docs/articles/vpns-example.md
In natverse/flycircuit: Functions to support the analysis of the FlyCircuit single neuron dataset
A short guide to analysing visual projection neurons
Set up environment
# Allow production of figures using RGL
library(knitr)
knit_hooks$set(rgl = hook_rgl)
opts_chunk$set(dev = c("png", "pdf"))
# sidestep a bug in knitr that fails to produce output dir for rgl snapshots
dir.create("figure")
Load flycircuit and nat packages
library(flycircuit)
## Loading required package: rgl
library(nat)
Load VPN NBLAST scores
Download NBLAST scores for VPNs and load them into the workspace.
# Download scores...
fc_download_data("http://jefferislab.org/si/nblast/flycircuit/vpnsblastcv2.5.ff",
type = "ff")
## [1] TRUE
# ...and set an option to use them as the default
options(flycircuit.scoremat = "vpnsblastcv2.5.ff")
Show the top 10 scores for the a neuron:
scores = fc_nblast("ChaMARCM-F000003_seg001")
## attaching: vpnsblastcv2.5
## opening ff /Library/Frameworks/R.framework/Versions/3.0/Resources/library/flycircuit/extdata/ff/vpnsblastcv2.5.ff
sort(scores, decreasing = TRUE)[1:10]
## ChaMARCM-F000003_seg001 GadMARCM-F000623_seg002
## 6253 3607
## ChaMARCM-F000289_seg001 FruMARCM-M000008_seg001
## 3470 3411
## ChaMARCM-F000826_seg001 DvGlutMARCM-F002277_seg001
## 3343 3321
## DvGlutMARCM-F002956_seg001 ChaMARCM-F000087_seg002
## 3302 3251
## DvGlutMARCM-F004615_seg001 DvGlutMARCM-F004068_seg001
## 3232 3150
Notice that the top score was of course the
Download VPN morphologies
At the moment we have the NBLAST scores for the VPNs, but no other information about them.
Let's download the neurons. Or rather the neurons, but an object that we can save to our
local disk that contains information about what neurons are present.
# Download the data
vpns <- read.neuronlistfh("http://jefferislab.org/si/nblast/flycircuit/vpns.rds",
getOption("flycircuit.datadir"))
# show what kind of data we have for the neurons
head(vpns)
## idid gene_name soma_side
## 5HT1bMARCM-F000019_seg001 11625 5HT1bMARCM-F000019_seg001 R
## 5HT1bMARCM-F000024_seg001 11193 5HT1bMARCM-F000024_seg001 L
## 5HT1bMARCM-F000026_seg001 11196 5HT1bMARCM-F000026_seg001 L
## 5HT1bMARCM-M000046_seg001 2500 5HT1bMARCM-M000046_seg001 L
## ChaMARCM-F000003_seg001 11568 ChaMARCM-F000003_seg001 L
## ChaMARCM-F000008_seg001 6140 ChaMARCM-F000008_seg001 R
## flipped
## 5HT1bMARCM-F000019_seg001 TRUE
## 5HT1bMARCM-F000024_seg001 FALSE
## 5HT1bMARCM-F000026_seg001 FALSE
## 5HT1bMARCM-M000046_seg001 FALSE
## ChaMARCM-F000003_seg001 FALSE
## ChaMARCM-F000008_seg001 TRUE
## neuronidurl
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=11625
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=11193
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=11196
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=2500
