update cols / docs for nerve meshes

R/data.R

@@ -67,12 +67,16 @@
 #' @rdname MANC.tissue.surf
 "MANC.tissue.surf.sym"
 
-#' Simplified meshes of 35 Male VNC nerves.
+#'Simplified meshes of 35 Male VNC nerves.
+#'
+#'@name MANC.tissue.surf
+#'@docType data
+#'@description \code{MANC.nerves} contains meshes of 35 nerves: 17 symmetric
+#'  pairs \code{(L)/(R)} and \code{AbNT}. These were hand-drawn based on the
+#'  MANC grayscale data, guided by motor neuron and sensory neuron axon
+#'  reconstructions. Abbreviated names follow the conventions established in
+#'  Court et al., 2020 and are defined in Table 2 of Takemura et al., 2023.
 #'
-#' @name MANC.tissue.surf
-#' @docType data
-#' @description \code{MANC.nerves} contains mesh of 35 MANC nerves:
-#' 15 symmetric ("L"/"R") and "AbNT".
 #' @examples
 #' \dontrun{
 #' # Depends on nat

data-raw/manc-meshes.R

@@ -0,0 +1,67 @@
+# see
+# https://flyconnectome.slack.com/archives/C01AETN5W15/p1675441690566929
+u2="https://clio-ng.janelia.org/#!gs://flyem-user-links/short/2023-08-01.060515.json"
+nsc=fafbseg::ngl_decode_scene(flyem_expand_url(u2))
+nsc$layers$`nerves-202301`
+
+neuprintr::neuprint_ROI_mesh("PrN(L)", conn=manc_neuprint())
+neuprintr::neuprint_ROI_hierarchy(conn = manc_neuprint())
+
+nsc$layers$`nerves-202301` %>% dput
+
+rois=neuprintr::neuprint_ROIs(conn = manc_neuprint())
+nerve.rois=grep("N[1-4]{0,1}(T|[(LR)]{0,})$", rois, value = T)
+
+library(nat)
+nerve.meshes=nlapply(nerve.rois, neuprintr::neuprint_ROI_mesh, conn=manc_neuprint())
+names(nerve.meshes)=nerve.rois
+
+# test but not used in the end
+nerve.meshes.simp <- nlapply(nerve.meshes, function(x) {
+ nrvmesh.simp <- Rvcg::vcgQEdecim(x, percent = 0.2)
+ nrvmesh.simp = addNormals(nrvmesh.simp)
+ nrvmesh.simp
+})
+
+# MANC.nerves=do.call(c, mapply(as.hxsurf, nerve.meshes,region=nerve.rois, SIMPLIFY = F))*8/1000
+
+cols=readr::read_table(file="
+Region Colour
+AbN1(L)   #7300FF
+AbN1(R)   #9900FF
+AbN2(L)   #00FF73
+AbN2(R)   #00FFB3
+AbN3(L)   #00B3A2
+AbN3(R)   #009980
+AbN4(L)   #FF6300
+AbN4(R)   #FF9400
+AbNT      #D600FF
+ADMN(L)   #00CC60
+ADMN(R)   #009933
+CvN(L)    #FF00A0
+CvN(R)    #FF0080
+DMetaN(L) #FF4500
+DMetaN(R) #FF2200
+DProN(L)  #a7faf7
+DProN(R)  #bff5f3
+MesoAN(L) #0084ff
+MesoAN(R) #0095ff
+MesoLN(L) #52FF00
+MesoLN(R) #21FF00
+MetaLN(L) #faed05
+MetaLN(R) #fff830
+PDMN(L)   #FFBB00
+PDMN(R)   #FFDD00
+PrN(L)    #0e0114
+PrN(R)    #09020d
+ProAN(L)  #BBAA00
+ProAN(R)  #998800
+ProCN(L)  #f788f2
+ProCN(R)  #f274ec
+ProLN(L)  #FF0000
+ProLN(R)  #CC0000
+VProN(L)  #10FF00
+VProN(R)  #00CC00")
+
+MANC.nerves=do.call(c, mapply(as.hxsurf, nerve.meshes[cols$Region],region=cols$Region,col=cols$Colour, SIMPLIFY = F))*8/1000
+usethis::use_data(MANC.nerves, internal = F, version = 2, overwrite = T)