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processLHNs.R
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processLHNs.R
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# Process LHN data
# Get Data
message("Reading in raw neuron skeleton data!")
load("data-raw/SF_dye_fills_FCWB.rda")
load("data-raw/Segmented_FlyCircuit_LHNs_FCWB.rda")
JFRCSH_clusters=read.neurons("data-raw/swc/Clusters_JFRCSH")
SF_clusters=read.neurons("data-raw/swc/Clusters_SF")
JFRCSH.DS_clusters=read.neurons("data-raw/swc/Clusters_JFRC2013DS")
# Get data together in FCWB brainspace
library(nat.flybrains)
JFRCSH_clusters.FCWB= nat.templatebrains::xform_brain(JFRCSH_clusters, sample=JFRC2, ref=FCWB)
JFRCSH.DS_clusters.FCWB= nat.templatebrains::xform_brain(JFRCSH.DS_clusters, sample=JFRC2013DS, ref=FCWB)
SF_clusters.FCWB= nat.templatebrains::xform_brain(SF_clusters, IS2, FCWB)
names(JFRCSH_clusters.FCWB)=sub("-000.swc","",x=names(JFRCSH_clusters.FCWB))
names(JFRCSH.DS_clusters.FCWB)=sub("-000.swc","",x=names(JFRCSH.DS_clusters.FCWB))
names(SF_clusters.FCWB)=sub("-000.swc","",x=names(SF_clusters.FCWB))
most.lhns=c(fc.lhns,dye.fills,JFRCSH_clusters.FCWB,JFRCSH.DS_clusters.FCWB,SF_clusters.FCWB)
# Prepare meta data frame
df = most.lhns[,c("id","sex","LH_side")]
df$id = names(most.lhns)
df$id[is.na(df$id)] = "dyefill"
df$pnt=NA
df$anatomy.group=NA
df$cell.type = NA
df$coreLH= TRUE
df$good.trace = TRUE
df$dendritic.cable.in.lh = NA
df$dendritic.cable = NA
###### Bad Cells ######
badly.traced = c("5HT1A-F-200014", "Gad1-F-300266", "npf-F-000002", "VGlut-F-300400",
"120714c4","131206c0","Cha-F-200386","120605c0",
"VGlut-F-900127", "VGlut-F-500145", "VGlut-F-500393", "5HT1A-F-200014",
"Gad1-F-300266", "npf-F-300047", "npf-M-200017", "npf-M-300045",
"npf-M-300051", "Cha-F-800106", "fru-M-700211", "Gad1-F-500038", "VGlut-F-500323",
"Gad1-F-200366", "Gad1-F-000381", "Gad1-F-000349", "fru-M-800040",
"fru-F-600043", "5HT1A-F-800008", "Cha-F-200378", "Cha-F-300146",
"Cha-F-400324", "VGlut-F-500032", "Cha-F-000395", "Cha-F-000515",
"Cha-F-800134", "Gad1-F-000101", "Cha-F-200357", "VGlut-F-500253","Gad1-F-200431", "Gad1-F-100264", "Cha-F-100357", "Cha-F-600061","VGlut-F-500148",
"VGlut-F-200021", "VGlut-F-200382", "fru-F-500093", "Cha-F-400240",
"fru-M-700211")
df[names(c(JFRCSH_clusters.FCWB,JFRCSH.DS_clusters.FCWB,SF_clusters.FCWB)),]$good.trace = FALSE
df[badly.traced,]$good.trace = FALSE
###### Not LH proper ######
notLH= c("Cha-F-100387", "Cha-F-700265", "VGlut-F-200296", "Gad1-F-200198",
"Cha-F-600251", "Cha-F-100373","fru-F-500116","VGlut-F-500325",
"Cha-F-300023","Cha-F-400287","fru-M-200431",
"fru-F-300161","fru-M-900027","fru-M-200444","fru-M-300186",
"npf-M-800005","fru-M-000139","VGlut-F-500325","Gad1-F-400161",
"fru-M-700136","fru-M-200432","fru-M-700108",
"fru-M-200206","fru-M-000344","TH-M-100044", "TH-M-100042"
, "fru-M-100344","fru-F-600242","Gad1-F-900064",
"TH-M-200031","npf-F-000008", "Gad1-F-800172", "Gad1-F-800120", "Gad1-F-700145", "fru-M-200400",
"Gad1-F-600274", "Gad1-F-600260", "Gad1-F-600254", "Gad1-F-600221",
