Setup for brain connectome data.
At the time of writing the main datasets of interest for coconatfly will be the hemibrain and flywire. Installing coconatfly will automatically install the natverse packages required for analysis. However, a few extra steps are still required.
# first install coconatfly
if(!requireNamespace('natmanager'))
install.packages('natmanager')
natmanager::install(pkgs = 'coconatfly')
# then get flywire data
fafbseg::download_flywire_release_data()If you have not already done so, you will also need to record a neuprint token to access hemibrain data. Go to https://neuprint.janelia.org/account, copy your Auth Token and then edit your R environ file to do
usethis::edit_r_environ()and add a line like this:
neuprint_token="eyJhbH0lc9OqzJ6evvcJ23KmIi.eyJlb6B8nUg8senJO1ZVzHb6uQ1fvncAiWdFcTIwTQb0xOcxa3TjKHVdLZ5OAtHzjWJJLqpQjiTikWryIfgUHCKoq31RSdDMqD7mah0RWCFaEPrTDdPm7OfRBizNdoqyyWAE61g9FWb2CAh8kAfcsb3ylVG3MwFOYpX91ayWxtp1prfjtm9dte9mFddGdWdr8444Rrun8cLksyELl93utdnGAQReSgiNy-jDLujyRCSRCAOq23X049gRA9QtJcOKCDtdiFyQhMKzLk8EISt7Cnn9AS1"Replacing with your auth token and being sure that is all on one line with a line break after the last quotation mark.
Set up for VNC data
For VNC data, the main datasets are FANC and MANC. MANC data will be available if you have set up your neuprint access token as described in the brain section. For FANC data you will need a separate CAVE access token. Essentially this is covered by:
fancr::fanc_set_token()
# check all is good
fancr::dr_fanc()Dataset status
You can get a useful overview of the current status of your access to
different datasets with the dr_coconatfly() command.
library(coconatfly)
dr_coconatfly()
#> dataset installed
#> 1 hemibrain TRUE
#> 2 manc TRUE
#> 3 malecns TRUE
#> 4 opticlobe TRUE
#> 5 flywire TRUE
#> 6 fanc TRUE
#> 7 banc TRUE
#> server
#> 1 https://neuprint.janelia.org
#> 2 https://neuprint.janelia.org
#> 3 https://neuprint-cns.janelia.org
#> 4 https://neuprint.janelia.org
#> 5 local dump
#> 6 https://cave.fanc-fly.com/segmentation/table/mar2021_prod
#> 7 middleauth+https://cave.fanc-fly.com/segmentation/table/wclee_fly_cns_001
#> version
#> 1 hemibrain:v1.2.1
#> 2 manc:v1.2.1
#> 3 cns
#> 4 optic-lobe:v1.0.1
#> 5 783
#> 6 1195
#> 7 452
#> For additional information (inc auth issues) for flywire or fanc datasets, try:
#> `fafbseg::dr_fafbseg()` or `fancr::dr_fanc()`Brain example
Ok with that in place, let’s check if we can use connectome data, starting with the brain.
We use cf_ids() to specify neurons in different
datasets:
cf_ids(hemibrain = 'ORN_DA2', expand = TRUE)
#> hemibrain [35 ids]: 1669017843 1669699714 1669946117 1670382036 1670386270 1670390647 1669358817 1671659809 1702107389 1702802179 ...We can ask for the same specific cell type across datasets, here MBON01, mushroom body output neuron 1 (aka M6 or MBON-gamma5beta’2a).