## ChaMARCM-F000003_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=11568
## ChaMARCM-F000008_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=6140
## Name Driver
## 5HT1bMARCM-F000019_seg001 5-HT1B-F-400000 5-HT1B-Gal4
## 5HT1bMARCM-F000024_seg001 5-HT1B-F-500013 5-HT1B-Gal4
## 5HT1bMARCM-F000026_seg001 5-HT1B-F-500016 5-HT1B-Gal4
## 5HT1bMARCM-M000046_seg001 5-HT1B-M-400004 5-HT1B-Gal4
## ChaMARCM-F000003_seg001 Cha-F-200000 Cha-Gal4
## ChaMARCM-F000008_seg001 Cha-F-000004 Cha-Gal4
## Gender_Age
## 5HT1bMARCM-F000019_seg001 Female / Adult 5~15 days
## 5HT1bMARCM-F000024_seg001 Female / Adult 5~15 days
## 5HT1bMARCM-F000026_seg001 Female / Adult 5~15 days
## 5HT1bMARCM-M000046_seg001 Male / Adult 5~15 days
## ChaMARCM-F000003_seg001 Female / Adult 5~15 days
## ChaMARCM-F000008_seg001 Female / Adult 5~15 days
## Soma_Coordinate
## 5HT1bMARCM-F000019_seg001 X: -212 , Y: -70 , Z: -90
## 5HT1bMARCM-F000024_seg001 X: 217 , Y: -61 , Z: -93
## 5HT1bMARCM-F000026_seg001 X: 258 , Y: -40 , Z: -118
## 5HT1bMARCM-M000046_seg001 X: 201 , Y: -49 , Z: -107
## ChaMARCM-F000003_seg001 X: 147 , Y: -160 , Z: -58
## ChaMARCM-F000008_seg001 X: -194 , Y: -167 , Z: -11
## Putative_neurotransmitter Putative_birth_time
## 5HT1bMARCM-F000019_seg001 unknown day 4
## 5HT1bMARCM-F000024_seg001 unknown day 5
## 5HT1bMARCM-F000026_seg001 unknown day 5
## 5HT1bMARCM-M000046_seg001 unknown day 4
## ChaMARCM-F000003_seg001 Acetylcholine day 2
## ChaMARCM-F000008_seg001 Acetylcholine embryo
## Author Stock Lineage Gender
## 5HT1bMARCM-F000019_seg001 AS_Chiang 5-HT1B-Gal4 F
## 5HT1bMARCM-F000024_seg001 AS_Chiang 5-HT1B-Gal4 F
## 5HT1bMARCM-F000026_seg001 AS_Chiang 5-HT1B-Gal4 F
## 5HT1bMARCM-M000046_seg001 AS_Chiang 5-HT1B-Gal4 M
## ChaMARCM-F000003_seg001 AS_Chiang Cha-Gal4 F
## ChaMARCM-F000008_seg001 AS_Chiang Cha-Gal4 F
## Age Date Soma_X Soma_Y Soma_Z
## 5HT1bMARCM-F000019_seg001 Adult 5~15 days 2009-05-26 -212 -70 -90
## 5HT1bMARCM-F000024_seg001 Adult 5~15 days 2009-05-31 217 -61 -93
## 5HT1bMARCM-F000026_seg001 Adult 5~15 days 2009-05-31 258 -40 -118
## 5HT1bMARCM-M000046_seg001 Adult 5~15 days 2009-05-26 201 -49 -107
## ChaMARCM-F000003_seg001 Adult 5~15 days 2009-05-26 147 -160 -58
## ChaMARCM-F000008_seg001 Adult 5~15 days 2010-01-25 -194 -167 -11
## lsmjpgurl
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/5HT1bMARCM-F000019_seg001_lsm.jpg
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/5HT1bMARCM-F000024_seg001_lsm.jpg
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/5HT1bMARCM-F000026_seg001_lsm.jpg
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/5HT1bMARCM-M000046_seg001_lsm.jpg
## ChaMARCM-F000003_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/ChaMARCM-F000003_seg001_lsm.jpg
## ChaMARCM-F000008_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/ChaMARCM-F000008_seg001_lsm.jpg
## lsmjpg300url
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/5HT1bMARCM-F000019_seg001_lsm.jpg
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/5HT1bMARCM-F000024_seg001_lsm.jpg
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/5HT1bMARCM-F000026_seg001_lsm.jpg
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/5HT1bMARCM-M000046_seg001_lsm.jpg
## ChaMARCM-F000003_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/ChaMARCM-F000003_seg001_lsm.jpg
## ChaMARCM-F000008_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/ChaMARCM-F000008_seg001_lsm.jpg
## ziplsmurl
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/zipLSM/5HT1bMARCM-F000019_seg001.lsm.zip
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/zipLSM/5HT1bMARCM-F000024_seg001.lsm.zip
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/zipLSM/5HT1bMARCM-F000026_seg001.lsm.zip