"Gad1-F-500349", "Gad1-F-500326", "Gad1-F-500302", "Gad1-F-500207",
"Gad1-F-500201", "Gad1-F-500192", "Gad1-F-500112", "Gad1-F-400406",
"Gad1-F-400220", "Gad1-F-400154", "Gad1-F-400144", "Gad1-F-400128",
"Gad1-F-300311", "Gad1-F-300243", "Gad1-F-300212", "Gad1-F-300193",
"Gad1-F-300190", "Gad1-F-200459", "Gad1-F-200458", "Gad1-F-200380",
"Gad1-F-200320", "Gad1-F-200213", "Gad1-F-200169", "Gad1-F-100358",
"5HT1A-F-100016", "5HT1A-F-300001", "5HT1A-F-300035", "Cha-F-000428",
"Cha-F-000432", "Cha-F-000452", "Cha-F-000506", "Cha-F-100420",
"Cha-F-100425", "Cha-F-300347", "Cha-F-400277", "Cha-F-400301",
"Cha-F-600245", "Cha-F-700082", "Cha-F-800107", "Cha-F-800145",
"E0585-F-000006", "E0585-F-300019", "E0585-F-400016", "E0585-F-600005",
"fru-F-000155", "fru-F-000201", "fru-F-100122", "fru-F-300158",
"fru-F-300189", "fru-F-300212", "fru-F-300225", "fru-F-400364",
"fru-F-400374", "fru-F-400494", "fru-F-500285", "fru-F-500330",
"fru-F-500333", "fru-F-500370", "fru-F-500557", "fru-F-500588",
"fru-F-600297", "fru-F-700234", "Gad1-F-000142", "Gad1-F-000176",
"Gad1-F-000231", "Gad1-F-000275", "Gad1-F-000434", "Gad1-F-100110",
"Gad1-F-100150", "Gad1-F-100153", "Cha-F-400224", "Cha-F-200232",
"VGlut-F-600076", "fru-F-400084", "fru-F-700115", "fru-F-200100",
"TH-F-300067", "Trh-M-700054", "Trh-M-700040", "Trh-M-700010",
"Trh-M-500187", "Trh-M-500168", "Trh-M-500155", "Trh-M-500142",
"Trh-M-500128", "Trh-M-500078", "Trh-M-400045", "Trh-M-400020",
"Trh-M-300024", "Trh-M-200030", "Trh-M-100082", "Trh-M-000109",
"TH-M-600000", "TH-M-500005", "TH-M-500000", "TH-M-300056", "TH-M-300053",
"TH-M-300023", "TH-M-300013", "TH-M-200087", "TH-M-200076", "TH-M-200060",
"TH-M-200058", "TH-M-200037", "TH-M-200009", "TH-M-100077", "TH-M-100062",
"TH-M-000048", "TH-M-000032", "TH-M-000016", "npf-M-800002",
"npf-M-400010", "npf-M-400004", "npf-M-300037", "npf-M-200043",
"npf-M-200039", "npf-M-200036", "npf-M-200028", "npf-M-200027",
"npf-M-200016", "npf-M-200015", "npf-M-200002", "npf-M-200001",
"fru-M-800150", "fru-M-800106", "fru-M-800088", "fru-M-800059",
"fru-M-800038", "fru-M-700247", "fru-M-700136", "fru-M-600210",
"fru-M-600026", "fru-M-500385", "fru-M-500381", "fru-M-500372",
"fru-M-500318", "fru-M-500305", "fru-M-500270", "fru-M-500269",
"fru-M-500107", "fru-M-500089", "fru-M-500075", "fru-M-500012",
"fru-M-500009", "fru-M-400399", "fru-M-400371", "fru-M-400342",
"fru-M-400295", "fru-M-400274", "fru-M-400224", "fru-M-400217",
"fru-M-400214", "fru-M-400115", "fru-M-400107", "fru-M-300381",
"fru-M-300362", "fru-M-300344", "fru-M-300251", "fru-M-300250",
"fru-M-300189", "fru-M-300186", "fru-M-300111", "fru-M-300043",
"fru-M-300038", "fru-M-300030", "fru-M-300015", "fru-M-300002",
"fru-M-200492", "fru-M-200458", "fru-M-200444", "fru-M-200431",
"fru-M-200400", "fru-M-200380", "fru-M-200302", "fru-M-200299",
"fru-M-200239", "fru-M-200228", "fru-M-200206", "fru-M-200156",
"fru-M-200145", "fru-M-200113", "fru-M-200086", "fru-M-100387",
"fru-M-100342", "fru-M-100332", "fru-M-100295", "fru-M-100290",
