [123] "position_time" "reviewer"
#> [125] "long_tract_user" "predicted_nt_time"
#> [127] "predicted_nt_prob" "soma_neuromere_time"
#> [129] "subclassabbr_time" "neuropils_axonal_user"
#> [131] "origin_time" "nt_glutamate_prob"
#> [133] "predicted_nt_prob_time" "nt_gaba_prob_time"
#> [135] "receptor_type_user" "type"
#> [137] "modality_time" "group_old_time"
#> [139] "to_review" "soma_neuromere"
#> [141] "serial" "transmission_user"
#> [143] "serial_motif_user" "tag"
#> [145] "neuropils_axonal_time" "target"
#> [147] "nt_unknown_prob_user" "instance"
#> [149] "to_review_user" "tosoma_position_user"
#> [151] "hemilineage_user" "birthtime_user"
#> [153] "exit_nerve_time" "long_tract_time"
#> [155] "origin_user" "status_user"
#> [157] "status_time" "nt_unknown_prob_time"
#> [159] "entry_nerve" "soma_side_user"