Specify ids for fly connectome datasets
Usage
cf_ids(
query = NULL,
datasets = c("brain", "vnc", "hemibrain", "flywire", "malecns", "manc", "fanc",
"opticlobe", "banc", "yakubavnc"),
expand = FALSE,
keys = FALSE,
hemibrain = NULL,
flywire = NULL,
malecns = NULL,
manc = NULL,
fanc = NULL,
opticlobe = NULL,
banc = NULL,
yakubavnc = NULL,
...
)
# S3 method for class 'cidlist'
c(..., unique = TRUE)Arguments
- query
A query (e.g. cell type name or regular expression)
- datasets
Character vector naming datasets to which the
queryshould be applied.- expand
Whether to expand any queries into the matching ids (this will involve one or more calls to corresponding servers). Default
FALSE.- keys
Whether to turn the ids into keys
hb:12345right away. DefaultFALSEbut you may find this useful e.g. for combining lists of neurons (see examples).- hemibrain
Pass hemibrain specific query or ids to this argument
- flywire
Pass flywire specific query or ids to this argument
- malecns
Pass malecns specific query or ids to this argument
- manc
Pass manc specific query or ids to this argument
- fanc
Pass fanc ids to this argument (at present we do not support metadata queries for fanc)
- opticlobe
Pass opticlobe specific query or ids to this argument
- banc
Pass banc ids to this argument (we only support basic metadata queries for banc)
- yakubavnc
Pass yakuba VNC specific query or ids to this argument
- ...
One or more lists generated by
cf_idsthat should be joined together- unique
Whether to remove duplicated ids when combining cf_id lists with
c.cidlist
Details
You will often want to perform a query, most commonly for a cell
type or cell class, rather than specific numeric ids. The
most flexible way to do this is to use a regular expression (regex) query,
specified with an initial "/".
All neuprint datasets (hemibrain, malevnc, opticlobe, malecns) use the same
query syntax although some fields may be dataset specific (see examples).
The regex syntax for CAVE datasets (flywire, fanc, banc) should be the same
although you may find some wrinkles because the underlying data stores are
different. Note that we do not yet translate all the different fields
across datasets for queries, although this is a goal. For example the
neuprint/fanc/banc class field is equivalent to flywire
super_class. Similarly the values are not guaranteed to be the same.
Where flywire uses super_class=="descending") the manc uses
class=="descending neuron").
Therefore to find all DNs in these two datasets you will need to do:
cf_ids(manc='/class:descending.*',
flywire='/super_class:descending.*')
Feel free to make an issue if you find something that doesn't feel right or can suggest an improvement.
Additional datasets
coconatfly allows can be extended by
registering additional datasets using the
coconat::register_dataset function. You can use cf_ids
to support these additional datasets by passing additional named arguments.
The only inconvenience is that these will not be available for command
completion by your editor.
See also
Other ids:
keys()
Examples
# \donttest{
cf_ids("DA2_lPN", datasets='brain')
#> banc [1 ids]: DA2_lPN
#> flywire [1 ids]: DA2_lPN
#> hemibrain [1 ids]: DA2_lPN
#> malecns [1 ids]: DA2_lPN
# / introduces a regular expression
cf_ids("/MBON.+", datasets='brain')
#> banc [1 ids]: /MBON.+
#> flywire [1 ids]: /MBON.+
#> hemibrain [1 ids]: /MBON.+
#> malecns [1 ids]: /MBON.+
# expand query into actual ids
cf_ids("/type:MBON.+", datasets='brain', expand=TRUE)
#> Warning: Unable to process query for dataset:banc
#> banc [0 ids]:
#> flywire [96 ids]: 720575940624185095 720575940624117245 720575940638526278 720575940629585602 720575940637934308 720575940632118343 720575940609959637 720575940638163428 720575940630496374 720575940642142861 ...
#> hemibrain [71 ids]: 612371421 673509195 424789697 5813022341 487925037 612738462 487925063 613079053 1386512867 799586652 ...
#> malecns [98 ids]: 520151 10013 522444 522749 519373 521526 525780 530875 519371 10495 ...
