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()
#> Error in clio_auth() :
#> Clio/Google auth failure. Do you have access rights to VNC clio?
#> Try specifying the email linked to clio in a call to `clio_auth` or setting `options(malevnc.clio_email)`!
#> Warning in fun(libname, pkgname): Trouble choosing default malecns dataset.
#> Try running dr_malecns() and then ask on #code or file an issue at
#> https://github.com/flyconnectome/malecns/issues
#> Error : Unable to find chunked graph credentials!
#> Please set by doing:
#> flywire_set_token()/fanc_set_token() etc
#> For further details see:
#> https://github.com/seung-lab/cloud-volume#chunkedgraph-secretjson
#> Error in fanc_scene() :
#> It looks like you do not have a stored token. Please use `fanc_set_token()` to make one.
#> Error : Unable to find chunked graph credentials!
#> Please set by doing:
#> flywire_set_token()/fanc_set_token() etc
#> For further details see:
#> https://github.com/seung-lab/cloud-volume#chunkedgraph-secretjson
#> dataset installed server version
#> 1 hemibrain TRUE https://neuprint.janelia.org hemibrain:v1.2.1
#> 2 manc TRUE https://neuprint.janelia.org manc:v1.2.1
#> 3 malecns TRUE <NA> <NA>
#> 4 opticlobe TRUE https://neuprint.janelia.org optic-lobe:v1.0
#> 5 flywire TRUE local dump 783
#> 6 fanc TRUE <NA> <NA>
#> 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 type group instance dataset
#> 1 720575940624117245 R central MBON01 <NA> MBON01_R flywire
#> 2 720575940643309197 L central MBON01 <NA> MBON01_L flywire
#> 3 612371421 R <NA> MBON01 <NA> MBON01(y5B'2a)_R hemibrain
#> 4 673509195 L <NA> MBON01 <NA> MBON01(y5B'2a)_L hemibrain
#> key
#> 1 fw:720575940624117245
#> 2 fw:720575940643309197
#> 3 hb:612371421
#> 4 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 type group
#> 1 720575940624185095 L central MBON02 <NA>
#> 2 720575940624117245 R central MBON01 <NA>
#> 3 720575940638526278 R central MBON32 <NA>
#> 4 720575940629585602 R central MBON10 <NA>
#> 5 720575940637934308 R central MBON30 <NA>
#> 6 720575940632118343 L central MBON10 <NA>
#> 7 720575940609959637 L central MBON32 <NA>
#> 8 720575940638163428 L central MBON06 <NA>
#> 9 720575940630496374 R central MBON05 <NA>
#> 10 720575940642142861 L central MBON10 <NA>
#> 11 720575940611344078 R central MBON20 <NA>
#> 12 720575940634822751 R central MBON17-like <NA>
#> 13 720575940617552340 R central MBON02 <NA>
#> 14 720575940624280328 R central MBON33 <NA>
#> 15 720575940617567206 L central MBON23 <NA>
#> 16 720575940643700640 R central MBON29 <NA>
#> 17 720575940615221811 R central MBON10 <NA>
#> 18 720575940614026193 R central MBON14 <NA>
#> 19 720575940633209647 L central MBON10 <NA>
#> 20 720575940623001480 R central MBON12 <NA>
#> 21 720575940608304220 R central MBON15-like <NA>