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/zipLSM/5HT1bMARCM-M000046_seg001.lsm.zip
## ChaMARCM-F000003_seg001 http://flycircuit.tw/zipLSM/ChaMARCM-F000003_seg001.lsm.zip
## ChaMARCM-F000008_seg001 http://flycircuit.tw/zipLSM/ChaMARCM-F000008_seg001.lsm.zip
## lsm ziplsmsize
## 5HT1bMARCM-F000019_seg001 5HT1bMARCM-F000019_seg001.lsm 118198735
## 5HT1bMARCM-F000024_seg001 5HT1bMARCM-F000024_seg001.lsm 131777383
## 5HT1bMARCM-F000026_seg001 5HT1bMARCM-F000026_seg001.lsm 104434363
## 5HT1bMARCM-M000046_seg001 5HT1bMARCM-M000046_seg001.lsm 105427290
## ChaMARCM-F000003_seg001 ChaMARCM-F000003_seg001.lsm 76352938
## ChaMARCM-F000008_seg001 ChaMARCM-F000008_seg001.lsm 107805672
## flashurl
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/lsm_movie/female/5HT1bMARCM-F000019_seg001_lsm.flv
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/lsm_movie/female/5HT1bMARCM-F000024_seg001_lsm.flv
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/lsm_movie/female/5HT1bMARCM-F000026_seg001_lsm.flv
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/lsm_movie/male/5HT1bMARCM-M000046_seg001_lsm.flv
## ChaMARCM-F000003_seg001 http://flycircuit.tw/lsm_movie/female/ChaMARCM-F000003_seg001_lsm.flv
## ChaMARCM-F000008_seg001 http://flycircuit.tw/lsm_movie/female/ChaMARCM-F000008_seg001_lsm.flv
## flashsize download_time
## 5HT1bMARCM-F000019_seg001 2224773 2011-01-26 09:33:49
## 5HT1bMARCM-F000024_seg001 2482342 2011-01-26 03:12:52
## 5HT1bMARCM-F000026_seg001 2253510 2011-01-26 03:12:59
## 5HT1bMARCM-M000046_seg001 2442094 2011-01-25 21:45:29
## ChaMARCM-F000003_seg001 2370166 2011-01-26 09:33:33
## ChaMARCM-F000008_seg001 2341834 2011-01-26 00:39:38
## last_updated SpaceCoding rAL lAL rAMMC
## 5HT1bMARCM-F000019_seg001 2011-01-28 18:13:54 PPPPUU3333 0 0 0
## 5HT1bMARCM-F000024_seg001 2011-01-28 18:13:54 pppsss444 0 0 0
## 5HT1bMARCM-F000026_seg001 2011-01-28 18:13:54 pppp444 0 0 0
## 5HT1bMARCM-M000046_seg001 2011-01-28 18:13:54 ffffpppqqqqq 0 0 0
## ChaMARCM-F000003_seg001 2011-01-28 18:13:54 ppppuuu 0 0 0
## ChaMARCM-F000008_seg001 2011-01-28 18:13:54 PPPPQUUUU 0 0 0
## lAMMC rCAL lCAL rCCP lCCP rCMP lCMP rCVLP lCVLP
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 3283
## ChaMARCM-F000003_seg001 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 0
## rDLP lDLP rDMP lDMP rEB lEB rFB lFB rFSPP lFSPP
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000003_seg001 0 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 0 0
## rIDFP lIDFP rIDLP lIDLP rLAT lLAT rLH lLH rLOB
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 7057
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000003_seg001 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 11158
## lLOB rLOP lLOP rMB lMB rMED lMED rNOD lNOD rOG
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 0 59
## 5HT1bMARCM-F000024_seg001 2341 0 0 0 0 0 921 0 0 0
## 5HT1bMARCM-F000026_seg001 7676 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 1696 0 47378 0 0 0 0 0 0 0
## ChaMARCM-F000003_seg001 8838 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 5 0 0 0 0 0 0 0 3636
## lOG rOPTU lOPTU rPAN lPAN rPCB lPCB rSDFP lSDFP
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000003_seg001 1892 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 0