# return keys directly
cf_ids("/type:MBON.+", keys=TRUE)
#> Warning: Unable to process query for dataset:banc
#> [1] "fw:720575940624185095" "fw:720575940624117245" "fw:720575940638526278"
#> [4] "fw:720575940629585602" "fw:720575940637934308" "fw:720575940632118343"
#> [7] "fw:720575940609959637" "fw:720575940638163428" "fw:720575940630496374"
#> [10] "fw:720575940642142861" "fw:720575940611344078" "fw:720575940634822751"
#> [13] "fw:720575940617552340" "fw:720575940624280328" "fw:720575940617567206"
#> [16] "fw:720575940643700640" "fw:720575940615221811" "fw:720575940614026193"
#> [19] "fw:720575940633209647" "fw:720575940623001480" "fw:720575940608304220"
#> [22] "fw:720575940614595218" "fw:720575940636992368" "fw:720575940621828443"
#> [25] "fw:720575940637902938" "fw:720575940638774606" "fw:720575940639697827"
#> [28] "fw:720575940626833021" "fw:720575940618008859" "fw:720575940635841143"
#> [31] "fw:720575940618249797" "fw:720575940629856515" "fw:720575940623905719"
#> [34] "fw:720575940629529722" "fw:720575940624659943" "fw:720575940624590316"
#> [37] "fw:720575940645304430" "fw:720575940612196850" "fw:720575940630767959"
#> [40] "fw:720575940635082347" "fw:720575940628757547" "fw:720575940627144069"
#> [43] "fw:720575940610647416" "fw:720575940622093436" "fw:720575940624696810"
#> [46] "fw:720575940629422086" "fw:720575940647328900" "fw:720575940650386553"
#> [49] "fw:720575940639556467" "fw:720575940612455338" "fw:720575940617749538"
#> [52] "fw:720575940617760257" "fw:720575940619810389" "fw:720575940634482783"
#> [55] "fw:720575940644615716" "fw:720575940626109315" "fw:720575940623377802"
#> [58] "fw:720575940626744921" "fw:720575940623464316" "fw:720575940622979277"
#> [61] "fw:720575940614892182" "fw:720575940620715224" "fw:720575940643863496"
#> [64] "fw:720575940621777391" "fw:720575940606953858" "fw:720575940630075703"
#> [67] "fw:720575940652390134" "fw:720575940632535756" "fw:720575940643696288"
#> [70] "fw:720575940623201833" "fw:720575940635063135" "fw:720575940616463477"
#> [73] "fw:720575940629981440" "fw:720575940623182847" "fw:720575940626315010"
#> [76] "fw:720575940632943277" "fw:720575940624539284" "fw:720575940620464321"
#> [79] "fw:720575940628783363" "fw:720575940643309197" "fw:720575940614392999"
#> [82] "fw:720575940617302365" "fw:720575940622997453" "fw:720575940624694503"
#> [85] "fw:720575940628734376" "fw:720575940610964946" "fw:720575940607155890"
#> [88] "fw:720575940623381956" "fw:720575940630864847" "fw:720575940638028607"
#> [91] "fw:720575940621164720" "fw:720575940623841463" "fw:720575940631177803"
#> [94] "fw:720575940624489964" "fw:720575940616398303" "fw:720575940623750325"
#> [97] "hb:612371421" "hb:673509195" "hb:424789697"
#> [100] "hb:5813022341" "hb:487925037" "hb:612738462"
#> [103] "hb:487925063" "hb:613079053" "hb:1386512867"
#> [106] "hb:799586652" "hb:422725634" "hb:5813061512"
#> [109] "hb:1234386037" "hb:611477605" "hb:733036127"
#> [112] "hb:920470959" "hb:1016835041" "hb:1048215779"
#> [115] "hb:1078693835" "hb:613719036" "hb:672352543"
#> [118] "hb:768555687" "hb:424767514" "hb:517518166"
#> [121] "hb:704466265" "hb:861665641" "hb:1139667240"
#> [124] "hb:300972942" "hb:394225044" "hb:5813067721"
#> [127] "hb:5813068729" "hb:642664141" "hb:673702721"
#> [130] "hb:457175171" "hb:579916831" "hb:673366098"
#> [133] "hb:5812981264" "hb:5812981543" "hb:457196444"
#> [136] "hb:5813020828" "hb:423774471" "hb:517854468"
#> [139] "hb:792368888" "hb:5813022896" "hb:985813153"
#> [142] "hb:5813042659" "hb:985131499" "hb:423382015"
#> [145] "hb:487143497" "hb:550081497" "hb:612742248"
#> [148] "hb:612422902" "hb:912951014" "hb:895441451"