#> 22 720575940614595218 L central MBON28 <NA>
#> 23 720575940636992368 R central MBON31 <NA>
#> 24 720575940621828443 L central MBON12 <NA>
#> 25 720575940637902938 L central MBON35 <NA>
#> 26 720575940638774606 L central MBON17 <NA>
#> 27 720575940639697827 R central MBON14 <NA>
#> 28 720575940626833021 L central MBON19 <NA>
#> 29 720575940618008859 L central MBON30 <NA>
#> 30 720575940635841143 L central MBON15 <NA>
#> 31 720575940618249797 R central MBON27 <NA>
#> 32 720575940629856515 L central MBON09 <NA>
#> 33 720575940623905719 R central MBON12 <NA>
#> 34 720575940629529722 L central MBON10 <NA>
#> 35 720575940624659943 L central MBON25,MBON34 <NA>
#> 36 720575940624590316 R central MBON03 <NA>
#> 37 720575940645304430 L central MBON13 <NA>
#> 38 720575940612196850 R central MBON15-like <NA>
#> 39 720575940630767959 L central MBON15 <NA>
#> 40 720575940635082347 L central MBON15-like <NA>
#> 41 720575940628757547 L central MBON15-like <NA>
#> 42 720575940627144069 R central MBON25,MBON34 <NA>
#> 43 720575940610647416 R central MBON10 <NA>
#> 44 720575940622093436 R central MBON15 <NA>
#> 45 720575940624696810 L central MBON15-like <NA>
#> 46 720575940629422086 L central MBON09 <NA>
#> 47 720575940647328900 R central MBON10 <NA>
#> 48 720575940650386553 L central MBON17-like <NA>
#> 49 720575940639556467 R central MBON10 <NA>
#> 50 720575940612455338 R central MBON15 <NA>
#> 51 720575940617749538 R central MBON11 <NA>
#> 52 720575940617760257 R central MBON17 <NA>
#> 53 720575940619810389 R central MBON25,MBON34 <NA>
#> 54 720575940634482783 R central MBON19 <NA>
#> 55 720575940644615716 L central MBON31 <NA>
#> 56 720575940626109315 R central MBON19 <NA>
#> 57 720575940623377802 L central MBON16 <NA>
#> 58 720575940626744921 R central MBON16 <NA>
#> 59 720575940623464316 R central MBON24 <NA>
#> 60 720575940622979277 L central MBON27 <NA>
#> 61 720575940614892182 R central MBON28 <NA>
#> 62 720575940620715224 L central MBON21 <NA>
#> 63 720575940643863496 L central MBON20 <NA>
#> 64 720575940621777391 R central MBON21 <NA>
#> 65 720575940606953858 R central MBON23 <NA>
#> 66 720575940630075703 L central MBON12 <NA>
#> 67 720575940652390134 L central MBON07 <NA>
#> 68 720575940632535756 L central MBON14 <NA>
#> 69 720575940643696288 L central MBON14 <NA>
#> 70 720575940623201833 L central MBON11 <NA>
#> 71 720575940635063135 R central MBON22 <NA>
#> 72 720575940616463477 L central MBON22 <NA>
#> 73 720575940629981440 L central MBON26 <NA>
#> 74 720575940623182847 L central MBON33 <NA>
#> 75 720575940626315010 R central MBON13 <NA>
#> 76 720575940632943277 R central MBON35 <NA>
#> 77 720575940624539284 L central MBON18 <NA>
#> 78 720575940620464321 L central MBON04 <NA>
#> 79 720575940628783363 R central MBON07 <NA>
#> 80 720575940643309197 L central MBON01 <NA>