## rSOG lSOG rSPP lSPP rVLP lVLP rVMP lVMP X
## 5HT1bMARCM-F000019_seg001 0 0 0 0 3248 0 0 0 408.6
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 2712 0 0 415.4
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 1713 0 0 440.5
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 412.1
## ChaMARCM-F000003_seg001 0 0 0 0 0 0 0 0 372.9
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 398.9
## Y Z
## 5HT1bMARCM-F000019_seg001 150.4 84.57
## 5HT1bMARCM-F000024_seg001 144.7 85.29
## 5HT1bMARCM-F000026_seg001 134.9 96.17
## 5HT1bMARCM-M000046_seg001 142.8 88.28
## ChaMARCM-F000003_seg001 198.7 68.02
## ChaMARCM-F000008_seg001 199.6 49.04
We'll be plotting these neurons a lot, so let's set an option that will save us some typing:
options(nat.default.neuronlist = "vpns")
# also make sure default view is frontal to fly brain
r3dDefaults$userMatrix = structure(c(1, 0, 0, 0, 0, -1, 0, 0, 0, 0, -1, 0, 0,
0, 0, 1), .Dim = c(4L, 4L))
Simple plot
Let's plot (automagically downloading) the first 3 neurons
open3d()
## glX
## 1
plot3d(vpns[1:3])
# and add brain surface
fcwbsurf()
Cluster cells by morphology
Let's find all the bilateral lobula complex neurons, insisting on at least 500
voxels in each optic lobula complex.
bilateral = subset(vpns, (rLOP + rLOB) > 500 & (lLOP + lLOB) > 500, rval = "names")
hcbilateral <- hclustfc(bilateral)
# two big clusters
library(dendroextras)
plot(colour_clusters(hcbilateral, k = 2))
# or 7 finer scale ones
plot(colour_clusters(hcbilateral, k = 7))
Plot 2 major clusters
Now let's look at the two major clusters:
open3d()
## glX
## 2
plot3d(hcbilateral, k = 2, db = vpns)
# add lobula
fcwbnpsurf("LO_L", alpha = 0.5)
Looks like Lobula vs Medulla (not that much in Lobula Plate)
# remove lobula
pop3d()
# ... and add lobula plate
fcwbnpsurf("LOP_L", alpha = 0.5)
Plot 7 finer scale clusters
clear3d()
plot3d(hcbilateral, k = 7, db = vpns)
More NBLASTing
How do other neurons compare with 5HT1bMARCM-F000019_seg001? Let's NBLAST it against all the other neurons and look at the distribution of scores.
results <- fc_nblast(names(vpns)[1], names(vpns))
hist(results, breaks = 100)
The little bump at 5717.3936 is for 5HT1bMARCM-F000019_seg001 itself, which has the highest score possible as there should be no distance between it and itself. Let's plot the next four hits, along with the query neuron in black, to see how similar they are:
open3d()
## glX
## 3
plot3d(names(vpns)[1], col = "black")
plot3dfc(names(sort(results, decreasing = TRUE)[2:5]))
Hmm, they look pretty similar. Let's plot the four worst hits for comparison:
open3d()
## glX
## 4
plot3d(names(vpns)[1], col = "black")
plot3dfc(names(sort(results)[1:4]))
Definitely different.
natverse/flycircuit documentation built on Jan. 26, 2023, 6:46 p.m.
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A short guide to analysing visual projection neurons
Set up environment
# Allow production of figures using RGL
library(knitr)
knit_hooks$set(rgl = hook_rgl)
opts_chunk$set(dev = c("png", "pdf"))
# sidestep a bug in knitr that fails to produce output dir for rgl snapshots
dir.create("figure")
Load flycircuit and nat packages
library(flycircuit)
## Loading required package: rgl
library(nat)
Load VPN NBLAST scores
Download NBLAST scores for VPNs and load them into the workspace.