#> [151] "hb:5813061538" "hb:5813117385" "hb:457196643"
#> [154] "hb:5813058048" "hb:5813052909" "hb:5813022234"
#> [157] "hb:5813040205" "hb:706948318" "hb:894020730"
#> [160] "hb:642732835" "hb:643847447" "hb:518670779"
#> [163] "hb:547552266" "hb:1173814525" "hb:5813033000"
#> [166] "hb:518930199" "hb:611089775" "mc:520151"
#> [169] "mc:10013" "mc:522444" "mc:522749"
#> [172] "mc:519373" "mc:521526" "mc:525780"
#> [175] "mc:530875" "mc:519371" "mc:10495"
#> [178] "mc:10079" "mc:12690" "mc:15626"
#> [181] "mc:18603" "mc:12859" "mc:515338"
#> [184] "mc:18713" "mc:19267" "mc:523060"
#> [187] "mc:21242" "mc:579919" "mc:558665"
#> [190] "mc:133427" "mc:70924" "mc:59057"
#> [193] "mc:62162" "mc:39608" "mc:524733"
#> [196] "mc:49262" "mc:531829" "mc:10704"
#> [199] "mc:11402" "mc:13728" "mc:13768"
#> [202] "mc:519368" "mc:521086" "mc:12726"
#> [205] "mc:514853" "mc:11873" "mc:19366"
#> [208] "mc:17946" "mc:10267" "mc:520395"
#> [211] "mc:38853" "mc:58401" "mc:11777"
#> [214] "mc:31083" "mc:44619" "mc:187741"
#> [217] "mc:38859" "mc:562782" "mc:520186"
#> [220] "mc:31016" "mc:41692" "mc:513387"
#> [223] "mc:513391" "mc:14221" "mc:512788"
#> [226] "mc:36094" "mc:47551" "mc:33617"
#> [229] "mc:26853" "mc:10804" "mc:11145"
#> [232] "mc:523628" "mc:10826" "mc:11990"
#> [235] "mc:12918" "mc:20835" "mc:512789"
#> [238] "mc:18406" "mc:15708" "mc:87077"
#> [241] "mc:394860" "mc:76585" "mc:110448"
#> [244] "mc:160320" "mc:556300" "mc:11176"
#> [247] "mc:524893" "mc:515034" "mc:519128"
#> [250] "mc:28622" "mc:26485" "mc:519619"
#> [253] "mc:523987" "mc:515015" "mc:513174"
#> [256] "mc:11805" "mc:10816" "mc:519131"
#> [259] "mc:11455" "mc:523043" "mc:11785"
#> [262] "mc:208566" "mc:92112" "mc:508595"
#> [265] "mc:10599"
# one way of combining separate lists of neurons
hbids=c(264083994, 5813022274)
c(cf_ids("/type:MBON1.+", keys=TRUE), cf_ids(hemibrain = hbids, keys = TRUE))
#> Warning: Unable to process query for dataset:banc
#> [1] "fw:720575940629585602" "fw:720575940632118343" "fw:720575940642142861"
#> [4] "fw:720575940634822751" "fw:720575940615221811" "fw:720575940614026193"
#> [7] "fw:720575940633209647" "fw:720575940623001480" "fw:720575940608304220"
#> [10] "fw:720575940621828443" "fw:720575940638774606" "fw:720575940639697827"
#> [13] "fw:720575940626833021" "fw:720575940635841143" "fw:720575940623905719"
#> [16] "fw:720575940629529722" "fw:720575940645304430" "fw:720575940612196850"
#> [19] "fw:720575940630767959" "fw:720575940635082347" "fw:720575940628757547"
#> [22] "fw:720575940610647416" "fw:720575940622093436" "fw:720575940624696810"
#> [25] "fw:720575940647328900" "fw:720575940650386553" "fw:720575940639556467"
#> [28] "fw:720575940612455338" "fw:720575940617749538" "fw:720575940617760257"
#> [31] "fw:720575940634482783" "fw:720575940626109315" "fw:720575940623377802"
#> [34] "fw:720575940626744921" "fw:720575940630075703" "fw:720575940632535756"
#> [37] "fw:720575940643696288" "fw:720575940623201833" "fw:720575940626315010"
#> [40] "fw:720575940624539284" "fw:720575940622997453" "fw:720575940623841463"
#> [43] "hb:613719036" "hb:672352543" "hb:768555687"
#> [46] "hb:424767514" "hb:517518166" "hb:704466265"
#> [49] "hb:861665641" "hb:1139667240" "hb:300972942"
#> [52] "hb:394225044" "hb:5813067721" "hb:5813068729"
#> [55] "hb:642664141" "hb:673702721" "hb:457175171"
#> [58] "hb:579916831" "hb:673366098" "hb:5812981264"
#> [61] "hb:5812981543" "hb:457196444" "hb:5813020828"
#> [64] "hb:423774471" "hb:517854468" "mc:579919"
#> [67] "mc:558665" "mc:133427" "mc:70924"
#> [70] "mc:59057" "mc:62162" "mc:39608"
#> [73] "mc:524733" "mc:49262" "mc:531829"
#> [76] "mc:10704" "mc:11402" "mc:13728"
#> [79] "mc:13768" "mc:519368" "mc:521086"