#> 81 720575940614392999 L central MBON29 <NA>
#> 82 720575940617302365 L central MBON07 <NA>
#> 83 720575940622997453 R central MBON18 <NA>
#> 84 720575940624694503 L central MBON03 <NA>
#> 85 720575940628734376 R central MBON04 <NA>
#> 86 720575940610964946 R central MBON09 <NA>
#> 87 720575940607155890 R central MBON26 <NA>
#> 88 720575940623381956 R central MBON07 <NA>
#> 89 720575940630864847 R central MBON09 <NA>
#> 90 720575940638028607 R central MBON06 <NA>
#> 91 720575940621164720 L central MBON05 <NA>
#> 92 720575940623841463 L central MBON19 <NA>
#> 93 720575940631177803 L central MBON24 <NA>
#> 94 720575940624489964 R central MBON25,MBON34 <NA>
#> 95 720575940616398303 L central MBON25,MBON34 <NA>
#> 96 720575940623750325 L central MBON25,MBON34 <NA>
#> 97 612371421 R <NA> MBON01 <NA>
#> 98 673509195 L <NA> MBON01 <NA>
#> 99 424789697 R <NA> MBON02 <NA>
#> 100 5813022341 L <NA> MBON02 <NA>
#> 101 487925037 R <NA> MBON03 <NA>
#> 102 612738462 L <NA> MBON03 <NA>
#> 103 487925063 R <NA> MBON04 <NA>
#> 104 613079053 L <NA> MBON04 <NA>
#> 105 1386512867 R <NA> MBON05 <NA>
#> 106 799586652 L <NA> MBON05 <NA>
#> 107 422725634 L <NA> MBON06 <NA>
#> 108 5813061512 R <NA> MBON06 <NA>
#> 109 1234386037 R <NA> MBON07 <NA>
#> 110 611477605 L <NA> MBON07 <NA>
#> 111 733036127 R <NA> MBON07 <NA>
#> 112 920470959 L <NA> MBON07 <NA>
#> 113 1016835041 L <NA> MBON09 <NA>
#> 114 1048215779 L <NA> MBON09 <NA>
#> 115 1078693835 R <NA> MBON09 <NA>
#> 116 613719036 R <NA> MBON10 <NA>
#> 117 672352543 R <NA> MBON10 <NA>
#> 118 768555687 R <NA> MBON10 <NA>
#> 119 424767514 R <NA> MBON11 <NA>
#> 120 517518166 L <NA> MBON11 <NA>
#> 121 704466265 R <NA> MBON12 <NA>
#> 122 861665641 R <NA> MBON12 <NA>
#> 123 1139667240 R <NA> MBON13 <NA>
#> 124 300972942 R <NA> MBON14 <NA>
#> 125 394225044 L <NA> MBON14 <NA>
#> 126 5813067721 L <NA> MBON14 <NA>
#> 127 5813068729 R <NA> MBON14 <NA>
#> 128 642664141 R <NA> MBON15 <NA>
#> 129 673702721 R <NA> MBON15 <NA>
#> 130 457175171 R <NA> MBON15-like <NA>
#> 131 579916831 R <NA> MBON15-like <NA>
#> 132 673366098 R <NA> MBON16 <NA>
#> 133 5812981264 R <NA> MBON17 <NA>
#> 134 5812981543 R <NA> MBON17-like <NA>
#> 135 457196444 L <NA> MBON18 <NA>
#> 136 5813020828 R <NA> MBON18 <NA>
#> 137 423774471 R <NA> MBON19 <NA>
#> 138 517854468 R <NA> MBON19 <NA>
#> 139 792368888 R <NA> MBON20 <NA>
#> 140 5813022896 R <NA> MBON21 <NA>
#> 141 985813153 L <NA> MBON21 <NA>
#> 142 5813042659 R <NA> MBON22 <NA>
#> 143 985131499 L <NA> MBON22 <NA>
#> 144 423382015 R <NA> MBON23 <NA>
#> 145 487143497 R <NA> MBON24 <NA>
#> 146 550081497 L <NA> MBON24 <NA>
#> 147 612742248 L <NA> MBON25 <NA>
#> 148 612422902 R <NA> MBON25 <NA>
#> 149 912951014 L <NA> MBON26 <NA>
#> 150 895441451 R <NA> MBON26 <NA>
#> 151 5813061538 L <NA> MBON27 <NA>
#> 152 5813117385 R <NA> MBON27 <NA>