cf_meta(cf_ids('MBON01', datasets = c("flywire", "hemibrain")))
#> Loading required namespace: git2r
#> id side class subclass subsubclass type lineage
#> 1 720575940624117245 R central MBON <NA> MBON01 putative_primary
#> 2 720575940643309197 L central MBON <NA> MBON01 putative_primary
#> 3 612371421 R <NA> <NA> <NA> MBON01 ADM07
#> 4 673509195 L <NA> <NA> <NA> MBON01 ADM07
#> group instance dataset key
#> 1 <NA> MBON01_R flywire fw:720575940624117245
#> 2 <NA> MBON01_L flywire fw:720575940643309197
#> 3 <NA> MBON01(y5B'2a)_R hemibrain hb:612371421
#> 4 <NA> MBON01(y5B'2a)_L hemibrain hb:673509195We can do a regular expression query returning all MBONs:
mbonmeta=cf_meta(cf_ids('/type:MBON.+', datasets = c("flywire", "hemibrain")))
mbonmeta
#> id side class subclass subsubclass type
#> 1 720575940624185095 L central MBON <NA> MBON02
#> 2 720575940624117245 R central MBON <NA> MBON01
#> 3 720575940638526278 R central MBON <NA> MBON32
#> 4 720575940629585602 R central MBON <NA> MBON10
#> 5 720575940637934308 R central MBON <NA> MBON30
#> 6 720575940632118343 L central MBON <NA> MBON10
#> 7 720575940609959637 L central MBON <NA> MBON32
#> 8 720575940638163428 L central MBON <NA> MBON06
#> 9 720575940630496374 R central MBON <NA> MBON05
#> 10 720575940642142861 L central MBON <NA> MBON10
#> 11 720575940611344078 R central MBON <NA> MBON20
#> 12 720575940634822751 R central MBON <NA> MBON17-like
#> 13 720575940617552340 R central MBON <NA> MBON02
#> 14 720575940624280328 R central MBON <NA> MBON33
#> 15 720575940617567206 L central MBON <NA> MBON23
#> 16 720575940643700640 R central MBON <NA> MBON29
#> 17 720575940615221811 R central MBON <NA> MBON10
#> 18 720575940614026193 R central MBON <NA> MBON14
#> 19 720575940633209647 L central MBON <NA> MBON10
#> 20 720575940623001480 R central MBON <NA> MBON12
#> 21 720575940608304220 R central MBON <NA> MBON15-like
#> 22 720575940614595218 L central MBON <NA> MBON28
#> 23 720575940636992368 R central MBON <NA> MBON31
#> 24 720575940621828443 L central MBON <NA> MBON12
#> 25 720575940637902938 L central MBON <NA> MBON35
#> 26 720575940638774606 L central MBON <NA> MBON17
#> 27 720575940639697827 R central MBON <NA> MBON14
#> 28 720575940626833021 L central MBON <NA> MBON19
#> 29 720575940618008859 L central MBON <NA> MBON30
#> 30 720575940635841143 L central MBON <NA> MBON15
#> 31 720575940618249797 R central MBON <NA> MBON27
#> 32 720575940629856515 L central MBON <NA> MBON09
#> 33 720575940623905719 R central MBON <NA> MBON12
#> 34 720575940629529722 L central MBON <NA> MBON10
#> 35 720575940624659943 L central MBON <NA> MBON25,MBON34
#> 36 720575940624590316 R central MBON <NA> MBON03
#> 37 720575940645304430 L central MBON <NA> MBON13
#> 38 720575940612196850 R central MBON <NA> MBON15-like
#> 39 720575940630767959 L central MBON <NA> MBON15
#> 40 720575940635082347 L central MBON <NA> MBON15-like
#> 41 720575940628757547 L central MBON <NA> MBON15-like
#> 42 720575940627144069 R central MBON <NA> MBON25,MBON34
#> 43 720575940610647416 R central MBON <NA> MBON10
#> 44 720575940622093436 R central MBON <NA> MBON15