# Download scores...
fc_download_data("http://jefferislab.org/si/nblast/flycircuit/vpnsblastcv2.5.ff",
type = "ff")
## [1] TRUE
# ...and set an option to use them as the default
options(flycircuit.scoremat = "vpnsblastcv2.5.ff")
Show the top 10 scores for the a neuron:
scores = fc_nblast("ChaMARCM-F000003_seg001")
## attaching: vpnsblastcv2.5
## opening ff /Library/Frameworks/R.framework/Versions/3.0/Resources/library/flycircuit/extdata/ff/vpnsblastcv2.5.ff
sort(scores, decreasing = TRUE)[1:10]
## ChaMARCM-F000003_seg001 GadMARCM-F000623_seg002
## 6253 3607
## ChaMARCM-F000289_seg001 FruMARCM-M000008_seg001
## 3470 3411
## ChaMARCM-F000826_seg001 DvGlutMARCM-F002277_seg001
## 3343 3321
## DvGlutMARCM-F002956_seg001 ChaMARCM-F000087_seg002
## 3302 3251
## DvGlutMARCM-F004615_seg001 DvGlutMARCM-F004068_seg001
## 3232 3150
Notice that the top score was of course the
Download VPN morphologies
At the moment we have the NBLAST scores for the VPNs, but no other information about them. Let's download the neurons. Or rather the neurons, but an object that we can save to our local disk that contains information about what neurons are present.
# Download the data
vpns <- read.neuronlistfh("http://jefferislab.org/si/nblast/flycircuit/vpns.rds",
getOption("flycircuit.datadir"))
# show what kind of data we have for the neurons
head(vpns)
## idid gene_name soma_side
## 5HT1bMARCM-F000019_seg001 11625 5HT1bMARCM-F000019_seg001 R
## 5HT1bMARCM-F000024_seg001 11193 5HT1bMARCM-F000024_seg001 L
## 5HT1bMARCM-F000026_seg001 11196 5HT1bMARCM-F000026_seg001 L
## 5HT1bMARCM-M000046_seg001 2500 5HT1bMARCM-M000046_seg001 L
## ChaMARCM-F000003_seg001 11568 ChaMARCM-F000003_seg001 L
## ChaMARCM-F000008_seg001 6140 ChaMARCM-F000008_seg001 R
## flipped
## 5HT1bMARCM-F000019_seg001 TRUE
## 5HT1bMARCM-F000024_seg001 FALSE
## 5HT1bMARCM-F000026_seg001 FALSE
## 5HT1bMARCM-M000046_seg001 FALSE
## ChaMARCM-F000003_seg001 FALSE
## ChaMARCM-F000008_seg001 TRUE
## neuronidurl
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=11625
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=11193
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=11196
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=2500
## ChaMARCM-F000003_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=11568
## ChaMARCM-F000008_seg001 http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&idid=6140
## Name Driver
## 5HT1bMARCM-F000019_seg001 5-HT1B-F-400000 5-HT1B-Gal4
## 5HT1bMARCM-F000024_seg001 5-HT1B-F-500013 5-HT1B-Gal4
## 5HT1bMARCM-F000026_seg001 5-HT1B-F-500016 5-HT1B-Gal4
## 5HT1bMARCM-M000046_seg001 5-HT1B-M-400004 5-HT1B-Gal4
## ChaMARCM-F000003_seg001 Cha-F-200000 Cha-Gal4
## ChaMARCM-F000008_seg001 Cha-F-000004 Cha-Gal4
## Gender_Age
## 5HT1bMARCM-F000019_seg001 Female / Adult 5~15 days
## 5HT1bMARCM-F000024_seg001 Female / Adult 5~15 days
## 5HT1bMARCM-F000026_seg001 Female / Adult 5~15 days
## 5HT1bMARCM-M000046_seg001 Male / Adult 5~15 days
## ChaMARCM-F000003_seg001 Female / Adult 5~15 days