#> 153 457196643 R <NA> MBON28 <NA>
#> 154 5813058048 R <NA> MBON29 <NA>
#> 155 5813052909 L <NA> MBON29 <NA>
#> 156 5813022234 R <NA> MBON30 <NA>
#> 157 5813040205 L <NA> MBON30 <NA>
#> 158 706948318 L <NA> MBON31 <NA>
#> 159 894020730 R <NA> MBON31 <NA>
#> 160 642732835 R <NA> MBON32 <NA>
#> 161 643847447 L <NA> MBON32 <NA>
#> 162 518670779 L <NA> MBON33 <NA>
#> 163 547552266 R <NA> MBON33 <NA>
#> 164 1173814525 L <NA> MBON34 <NA>
#> 165 5813033000 R <NA> MBON34 <NA>
#> 166 518930199 R <NA> MBON35 <NA>
#> 167 611089775 L <NA> MBON35 <NA>
#> instance dataset key
#> 1 MBON02_L flywire fw:720575940624185095
#> 2 MBON01_R flywire fw:720575940624117245
#> 3 MBON32_R flywire fw:720575940638526278
#> 4 MBON10_R flywire fw:720575940629585602
#> 5 MBON30_R flywire fw:720575940637934308
#> 6 MBON10_L flywire fw:720575940632118343
#> 7 MBON32_L flywire fw:720575940609959637
#> 8 MBON06_L flywire fw:720575940638163428
#> 9 MBON05_R flywire fw:720575940630496374
#> 10 MBON10_L flywire fw:720575940642142861
#> 11 MBON20_R flywire fw:720575940611344078
#> 12 MBON17-like_R flywire fw:720575940634822751
#> 13 MBON02_R flywire fw:720575940617552340
#> 14 MBON33_R flywire fw:720575940624280328
#> 15 MBON23_L flywire fw:720575940617567206
#> 16 MBON29_R flywire fw:720575940643700640
#> 17 MBON10_R flywire fw:720575940615221811
#> 18 MBON14_R flywire fw:720575940614026193
#> 19 MBON10_L flywire fw:720575940633209647
#> 20 MBON12_R flywire fw:720575940623001480
#> 21 MBON15-like_R flywire fw:720575940608304220
#> 22 MBON28_L flywire fw:720575940614595218
#> 23 MBON31_R flywire fw:720575940636992368
#> 24 MBON12_L flywire fw:720575940621828443
#> 25 MBON35_L flywire fw:720575940637902938
#> 26 MBON17_L flywire fw:720575940638774606
#> 27 MBON14_R flywire fw:720575940639697827
#> 28 MBON19_L flywire fw:720575940626833021
#> 29 MBON30_L flywire fw:720575940618008859
#> 30 MBON15_L flywire fw:720575940635841143
#> 31 MBON27_R flywire fw:720575940618249797
#> 32 MBON09_L flywire fw:720575940629856515
#> 33 MBON12_R flywire fw:720575940623905719
#> 34 MBON10_L flywire fw:720575940629529722
#> 35 MBON25,MBON34_L flywire fw:720575940624659943
#> 36 MBON03_R flywire fw:720575940624590316
#> 37 MBON13_L flywire fw:720575940645304430
#> 38 MBON15-like_R flywire fw:720575940612196850
#> 39 MBON15_L flywire fw:720575940630767959
#> 40 MBON15-like_L flywire fw:720575940635082347
#> 41 MBON15-like_L flywire fw:720575940628757547
#> 42 MBON25,MBON34_R flywire fw:720575940627144069
#> 43 MBON10_R flywire fw:720575940610647416
#> 44 MBON15_R flywire fw:720575940622093436
#> 45 MBON15-like_L flywire fw:720575940624696810
#> 46 MBON09_L flywire fw:720575940629422086
#> 47 MBON10_R flywire fw:720575940647328900
#> 48 MBON17-like_L flywire fw:720575940650386553
#> 49 MBON10_R flywire fw:720575940639556467