#> 45 720575940624696810 L central MBON <NA> MBON15-like
#> 46 720575940629422086 L central MBON <NA> MBON09
#> 47 720575940647328900 R central MBON <NA> MBON10
#> 48 720575940650386553 L central MBON <NA> MBON17-like
#> 49 720575940639556467 R central MBON <NA> MBON10
#> 50 720575940612455338 R central MBON <NA> MBON15
#> 51 720575940617749538 R central MBON <NA> MBON11
#> 52 720575940617760257 R central MBON <NA> MBON17
#> 53 720575940619810389 R central MBON <NA> MBON25,MBON34
#> 54 720575940634482783 R central MBON <NA> MBON19
#> 55 720575940644615716 L central MBON <NA> MBON31
#> 56 720575940626109315 R central MBON <NA> MBON19
#> 57 720575940623377802 L central MBON <NA> MBON16
#> 58 720575940626744921 R central MBON <NA> MBON16
#> 59 720575940623464316 R central MBON <NA> MBON24
#> 60 720575940622979277 L central MBON <NA> MBON27
#> 61 720575940614892182 R central MBON <NA> MBON28
#> 62 720575940620715224 L central MBON <NA> MBON21
#> 63 720575940643863496 L central MBON <NA> MBON20
#> 64 720575940621777391 R central MBON <NA> MBON21
#> 65 720575940606953858 R central MBON <NA> MBON23
#> 66 720575940630075703 L central MBON <NA> MBON12
#> 67 720575940652390134 L central MBON <NA> MBON07
#> 68 720575940632535756 L central MBON <NA> MBON14
#> 69 720575940643696288 L central MBON <NA> MBON14
#> 70 720575940623201833 L central MBON <NA> MBON11
#> 71 720575940635063135 R central MBON <NA> MBON22
#> 72 720575940616463477 L central MBON <NA> MBON22
#> 73 720575940629981440 L central MBON <NA> MBON26
#> 74 720575940623182847 L central MBON <NA> MBON33
#> 75 720575940626315010 R central MBON <NA> MBON13
#> 76 720575940632943277 R central MBON <NA> MBON35
#> 77 720575940624539284 L central MBON <NA> MBON18
#> 78 720575940620464321 L central MBON <NA> MBON04
#> 79 720575940628783363 R central MBON <NA> MBON07
#> 80 720575940643309197 L central MBON <NA> MBON01
#> 81 720575940614392999 L central MBON <NA> MBON29
#> 82 720575940617302365 L central MBON <NA> MBON07
#> 83 720575940622997453 R central MBON <NA> MBON18
#> 84 720575940624694503 L central MBON <NA> MBON03
#> 85 720575940628734376 R central MBON <NA> MBON04
#> 86 720575940610964946 R central MBON <NA> MBON09
#> 87 720575940607155890 R central MBON <NA> MBON26
#> 88 720575940623381956 R central MBON <NA> MBON07
#> 89 720575940630864847 R central MBON <NA> MBON09
#> 90 720575940638028607 R central MBON <NA> MBON06
#> 91 720575940621164720 L central MBON <NA> MBON05
#> 92 720575940623841463 L central MBON <NA> MBON19
#> 93 720575940631177803 L central MBON <NA> MBON24
#> 94 720575940624489964 R central MBON <NA> MBON25,MBON34
#> 95 720575940616398303 L central MBON <NA> MBON25,MBON34
#> 96 720575940623750325 L central MBON <NA> MBON25,MBON34
#> 97 612371421 R <NA> <NA> <NA> MBON01
#> 98 673509195 L <NA> <NA> <NA> MBON01
#> 99 424789697 R <NA> <NA> <NA> MBON02
#> 100 5813022341 L <NA> <NA> <NA> MBON02
#> 101 487925037 R <NA> <NA> <NA> MBON03
#> 102 612738462 L <NA> <NA> <NA> MBON03
#> 103 487925063 R <NA> <NA> <NA> MBON04
#> 104 613079053 L <NA> <NA> <NA> MBON04
#> 105 1386512867 R <NA> <NA> <NA> MBON05
