data-raw/hemibrain/startupHemibrain.R

In jefferislab/lhns: Skeleton data for neurons associated with the lateral horn of Drosophila melanogaster

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# Hemibrain LHNs #
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devtools::load_all(".")
library(neuprintr)
library(hemibrainr)
library(nat.jrcbrains)
source("data-raw/hemibrain/lh_hemibrain_functions.R")

# Google Sheet database
selected_file = "1OSlDtnR3B1LiB5cwI5x5Ql6LkZd8JOS5bBr-HTi0pOw"

# Information from Kei Ito
cbfs = read.csv("data-raw/csv/CBF-Lineage-mapping.csv")
ito.lhns = read.csv("data-raw/csv/ito_lhns.csv")
rownames(ito.lhns) = ito.lhns$body.ID

# All the newest names
namelist =  read.csv("data-raw/csv/Namelist-04162020.csv")
colnames(namelist) = c("bodyid","type","cbf","m.type","c.type")
rownames(namelist) = namelist$bodyid

# Get LH information
lh.info = neuprintr::neuprint_find_neurons(
  input_ROIs = "LH(R)",
  output_ROIs =  'LH(R)',
  all_segments = FALSE )

# Get LH meta data
lh.meta = neuprint_get_meta(unique(hemibrain.lhn.bodyids,ito.lhns$body.ID))
lh.meta = lh.meta[order(lh.meta$type),]
lh.meta = subset(lh.meta, bodyid%in%hemibrain.lhn.bodyids)
new.cts = ito.lhns$new.type.name[match(lh.meta$bodyid,ito.lhns$body.ID,)]
new.cts[is.na(new.cts)] = lh.meta$type[is.na(new.cts)]
lh.meta$type = new.cts

# Get neurons
db = hemibrainr::hemibrain_neurons()

# Get most.lhns
most.lhns.hemibrain = hemibrain_lm_lhns()
xyzmatrix(most.lhns.hemibrain) = xyzmatrix(most.lhns.hemibrain)*(1000/8)

# Get most.lhins
most.lhins.hemibrain = hemibrain_lm_lhns(cable = 'lhin')
xyzmatrix(most.lhins.hemibrain) = xyzmatrix(most.lhins.hemibrain)*(1000/8)

# Get all-by-all hemibrain NBLAST
# hemibrain_all_nblast = hemibrain_nblast(nblast="all")
# hemibrain_arbour_nblast = hemibrain_nblast(nblast="arbour")
# hemibrain_pnt_nblast = hemibrain_nblast(nblast="primary.neurites")
# hemibrain_spine_nblast = hemibrain_nblast(nblast="spines")

# Read the Google Sheet
# gs = hemibrainr:::gsheet_manipulation(FUN = googlesheets4::read_sheet,
#                          ss = selected_file,
#                          sheet = "lhns",
#                          return = TRUE)
# gs$bodyid = hemibrainr:::correct_id(gs$bodyid)
# rownames(gs) = gs$bodyid

## Get LH volume
hemibrain.lhr = hemibrain_roi_meshes("LH(R)")