#> 50 MBON15_R flywire fw:720575940612455338
#> 51 MBON11_R flywire fw:720575940617749538
#> 52 MBON17_R flywire fw:720575940617760257
#> 53 MBON25,MBON34_R flywire fw:720575940619810389
#> 54 MBON19_R flywire fw:720575940634482783
#> 55 MBON31_L flywire fw:720575940644615716
#> 56 MBON19_R flywire fw:720575940626109315
#> 57 MBON16_L flywire fw:720575940623377802
#> 58 MBON16_R flywire fw:720575940626744921
#> 59 MBON24_R flywire fw:720575940623464316
#> 60 MBON27_L flywire fw:720575940622979277
#> 61 MBON28_R flywire fw:720575940614892182
#> 62 MBON21_L flywire fw:720575940620715224
#> 63 MBON20_L flywire fw:720575940643863496
#> 64 MBON21_R flywire fw:720575940621777391
#> 65 MBON23_R flywire fw:720575940606953858
#> 66 MBON12_L flywire fw:720575940630075703
#> 67 MBON07_L flywire fw:720575940652390134
#> 68 MBON14_L flywire fw:720575940632535756
#> 69 MBON14_L flywire fw:720575940643696288
#> 70 MBON11_L flywire fw:720575940623201833
#> 71 MBON22_R flywire fw:720575940635063135
#> 72 MBON22_L flywire fw:720575940616463477
#> 73 MBON26_L flywire fw:720575940629981440
#> 74 MBON33_L flywire fw:720575940623182847
#> 75 MBON13_R flywire fw:720575940626315010
#> 76 MBON35_R flywire fw:720575940632943277
#> 77 MBON18_L flywire fw:720575940624539284
#> 78 MBON04_L flywire fw:720575940620464321
#> 79 MBON07_R flywire fw:720575940628783363
#> 80 MBON01_L flywire fw:720575940643309197
#> 81 MBON29_L flywire fw:720575940614392999
#> 82 MBON07_L flywire fw:720575940617302365
#> 83 MBON18_R flywire fw:720575940622997453
#> 84 MBON03_L flywire fw:720575940624694503
#> 85 MBON04_R flywire fw:720575940628734376
#> 86 MBON09_R flywire fw:720575940610964946
#> 87 MBON26_R flywire fw:720575940607155890
#> 88 MBON07_R flywire fw:720575940623381956
#> 89 MBON09_R flywire fw:720575940630864847
#> 90 MBON06_R flywire fw:720575940638028607
#> 91 MBON05_L flywire fw:720575940621164720
#> 92 MBON19_L flywire fw:720575940623841463
#> 93 MBON24_L flywire fw:720575940631177803
#> 94 MBON25,MBON34_R flywire fw:720575940624489964
#> 95 MBON25,MBON34_L flywire fw:720575940616398303
#> 96 MBON25,MBON34_L flywire fw:720575940623750325
#> 97 MBON01(y5B'2a)_R hemibrain hb:612371421
#> 98 MBON01(y5B'2a)_L hemibrain hb:673509195
#> 99 MBON02(B2B'2a)_R hemibrain hb:424789697
#> 100 MBON02(B2B'2a)_L hemibrain hb:5813022341
#> 101 MBON03(B'2mp)_R hemibrain hb:487925037
#> 102 MBON03(B'2mp)_L hemibrain hb:612738462
#> 103 MBON04(B'2mp_bilateral)_R hemibrain hb:487925063
#> 104 MBON04(B'2mp_bilateral)_L hemibrain hb:613079053
#> 105 MBON05(y4>y1y2)_R hemibrain hb:1386512867
#> 106 MBON05(y4>y1y2)(AVM07)_L hemibrain hb:799586652
#> 107 MBON06(B1>a)(AVM07)_L hemibrain hb:422725634
#> 108 MBON06(B1>a)_R hemibrain hb:5813061512
#> 109 MBON07(a1)_R hemibrain hb:1234386037
#> 110 MBON07(a1)_L hemibrain hb:611477605