#> 106 799586652 L <NA> <NA> <NA> MBON05
#> 107 422725634 L <NA> <NA> <NA> MBON06
#> 108 5813061512 R <NA> <NA> <NA> MBON06
#> 109 1234386037 R <NA> <NA> <NA> MBON07
#> 110 611477605 L <NA> <NA> <NA> MBON07
#> 111 733036127 R <NA> <NA> <NA> MBON07
#> 112 920470959 L <NA> <NA> <NA> MBON07
#> 113 1016835041 L <NA> <NA> <NA> MBON09
#> 114 1048215779 L <NA> <NA> <NA> MBON09
#> 115 1078693835 R <NA> <NA> <NA> MBON09
#> 116 613719036 R <NA> <NA> <NA> MBON10
#> 117 672352543 R <NA> <NA> <NA> MBON10
#> 118 768555687 R <NA> <NA> <NA> MBON10
#> 119 424767514 R <NA> <NA> <NA> MBON11
#> 120 517518166 L <NA> <NA> <NA> MBON11
#> 121 704466265 R <NA> <NA> <NA> MBON12
#> 122 861665641 R <NA> <NA> <NA> MBON12
#> 123 1139667240 R <NA> <NA> <NA> MBON13
#> 124 300972942 R <NA> <NA> <NA> MBON14
#> 125 394225044 L <NA> <NA> <NA> MBON14
#> 126 5813067721 L <NA> <NA> <NA> MBON14
#> 127 5813068729 R <NA> <NA> <NA> MBON14
#> 128 642664141 R <NA> <NA> <NA> MBON15
#> 129 673702721 R <NA> <NA> <NA> MBON15
#> 130 457175171 R <NA> <NA> <NA> MBON15-like
#> 131 579916831 R <NA> <NA> <NA> MBON15-like
#> 132 673366098 R <NA> <NA> <NA> MBON16
#> 133 5812981264 R <NA> <NA> <NA> MBON17
#> 134 5812981543 R <NA> <NA> <NA> MBON17-like
#> 135 457196444 L <NA> <NA> <NA> MBON18
#> 136 5813020828 R <NA> <NA> <NA> MBON18
#> 137 423774471 R <NA> <NA> <NA> MBON19
#> 138 517854468 R <NA> <NA> <NA> MBON19
#> 139 792368888 R <NA> <NA> <NA> MBON20
#> 140 5813022896 R <NA> <NA> <NA> MBON21
#> 141 985813153 L <NA> <NA> <NA> MBON21
#> 142 5813042659 R <NA> <NA> <NA> MBON22
#> 143 985131499 L <NA> <NA> <NA> MBON22
#> 144 423382015 R <NA> <NA> <NA> MBON23
#> 145 487143497 R <NA> <NA> <NA> MBON24
#> 146 550081497 L <NA> <NA> <NA> MBON24
#> 147 612742248 L <NA> <NA> <NA> MBON25
#> 148 612422902 R <NA> <NA> <NA> MBON25
#> 149 912951014 L <NA> <NA> <NA> MBON26
#> 150 895441451 R <NA> <NA> <NA> MBON26
#> 151 5813061538 L <NA> <NA> <NA> MBON27
#> 152 5813117385 R <NA> <NA> <NA> MBON27
#> 153 457196643 R <NA> <NA> <NA> MBON28
#> 154 5813058048 R <NA> <NA> <NA> MBON29
#> 155 5813052909 L <NA> <NA> <NA> MBON29
#> 156 5813022234 R <NA> <NA> <NA> MBON30
#> 157 5813040205 L <NA> <NA> <NA> MBON30
#> 158 706948318 L <NA> <NA> <NA> MBON31
#> 159 894020730 R <NA> <NA> <NA> MBON31
#> 160 642732835 R <NA> <NA> <NA> MBON32
#> 161 643847447 L <NA> <NA> <NA> MBON32
#> 162 518670779 L <NA> <NA> <NA> MBON33
#> 163 547552266 R <NA> <NA> <NA> MBON33
#> 164 1173814525 L <NA> <NA> <NA> MBON34
#> 165 5813033000 R <NA> <NA> <NA> MBON34
#> 166 518930199 R <NA> <NA> <NA> MBON35
#> 167 611089775 L <NA> <NA> <NA> MBON35
#> lineage group instance dataset
#> 1 putative_primary <NA> MBON02_L flywire
#> 2 putative_primary <NA> MBON01_R flywire
#> 3 putative_primary <NA> MBON32_R flywire
#> 4 EBa1 <NA> MBON10_R flywire
#> 5 putative_primary <NA> MBON30_R flywire
#> 6 EBa1 <NA> MBON10_L flywire
#> 7 putative_primary <NA> MBON32_L flywire
#> 8 putative_primary <NA> MBON06_L flywire
#> 9 putative_primary <NA> MBON05_R flywire
#> 10 EBa1 <NA> MBON10_L flywire
#> 11 putative_primary <NA> MBON20_R flywire
#> 12 DL1_dorsal <NA> MBON17-like_R flywire
#> 13 putative_primary <NA> MBON02_R flywire