## ChaMARCM-F000008_seg001 Female / Adult 5~15 days
## Soma_Coordinate
## 5HT1bMARCM-F000019_seg001 X: -212 , Y: -70 , Z: -90
## 5HT1bMARCM-F000024_seg001 X: 217 , Y: -61 , Z: -93
## 5HT1bMARCM-F000026_seg001 X: 258 , Y: -40 , Z: -118
## 5HT1bMARCM-M000046_seg001 X: 201 , Y: -49 , Z: -107
## ChaMARCM-F000003_seg001 X: 147 , Y: -160 , Z: -58
## ChaMARCM-F000008_seg001 X: -194 , Y: -167 , Z: -11
## Putative_neurotransmitter Putative_birth_time
## 5HT1bMARCM-F000019_seg001 unknown day 4
## 5HT1bMARCM-F000024_seg001 unknown day 5
## 5HT1bMARCM-F000026_seg001 unknown day 5
## 5HT1bMARCM-M000046_seg001 unknown day 4
## ChaMARCM-F000003_seg001 Acetylcholine day 2
## ChaMARCM-F000008_seg001 Acetylcholine embryo
## Author Stock Lineage Gender
## 5HT1bMARCM-F000019_seg001 AS_Chiang 5-HT1B-Gal4 F
## 5HT1bMARCM-F000024_seg001 AS_Chiang 5-HT1B-Gal4 F
## 5HT1bMARCM-F000026_seg001 AS_Chiang 5-HT1B-Gal4 F
## 5HT1bMARCM-M000046_seg001 AS_Chiang 5-HT1B-Gal4 M
## ChaMARCM-F000003_seg001 AS_Chiang Cha-Gal4 F
## ChaMARCM-F000008_seg001 AS_Chiang Cha-Gal4 F
## Age Date Soma_X Soma_Y Soma_Z
## 5HT1bMARCM-F000019_seg001 Adult 5~15 days 2009-05-26 -212 -70 -90
## 5HT1bMARCM-F000024_seg001 Adult 5~15 days 2009-05-31 217 -61 -93
## 5HT1bMARCM-F000026_seg001 Adult 5~15 days 2009-05-31 258 -40 -118
## 5HT1bMARCM-M000046_seg001 Adult 5~15 days 2009-05-26 201 -49 -107
## ChaMARCM-F000003_seg001 Adult 5~15 days 2009-05-26 147 -160 -58
## ChaMARCM-F000008_seg001 Adult 5~15 days 2010-01-25 -194 -167 -11
## lsmjpgurl
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/5HT1bMARCM-F000019_seg001_lsm.jpg
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/5HT1bMARCM-F000024_seg001_lsm.jpg
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/5HT1bMARCM-F000026_seg001_lsm.jpg
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/5HT1bMARCM-M000046_seg001_lsm.jpg
## ChaMARCM-F000003_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/ChaMARCM-F000003_seg001_lsm.jpg
## ChaMARCM-F000008_seg001 http://flycircuit.tw/flycircuitImage/LSM_upload/ChaMARCM-F000008_seg001_lsm.jpg
## lsmjpg300url
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/5HT1bMARCM-F000019_seg001_lsm.jpg
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/5HT1bMARCM-F000024_seg001_lsm.jpg
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/5HT1bMARCM-F000026_seg001_lsm.jpg
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/5HT1bMARCM-M000046_seg001_lsm.jpg
## ChaMARCM-F000003_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/ChaMARCM-F000003_seg001_lsm.jpg
## ChaMARCM-F000008_seg001 http://flycircuit.tw/flycircuitImage/LSM_300/ChaMARCM-F000008_seg001_lsm.jpg
## ziplsmurl
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/zipLSM/5HT1bMARCM-F000019_seg001.lsm.zip
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/zipLSM/5HT1bMARCM-F000024_seg001.lsm.zip
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/zipLSM/5HT1bMARCM-F000026_seg001.lsm.zip
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/zipLSM/5HT1bMARCM-M000046_seg001.lsm.zip