#> 111 MBON07(a1)_R hemibrain hb:733036127
#> 112 MBON07(a1)_L hemibrain hb:920470959
#> 113 MBON09(y3B'1)(AVM17)_L hemibrain hb:1016835041
#> 114 MBON09(y3B'1)(AVM17)_L hemibrain hb:1048215779
#> 115 MBON09(y3B'1)_R hemibrain hb:1078693835
#> 116 MBON10(B'1)_R hemibrain hb:613719036
#> 117 MBON10(B'1)_R hemibrain hb:672352543
#> 118 MBON10(B'1)_R hemibrain hb:768555687
#> 119 MBON11(y1pedc>a/B)_R hemibrain hb:424767514
#> 120 MBON11(y1pedc>a/B)(ADM05)_L hemibrain hb:517518166
#> 121 MBON12(y2a'1)_R hemibrain hb:704466265
#> 122 MBON12(y2a'1)_R hemibrain hb:861665641
#> 123 MBON13(a'2)_R hemibrain hb:1139667240
#> 124 MBON14(a3)_R hemibrain hb:300972942
#> 125 MBON14(a3)_L hemibrain hb:394225044
#> 126 MBON14(a3)_L hemibrain hb:5813067721
#> 127 MBON14(a3)_R hemibrain hb:5813068729
#> 128 MBON15(a'1)_R hemibrain hb:642664141
#> 129 MBON15(a'1)_R hemibrain hb:673702721
#> 130 MBON15-like(a'1a'2)_R hemibrain hb:457175171
#> 131 MBON15-like(a'1a'2)_R hemibrain hb:579916831
#> 132 MBON16(a'3ap)_R hemibrain hb:673366098
#> 133 MBON17(a'3m)_R hemibrain hb:5812981264
#> 134 MBON17-like(a'2a'3)_R hemibrain hb:5812981543
#> 135 MBON18(a2sc)(PDL05)_L hemibrain hb:457196444
#> 136 MBON18(a2sc)_R hemibrain hb:5813020828
#> 137 MBON19(a2p3p)_R hemibrain hb:423774471
#> 138 MBON19(a2p3p)_R hemibrain hb:517854468
#> 139 MBON20(y1y2)_R hemibrain hb:792368888
#> 140 MBON21(y4y5)_R hemibrain hb:5813022896
#> 141 MBON21(y4y5)(PVL06)_L hemibrain hb:985813153
#> 142 MBON22(calyx)_R hemibrain hb:5813042659
#> 143 MBON22(calyx)(PVL06)_L hemibrain hb:985131499
#> 144 MBON23(a2sp)_R hemibrain hb:423382015
#> 145 MBON24(B2y5)_R hemibrain hb:487143497
#> 146 MBON24(B2y5)(PDL05)_L hemibrain hb:550081497
#> 147 MBON25(y1y2)_L hemibrain hb:612742248
#> 148 MBON25(y1y2)_R hemibrain hb:612422902
#> 149 MBON26(B'2d)(PDM28)_L hemibrain hb:912951014
#> 150 MBON26(B'2d)_R hemibrain hb:895441451
#> 151 MBON27(y5d)(PVM03)_L hemibrain hb:5813061538
#> 152 MBON27(y5d)_R hemibrain hb:5813117385
#> 153 MBON16-like(a'3a)_R hemibrain hb:457196643
#> 154 MBON29(y4y5)_R hemibrain hb:5813058048
#> 155 MBON29(y4y5)(PVL06)_L hemibrain hb:5813052909
#> 156 MBON30(y1y2y3)_R hemibrain hb:5813022234
#> 157 MBON30(y1y2y3)(AVM07)_L hemibrain hb:5813040205
#> 158 MBON31(a'1a)(ADM10)_L hemibrain hb:706948318
#> 159 MBON31(a'1a)_R hemibrain hb:894020730
#> 160 MBON32(y2)_R hemibrain hb:642732835
#> 161 MBON32(y2)(ADM08)_L hemibrain hb:643847447
#> 162 MBON33(y2y3)(ADM05)_L hemibrain hb:518670779
#> 163 MBON33(y2y3)_R hemibrain hb:547552266
#> 164 MBON34(y2)_L hemibrain hb:1173814525
#> 165 MBON34(y2)_R hemibrain hb:5813033000
#> 166 MBON35(y2)_R hemibrain hb:518930199
#> 167 MBON35(y2)_L hemibrain 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. Dropping 929/1703 output partner types with total weight 17648/41972