#> 14 putative_primary <NA> MBON33_R flywire
#> 15 DL1_dorsal <NA> MBON23_L flywire
#> 16 DL2_ventral <NA> MBON29_R flywire
#> 17 EBa1 <NA> MBON10_R flywire
#> 18 FLAa2 <NA> MBON14_R flywire
#> 19 EBa1 <NA> MBON10_L flywire
#> 20 FLAa2 <NA> MBON12_R flywire
#> 21 DL1_dorsal <NA> MBON15-like_R flywire
#> 22 DL1_dorsal <NA> MBON28_L flywire
#> 23 putative_primary <NA> MBON31_R flywire
#> 24 FLAa2 <NA> MBON12_L flywire
#> 25 putative_primary <NA> MBON35_L flywire
#> 26 DL1_dorsal <NA> MBON17_L flywire
#> 27 FLAa2 <NA> MBON14_R flywire
#> 28 DL1_dorsal <NA> MBON19_L flywire
#> 29 putative_primary <NA> MBON30_L flywire
#> 30 DL1_dorsal <NA> MBON15_L flywire
#> 31 putative_primary <NA> MBON27_R flywire
#> 32 putative_primary <NA> MBON09_L flywire
#> 33 FLAa2 <NA> MBON12_R flywire
#> 34 EBa1 <NA> MBON10_L flywire
#> 35 SMPad3 <NA> MBON25,MBON34_L flywire
#> 36 putative_primary <NA> MBON03_R flywire
#> 37 FLAa2 <NA> MBON13_L flywire
#> 38 DL1_dorsal <NA> MBON15-like_R flywire
#> 39 DL1_dorsal <NA> MBON15_L flywire
#> 40 DL1_dorsal <NA> MBON15-like_L flywire
#> 41 DL1_dorsal <NA> MBON15-like_L flywire
#> 42 SMPad3 <NA> MBON25,MBON34_R flywire
#> 43 EBa1 <NA> MBON10_R flywire
#> 44 DL1_dorsal <NA> MBON15_R flywire
#> 45 DL1_dorsal <NA> MBON15-like_L flywire
#> 46 putative_primary <NA> MBON09_L flywire
#> 47 EBa1 <NA> MBON10_R flywire
#> 48 DL1_dorsal <NA> MBON17-like_L flywire
#> 49 EBa1 <NA> MBON10_R flywire
#> 50 DL1_dorsal <NA> MBON15_R flywire
#> 51 putative_primary <NA> MBON11_R flywire
#> 52 DL1_dorsal <NA> MBON17_R flywire
#> 53 SMPad3 <NA> MBON25,MBON34_R flywire
#> 54 DL1_dorsal <NA> MBON19_R flywire
#> 55 putative_primary <NA> MBON31_L flywire
#> 56 DL1_dorsal <NA> MBON19_R flywire
#> 57 DL1_dorsal <NA> MBON16_L flywire
#> 58 DL1_dorsal <NA> MBON16_R flywire
#> 59 putative_primary <NA> MBON24_R flywire
#> 60 putative_primary <NA> MBON27_L flywire
#> 61 DL1_dorsal <NA> MBON28_R flywire
#> 62 putative_primary <NA> MBON21_L flywire
#> 63 putative_primary <NA> MBON20_L flywire
#> 64 putative_primary <NA> MBON21_R flywire
#> 65 DL1_dorsal <NA> MBON23_R flywire
#> 66 FLAa2 <NA> MBON12_L flywire
#> 67 putative_primary <NA> MBON07_L flywire
#> 68 FLAa2 <NA> MBON14_L flywire
#> 69 FLAa2 <NA> MBON14_L flywire
#> 70 putative_primary <NA> MBON11_L flywire
#> 71 putative_primary <NA> MBON22_R flywire
#> 72 putative_primary <NA> MBON22_L flywire
#> 73 putative_primary <NA> MBON26_L flywire
#> 74 putative_primary <NA> MBON33_L flywire
#> 75 FLAa2 <NA> MBON13_R flywire
#> 76 putative_primary <NA> MBON35_R flywire
#> 77 DL1_dorsal <NA> MBON18_L flywire
#> 78 putative_primary <NA> MBON04_L flywire
#> 79 putative_primary <NA> MBON07_R flywire
#> 80 putative_primary <NA> MBON01_L flywire
#> 81 DL2_ventral <NA> MBON29_L flywire
#> 82 putative_primary <NA> MBON07_L flywire
#> 83 DL1_dorsal <NA> MBON18_R flywire
#> 84 putative_primary <NA> MBON03_L flywire
#> 85 putative_primary <NA> MBON04_R flywire
#> 86 putative_primary <NA> MBON09_R flywire
#> 87 putative_primary <NA> MBON26_R flywire
#> 88 putative_primary <NA> MBON07_R flywire
#> 89 putative_primary <NA> MBON09_R flywire