## ChaMARCM-F000003_seg001 http://flycircuit.tw/zipLSM/ChaMARCM-F000003_seg001.lsm.zip
## ChaMARCM-F000008_seg001 http://flycircuit.tw/zipLSM/ChaMARCM-F000008_seg001.lsm.zip
## lsm ziplsmsize
## 5HT1bMARCM-F000019_seg001 5HT1bMARCM-F000019_seg001.lsm 118198735
## 5HT1bMARCM-F000024_seg001 5HT1bMARCM-F000024_seg001.lsm 131777383
## 5HT1bMARCM-F000026_seg001 5HT1bMARCM-F000026_seg001.lsm 104434363
## 5HT1bMARCM-M000046_seg001 5HT1bMARCM-M000046_seg001.lsm 105427290
## ChaMARCM-F000003_seg001 ChaMARCM-F000003_seg001.lsm 76352938
## ChaMARCM-F000008_seg001 ChaMARCM-F000008_seg001.lsm 107805672
## flashurl
## 5HT1bMARCM-F000019_seg001 http://flycircuit.tw/lsm_movie/female/5HT1bMARCM-F000019_seg001_lsm.flv
## 5HT1bMARCM-F000024_seg001 http://flycircuit.tw/lsm_movie/female/5HT1bMARCM-F000024_seg001_lsm.flv
## 5HT1bMARCM-F000026_seg001 http://flycircuit.tw/lsm_movie/female/5HT1bMARCM-F000026_seg001_lsm.flv
## 5HT1bMARCM-M000046_seg001 http://flycircuit.tw/lsm_movie/male/5HT1bMARCM-M000046_seg001_lsm.flv
## ChaMARCM-F000003_seg001 http://flycircuit.tw/lsm_movie/female/ChaMARCM-F000003_seg001_lsm.flv
## ChaMARCM-F000008_seg001 http://flycircuit.tw/lsm_movie/female/ChaMARCM-F000008_seg001_lsm.flv
## flashsize download_time
## 5HT1bMARCM-F000019_seg001 2224773 2011-01-26 09:33:49
## 5HT1bMARCM-F000024_seg001 2482342 2011-01-26 03:12:52
## 5HT1bMARCM-F000026_seg001 2253510 2011-01-26 03:12:59
## 5HT1bMARCM-M000046_seg001 2442094 2011-01-25 21:45:29
## ChaMARCM-F000003_seg001 2370166 2011-01-26 09:33:33
## ChaMARCM-F000008_seg001 2341834 2011-01-26 00:39:38
## last_updated SpaceCoding rAL lAL rAMMC
## 5HT1bMARCM-F000019_seg001 2011-01-28 18:13:54 PPPPUU3333 0 0 0
## 5HT1bMARCM-F000024_seg001 2011-01-28 18:13:54 pppsss444 0 0 0
## 5HT1bMARCM-F000026_seg001 2011-01-28 18:13:54 pppp444 0 0 0
## 5HT1bMARCM-M000046_seg001 2011-01-28 18:13:54 ffffpppqqqqq 0 0 0
## ChaMARCM-F000003_seg001 2011-01-28 18:13:54 ppppuuu 0 0 0
## ChaMARCM-F000008_seg001 2011-01-28 18:13:54 PPPPQUUUU 0 0 0
## lAMMC rCAL lCAL rCCP lCCP rCMP lCMP rCVLP lCVLP
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 3283
## ChaMARCM-F000003_seg001 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 0
## rDLP lDLP rDMP lDMP rEB lEB rFB lFB rFSPP lFSPP
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000003_seg001 0 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 0 0
## rIDFP lIDFP rIDLP lIDLP rLAT lLAT rLH lLH rLOB
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 7057
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000003_seg001 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 11158
## lLOB rLOP lLOP rMB lMB rMED lMED rNOD lNOD rOG
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 0 59
## 5HT1bMARCM-F000024_seg001 2341 0 0 0 0 0 921 0 0 0
## 5HT1bMARCM-F000026_seg001 7676 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 1696 0 47378 0 0 0 0 0 0 0
## ChaMARCM-F000003_seg001 8838 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 5 0 0 0 0 0 0 0 3636
## lOG rOPTU lOPTU rPAN lPAN rPCB lPCB rSDFP lSDFP
## 5HT1bMARCM-F000019_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 0 0 0 0
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 0