#> [82] "mc:12726" "mc:514853" "mc:11873"
#> [85] "mc:19366" "mc:17946" "mc:10267"
#> [88] "mc:520395" "mc:38853" "mc:58401"
#> [91] "mc:11777" "mc:31083" "mc:44619"
#> [94] "mc:187741" "mc:38859" "mc:562782"
#> [97] "mc:520186" "mc:31016" "mc:41692"
#> [100] "mc:513387" "mc:513391" "mc:14221"
#> [103] "mc:512788" "mc:36094" "mc:47551"
#> [106] "mc:33617" "mc:26853" "hb:264083994"
#> [109] "hb:5813022274"
# now equivalent to
keys(c(cf_ids("/type:MBON1.+"), cf_ids(hemibrain = hbids)))
#> Warning: Unable to process query for dataset:banc
#> [1] "fw:720575940629585602" "fw:720575940632118343" "fw:720575940642142861"
#> [4] "fw:720575940634822751" "fw:720575940615221811" "fw:720575940614026193"
#> [7] "fw:720575940633209647" "fw:720575940623001480" "fw:720575940608304220"
#> [10] "fw:720575940621828443" "fw:720575940638774606" "fw:720575940639697827"
#> [13] "fw:720575940626833021" "fw:720575940635841143" "fw:720575940623905719"
#> [16] "fw:720575940629529722" "fw:720575940645304430" "fw:720575940612196850"
#> [19] "fw:720575940630767959" "fw:720575940635082347" "fw:720575940628757547"
#> [22] "fw:720575940610647416" "fw:720575940622093436" "fw:720575940624696810"
#> [25] "fw:720575940647328900" "fw:720575940650386553" "fw:720575940639556467"
#> [28] "fw:720575940612455338" "fw:720575940617749538" "fw:720575940617760257"
#> [31] "fw:720575940634482783" "fw:720575940626109315" "fw:720575940623377802"
#> [34] "fw:720575940626744921" "fw:720575940630075703" "fw:720575940632535756"
#> [37] "fw:720575940643696288" "fw:720575940623201833" "fw:720575940626315010"
#> [40] "fw:720575940624539284" "fw:720575940622997453" "fw:720575940623841463"
#> [43] "hb:613719036" "hb:672352543" "hb:768555687"
#> [46] "hb:424767514" "hb:517518166" "hb:704466265"
#> [49] "hb:861665641" "hb:1139667240" "hb:300972942"
#> [52] "hb:394225044" "hb:5813067721" "hb:5813068729"
#> [55] "hb:642664141" "hb:673702721" "hb:457175171"
#> [58] "hb:579916831" "hb:673366098" "hb:5812981264"
#> [61] "hb:5812981543" "hb:457196444" "hb:5813020828"
#> [64] "hb:423774471" "hb:517854468" "hb:264083994"
#> [67] "hb:5813022274" "mc:579919" "mc:558665"
#> [70] "mc:133427" "mc:70924" "mc:59057"
#> [73] "mc:62162" "mc:39608" "mc:524733"
#> [76] "mc:49262" "mc:531829" "mc:10704"
#> [79] "mc:11402" "mc:13728" "mc:13768"
#> [82] "mc:519368" "mc:521086" "mc:12726"
#> [85] "mc:514853" "mc:11873" "mc:19366"
#> [88] "mc:17946" "mc:10267" "mc:520395"
#> [91] "mc:38853" "mc:58401" "mc:11777"
#> [94] "mc:31083" "mc:44619" "mc:187741"
#> [97] "mc:38859" "mc:562782" "mc:520186"
#> [100] "mc:31016" "mc:41692" "mc:513387"
#> [103] "mc:513391" "mc:14221" "mc:512788"
#> [106] "mc:36094" "mc:47551" "mc:33617"
#> [109] "mc:26853"
# queries on classes respecting dataset idiosyncrasies
cf_ids(manc="/class:descend.+", flywire="/super_class:descend.+", expand = TRUE)
#> flywire [1303 ids]: 720575940624402173 720575940627055303 720575940631082808 720575940623037720 720575940629543409 720575940618666142 720575940638109668 720575940630697078 720575940610610841 720575940618870881 ...
#> manc [1328 ids]: 28478 31361 156265 19821 22072 24087 29182 30346 31742 33545 ...
# }
c(cf_ids(flywire = 1, hemibrain = 2), cf_ids(hemibrain = 1:2, flywire=1:2))
#> flywire [2 ids]: 1 2
#> hemibrain [2 ids]: 2 1
c(cf_ids(flywire = 1, hemibrain = 2), cf_ids(hemibrain = 1:2, flywire=1:2), unique=FALSE)
#> flywire [3 ids]: 1 1 2
#> hemibrain [3 ids]: 2 1 2
# \donttest{
c(cf_ids(flywire = 1, hemibrain = 2), cf_ids(hemibrain = '/SMP55[0-9]', flywire=1:2))
#> flywire [2 ids]: 1 2
#> hemibrain [19 ids]: 2 452689494 579700707 328274638 392757094 605166418 298262663 361114148 669670654 613394707 ...
# }