#> 90 putative_primary <NA> MBON06_R flywire
#> 91 putative_primary <NA> MBON05_L flywire
#> 92 DL1_dorsal <NA> MBON19_L flywire
#> 93 putative_primary <NA> MBON24_L flywire
#> 94 SMPad3 <NA> MBON25,MBON34_R flywire
#> 95 SMPad3 <NA> MBON25,MBON34_L flywire
#> 96 SMPad3 <NA> MBON25,MBON34_L flywire
#> 97 ADM07 <NA> MBON01(y5B'2a)_R hemibrain
#> 98 ADM07 <NA> MBON01(y5B'2a)_L hemibrain
#> 99 ADM07 <NA> MBON02(B2B'2a)_R hemibrain
#> 100 ADM07 <NA> MBON02(B2B'2a)_L hemibrain
#> 101 ADM07 <NA> MBON03(B'2mp)_R hemibrain
#> 102 ADM07 <NA> MBON03(B'2mp)_L hemibrain
#> 103 ADM07 <NA> MBON04(B'2mp_bilateral)_R hemibrain
#> 104 ADM07 <NA> MBON04(B'2mp_bilateral)_L hemibrain
#> 105 AVM07 <NA> MBON05(y4>y1y2)_R hemibrain
#> 106 <NA> <NA> MBON05(y4>y1y2)(AVM07)_L hemibrain
#> 107 <NA> <NA> MBON06(B1>a)(AVM07)_L hemibrain
#> 108 AVM07 <NA> MBON06(B1>a)_R hemibrain
#> 109 <NA> <NA> MBON07(a1)_R hemibrain
#> 110 <NA> <NA> MBON07(a1)_L hemibrain
#> 111 ADM10 <NA> MBON07(a1)_R hemibrain
#> 112 <NA> <NA> MBON07(a1)_L hemibrain
#> 113 <NA> <NA> MBON09(y3B'1)(AVM17)_L hemibrain
#> 114 <NA> <NA> MBON09(y3B'1)(AVM17)_L hemibrain
#> 115 AVM17 <NA> MBON09(y3B'1)_R hemibrain
#> 116 AVM07 <NA> MBON10(B'1)_R hemibrain
#> 117 AVM07 <NA> MBON10(B'1)_R hemibrain
#> 118 AVM07 <NA> MBON10(B'1)_R hemibrain
#> 119 ADM05 <NA> MBON11(y1pedc>a/B)_R hemibrain
#> 120 <NA> <NA> MBON11(y1pedc>a/B)(ADM05)_L hemibrain
#> 121 <NA> <NA> MBON12(y2a'1)_R hemibrain
#> 122 <NA> <NA> MBON12(y2a'1)_R hemibrain
#> 123 <NA> <NA> MBON13(a'2)_R hemibrain
#> 124 <NA> <NA> MBON14(a3)_R hemibrain
#> 125 <NA> <NA> MBON14(a3)_L hemibrain
#> 126 <NA> <NA> MBON14(a3)_L hemibrain
#> 127 <NA> <NA> MBON14(a3)_R hemibrain
#> 128 PDL05 <NA> MBON15(a'1)_R hemibrain
#> 129 PDL05 <NA> MBON15(a'1)_R hemibrain
#> 130 PDL05 <NA> MBON15-like(a'1a'2)_R hemibrain
#> 131 PDL05 <NA> MBON15-like(a'1a'2)_R hemibrain
#> 132 PDL05 <NA> MBON16(a'3ap)_R hemibrain
#> 133 PDL05 <NA> MBON17(a'3m)_R hemibrain
#> 134 PDL05 <NA> MBON17-like(a'2a'3)_R hemibrain
#> 135 <NA> <NA> MBON18(a2sc)(PDL05)_L hemibrain
#> 136 PDL05 <NA> MBON18(a2sc)_R hemibrain
#> 137 PDL05 <NA> MBON19(a2p3p)_R hemibrain
#> 138 PDL19 <NA> MBON19(a2p3p)_R hemibrain
#> 139 AVM04 <NA> MBON20(y1y2)_R hemibrain
#> 140 PVL06 <NA> MBON21(y4y5)_R hemibrain
#> 141 <NA> <NA> MBON21(y4y5)(PVL06)_L hemibrain
#> 142 PVL06 <NA> MBON22(calyx)_R hemibrain
#> 143 <NA> <NA> MBON22(calyx)(PVL06)_L hemibrain
#> 144 PDL05 <NA> MBON23(a2sp)_R hemibrain
#> 145 PDL05 <NA> MBON24(B2y5)_R hemibrain
#> 146 <NA> <NA> MBON24(B2y5)(PDL05)_L hemibrain
#> 147 ADM07 <NA> MBON25(y1y2)_L hemibrain
#> 148 ADM07 <NA> MBON25(y1y2)_R hemibrain
#> 149 <NA> <NA> MBON26(B'2d)(PDM28)_L hemibrain
#> 150 PDM28 <NA> MBON26(B'2d)_R hemibrain
#> 151 <NA> <NA> MBON27(y5d)(PVM03)_L hemibrain
#> 152 PVM03 <NA> MBON27(y5d)_R hemibrain
#> 153 PDL05 <NA> MBON16-like(a'3a)_R hemibrain
#> 154 PVL06 <NA> MBON29(y4y5)_R hemibrain
#> 155 <NA> <NA> MBON29(y4y5)(PVL06)_L hemibrain
#> 156 AVM07 <NA> MBON30(y1y2y3)_R hemibrain
#> 157 <NA> <NA> MBON30(y1y2y3)(AVM07)_L hemibrain
#> 158 <NA> <NA> MBON31(a'1a)(ADM10)_L hemibrain