## ChaMARCM-F000003_seg001 1892 0 0 0 0 0 0 0 0
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 0
## rSOG lSOG rSPP lSPP rVLP lVLP rVMP lVMP X
## 5HT1bMARCM-F000019_seg001 0 0 0 0 3248 0 0 0 408.6
## 5HT1bMARCM-F000024_seg001 0 0 0 0 0 2712 0 0 415.4
## 5HT1bMARCM-F000026_seg001 0 0 0 0 0 1713 0 0 440.5
## 5HT1bMARCM-M000046_seg001 0 0 0 0 0 0 0 0 412.1
## ChaMARCM-F000003_seg001 0 0 0 0 0 0 0 0 372.9
## ChaMARCM-F000008_seg001 0 0 0 0 0 0 0 0 398.9
## Y Z
## 5HT1bMARCM-F000019_seg001 150.4 84.57
## 5HT1bMARCM-F000024_seg001 144.7 85.29
## 5HT1bMARCM-F000026_seg001 134.9 96.17
## 5HT1bMARCM-M000046_seg001 142.8 88.28
## ChaMARCM-F000003_seg001 198.7 68.02
## ChaMARCM-F000008_seg001 199.6 49.04
We'll be plotting these neurons a lot, so let's set an option that will save us some typing:
options(nat.default.neuronlist = "vpns")
# also make sure default view is frontal to fly brain
r3dDefaults$userMatrix = structure(c(1, 0, 0, 0, 0, -1, 0, 0, 0, 0, -1, 0, 0,
0, 0, 1), .Dim = c(4L, 4L))
Simple plot
Let's plot (automagically downloading) the first 3 neurons
open3d()
## glX
## 1
plot3d(vpns[1:3])
# and add brain surface
fcwbsurf()
Cluster cells by morphology
Let's find all the bilateral lobula complex neurons, insisting on at least 500 voxels in each optic lobula complex.
bilateral = subset(vpns, (rLOP + rLOB) > 500 & (lLOP + lLOB) > 500, rval = "names")
hcbilateral <- hclustfc(bilateral)
# two big clusters
library(dendroextras)
plot(colour_clusters(hcbilateral, k = 2))
# or 7 finer scale ones
plot(colour_clusters(hcbilateral, k = 7))
Plot 2 major clusters
Now let's look at the two major clusters:
open3d()
## glX
## 2
plot3d(hcbilateral, k = 2, db = vpns)
# add lobula
fcwbnpsurf("LO_L", alpha = 0.5)
Looks like Lobula vs Medulla (not that much in Lobula Plate)
# remove lobula
pop3d()
# ... and add lobula plate
fcwbnpsurf("LOP_L", alpha = 0.5)
Plot 7 finer scale clusters
clear3d()
plot3d(hcbilateral, k = 7, db = vpns)
More NBLASTing
How do other neurons compare with 5HT1bMARCM-F000019_seg001? Let's NBLAST it against all the other neurons and look at the distribution of scores.
results <- fc_nblast(names(vpns)[1], names(vpns))
hist(results, breaks = 100)
The little bump at 5717.3936 is for 5HT1bMARCM-F000019_seg001 itself, which has the highest score possible as there should be no distance between it and itself. Let's plot the next four hits, along with the query neuron in black, to see how similar they are:
open3d()
## glX
## 3
plot3d(names(vpns)[1], col = "black")
plot3dfc(names(sort(results, decreasing = TRUE)[2:5]))
Hmm, they look pretty similar. Let's plot the four worst hits for comparison:
open3d()
## glX
## 4
plot3d(names(vpns)[1], col = "black")
plot3dfc(names(sort(results)[1:4]))
Definitely different.
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