#> 159 ADM10 <NA> MBON31(a'1a)_R hemibrain
#> 160 ADM08 <NA> MBON32(y2)_R hemibrain
#> 161 <NA> <NA> MBON32(y2)(ADM08)_L hemibrain
#> 162 <NA> <NA> MBON33(y2y3)(ADM05)_L hemibrain
#> 163 ADM05 <NA> MBON33(y2y3)_R hemibrain
#> 164 ADM07 <NA> MBON34(y2)_L hemibrain
#> 165 ADM07 <NA> MBON34(y2)_R hemibrain
#> 166 ADM02 <NA> MBON35(y2)_R hemibrain
#> 167 <NA> <NA> MBON35(y2)_L hemibrain
#> key
#> 1 fw:720575940624185095
#> 2 fw:720575940624117245
#> 3 fw:720575940638526278
#> 4 fw:720575940629585602
#> 5 fw:720575940637934308
#> 6 fw:720575940632118343
#> 7 fw:720575940609959637
#> 8 fw:720575940638163428
#> 9 fw:720575940630496374
#> 10 fw:720575940642142861
#> 11 fw:720575940611344078
#> 12 fw:720575940634822751
#> 13 fw:720575940617552340
#> 14 fw:720575940624280328
#> 15 fw:720575940617567206
#> 16 fw:720575940643700640
#> 17 fw:720575940615221811
#> 18 fw:720575940614026193
#> 19 fw:720575940633209647
#> 20 fw:720575940623001480
#> 21 fw:720575940608304220
#> 22 fw:720575940614595218
#> 23 fw:720575940636992368
#> 24 fw:720575940621828443
#> 25 fw:720575940637902938
#> 26 fw:720575940638774606
#> 27 fw:720575940639697827
#> 28 fw:720575940626833021
#> 29 fw:720575940618008859
#> 30 fw:720575940635841143
#> 31 fw:720575940618249797
#> 32 fw:720575940629856515
#> 33 fw:720575940623905719
#> 34 fw:720575940629529722
#> 35 fw:720575940624659943
#> 36 fw:720575940624590316
#> 37 fw:720575940645304430
#> 38 fw:720575940612196850
#> 39 fw:720575940630767959
#> 40 fw:720575940635082347
#> 41 fw:720575940628757547
#> 42 fw:720575940627144069
#> 43 fw:720575940610647416
#> 44 fw:720575940622093436
#> 45 fw:720575940624696810
#> 46 fw:720575940629422086
#> 47 fw:720575940647328900
#> 48 fw:720575940650386553
#> 49 fw:720575940639556467
#> 50 fw:720575940612455338
#> 51 fw:720575940617749538
#> 52 fw:720575940617760257
#> 53 fw:720575940619810389
#> 54 fw:720575940634482783
#> 55 fw:720575940644615716
#> 56 fw:720575940626109315
#> 57 fw:720575940623377802
#> 58 fw:720575940626744921
#> 59 fw:720575940623464316
#> 60 fw:720575940622979277
#> 61 fw:720575940614892182
#> 62 fw:720575940620715224
#> 63 fw:720575940643863496
#> 64 fw:720575940621777391
#> 65 fw:720575940606953858
#> 66 fw:720575940630075703
#> 67 fw:720575940652390134
#> 68 fw:720575940632535756
#> 69 fw:720575940643696288
#> 70 fw:720575940623201833
#> 71 fw:720575940635063135
#> 72 fw:720575940616463477
#> 73 fw:720575940629981440
#> 74 fw:720575940623182847
#> 75 fw:720575940626315010
#> 76 fw:720575940632943277
#> 77 fw:720575940624539284
#> 78 fw:720575940620464321
#> 79 fw:720575940628783363
#> 80 fw:720575940643309197
#> 81 fw:720575940614392999
#> 82 fw:720575940617302365
#> 83 fw:720575940622997453
#> 84 fw:720575940624694503
#> 85 fw:720575940628734376
#> 86 fw:720575940610964946
#> 87 fw:720575940607155890
#> 88 fw:720575940623381956
#> 89 fw:720575940630864847
#> 90 fw:720575940638028607
#> 91 fw:720575940621164720
#> 92 fw:720575940623841463
#> 93 fw:720575940631177803
#> 94 fw:720575940624489964
#> 95 fw:720575940616398303
#> 96 fw:720575940623750325
#> 97 hb:612371421
#> 98 hb:673509195
#> 99 hb:424789697
#> 100 hb:5813022341
#> 101 hb:487925037
#> 102 hb:612738462
#> 103 hb:487925063
#> 104 hb:613079053
#> 105 hb:1386512867
#> 106 hb:799586652
#> 107 hb:422725634
#> 108 hb:5813061512
#> 109 hb:1234386037
#> 110 hb:611477605
#> 111 hb:733036127
#> 112 hb:920470959
#> 113 hb:1016835041
#> 114 hb:1048215779
#> 115 hb:1078693835
#> 116 hb:613719036
#> 117 hb:672352543
#> 118 hb:768555687
#> 119 hb:424767514
#> 120 hb:517518166
#> 121 hb:704466265
#> 122 hb:861665641
#> 123 hb:1139667240
#> 124 hb:300972942
#> 125 hb:394225044
#> 126 hb:5813067721
#> 127 hb:5813068729
#> 128 hb:642664141
#> 129 hb:673702721
#> 130 hb:457175171
#> 131 hb:579916831
#> 132 hb:673366098
#> 133 hb:5812981264
#> 134 hb:5812981543
#> 135 hb:457196444
#> 136 hb:5813020828
#> 137 hb:423774471
#> 138 hb:517854468
#> 139 hb:792368888
#> 140 hb:5813022896
#> 141 hb:985813153
#> 142 hb:5813042659
#> 143 hb:985131499
#> 144 hb:423382015
#> 145 hb:487143497
#> 146 hb:550081497
#> 147 hb:612742248
#> 148 hb:612422902
#> 149 hb:912951014
#> 150 hb:895441451
#> 151 hb:5813061538
#> 152 hb:5813117385
#> 153 hb:457196643
#> 154 hb:5813058048
#> 155 hb:5813052909
#> 156 hb:5813022234
#> 157 hb:5813040205
#> 158 hb:706948318
#> 159 hb:894020730
#> 160 hb:642732835
#> 161 hb:643847447
#> 162 hb:518670779
#> 163 hb:547552266
#> 164 hb:1173814525
#> 165 hb:5813033000
#> 166 hb:518930199
#> 167 hb:611089775and then do some simple summaries on the metadata returned by
cf_meta():
mbonmeta %>%
mutate(dss=paste0(abbreviate_datasets(dataset), side)) %>%
with(table(type, dss))
#> dss
#> type fwL fwR hbL hbR
#> MBON01 1 1 1 1
#> MBON02 1 1 1 1
#> MBON03 1 1 1 1
#> MBON04 1 1 1 1
#> MBON05 1 1 1 1
#> MBON06 1 1 1 1
#> MBON07 2 2 2 2
#> MBON09 2 2 2 1
#> MBON10 4 5 0 3
#> MBON11 1 1 1 1
#> MBON12 2 2 0 2
#> MBON13 1 1 0 1
#> MBON14 2 2 2 2
#> MBON15 2 2 0 2
#> MBON15-like 3 2 0 2
#> MBON16 1 1 0 1
#> MBON17 1 1 0 1
#> MBON17-like 1 1 0 1
#> MBON18 1 1 1 1
#> MBON19 2 2 0 2
#> MBON20 1 1 0 1
#> MBON21 1 1 1 1
#> MBON22 1 1 1 1
#> MBON23 1 1 0 1
#> MBON24 1 1 1 1
#> MBON25 0 0 1 1
#> MBON25,MBON34 3 3 0 0
#> MBON26 1 1 1 1
#> MBON27 1 1 1 1
#> MBON28 1 1 0 1
#> MBON29 1 1 1 1
#> MBON30 1 1 1 1
#> MBON31 1 1 1 1
#> MBON32 1 1 1 1
#> MBON33 1 1 1 1
#> MBON34 0 0 1 1
#> MBON35 1 1 1 1In general things look quite consistent across sides and datasets (although some neurons are of course missing from the LHS of the hemibrain).
Connectivity clustering
We can then then inspect the situation for MBON25 and MBON34 which
have been combined into a single compound type in FlyWire but were
regarded as two distinct types in hemibrain. Notice that we pipe
%>% the dataframe containing metadata to the
cf_cosine_plot function via a filter expression which picks
out our cell type of interest as well as few similarly numbered ones. We
use output connectivity clustering since we suspect the downstream cell
type interactions are more diagnostic for
mbonmeta %>%
filter(grepl("MBON(25|34|24|26|33|35)", type)) %>%
cf_cosine_plot(partners = 'out')
#> Matching types across datasets. Keeping 844/1844 output connections with total weight 24752/42677 (58%)