"fru-M-100193", "fru-M-100139", "fru-M-100136", "fru-M-100031",
"fru-M-100025", "fru-M-000360", "fru-M-000339", "fru-M-000291",
"fru-M-000227", "fru-M-000224", "fru-M-000179", "fru-M-000139",
"fru-M-000075", "fru-M-000050", "fru-M-000045", "fru-M-000042",
"fru-M-000040", "fru-M-000032", "fru-M-000027", "5HT1A-M-800011",
"5HT1A-M-500012", "5HT1A-M-400022", "VGlut-F-600694", "Gad1-F-800099",
"Gad1-F-600163", "Gad1-F-600108", "Gad1-F-500325", "Gad1-F-500200",
"Gad1-F-500172", "Gad1-F-400192", "Gad1-F-400161", "Gad1-F-200433",
"Gad1-F-200241", "Cha-F-000491", "Cha-F-100372", "Cha-F-200439",
"Cha-F-300350", "Cha-F-300384", "Cha-F-400296", "Cha-F-400328",
"Cha-F-500272", "Cha-F-500310", "Cha-F-700277", "E0585-F-000005",
"E0585-F-200004", "E0585-F-600004", "fru-F-000227", "fru-F-100125",
"fru-F-300136", "fru-F-400339", "fru-F-400527", "fru-F-500371",
"fru-F-500553", "fru-F-600136", "fru-F-700240", "fru-F-800103",
"Gad1-F-100112", "Gad1-F-100211", "Gad1-F-100223", "Gad1-F-100258",
"Gad1-F-100302", "Cha-F-300212", "Cha-F-000152", "VGlut-F-600218",
"VGlut-F-700413", "VGlut-F-500139", "VGlut-F-600075", "fru-F-000125",
"Gad1-F-100051", "Trh-M-700035", "Trh-M-600063", "Trh-M-500101",
"Trh-M-500055", "Trh-M-400120", "Trh-M-100087", "Trh-M-000175",
"Trh-M-000174", "TH-M-300052", "TH-M-100016", "TH-M-000045",
"TH-M-000023", "npf-M-800005", "npf-M-200061", "npf-M-200020",
"npf-M-200004", "fru-M-900027", "fru-M-900002", "fru-M-700135",
"fru-M-700116", "fru-M-600077", "fru-M-500224", "fru-M-500221",
"fru-M-500088", "fru-M-400067", "fru-M-300226", "fru-M-300165",
"fru-M-300088", "fru-M-300049", "fru-M-300008", "fru-M-200490",
"fru-M-200478", "fru-M-200448", "fru-M-200432", "fru-M-200402",
"fru-M-200260", "fru-M-200172", "fru-M-100345", "fru-M-100206",
"fru-M-100071", "fru-M-100056", "fru-M-000344", "fru-M-000167",
"fru-M-000133", "fru-M-000022", "fru-M-000002", "5HT1A-M-400013",
"5HT1A-M-300003", "fru-M-400080", "fru-M-800060", "fru-M-700108",
"Trh-M-500144", "fru-M-500259", "fru-F-000130", "Trh-M-100052",
"Gad1-F-200110", "VGlut-F-900053", "VGlut-F-000454", "Cha-F-500087",
"VGlut-F-000336", "VGlut-F-300515", "Trh-F-500222","Trh-M-500183")
df[unique(notLH),]$pnt = df[notLH,]$anatomy.group = df[notLH,]$cell.type = "notLHproper"
###### PNT PV6 ######
pv6 = c("Cha-F-800039", "Gad1-F-200219")
df[unique(pv6),]$pnt = "pv6"
pv6.a = "Cha-F-800039"
pv6.a.1 = "Cha-F-800039"
pv6.b = "Gad1-F-200219"
pv6.b.1 = "Gad1-F-200219"
df[pv6.a,]$anatomy.group = "pv6a"
df[pv6.b,]$anatomy.group = "pv6b"
df[pv6.a.1,]$cell.type = "pv6a1"
df[pv6.b.1,]$cell.type = "pv6b1"
###### PNT PV8 ######
### pv8
pv8 = c("fru-M-600077", "fru-M-200410","Trh-F-100061", "Trh-F-100060",
"Trh-M-100052", "Trh-F-000029","CL71R_47G10",
"Trh-F-000040", "Trh-F-100057", "Trh-F-000002", "Trh-M-100075",
"Trh-F-600087", "Trh-F-100091", "Trh-F-100072", "VGlut-F-200225",
"fru-M-000012", "fru-M-300184", "fru-M-100059", "Trh-F-200008",
"Trh-M-300118","Trh-M-100010","CL150R_JK733SF457")
df[unique(pv8),]$pnt = "pv8"
pv8.a = c("Trh-F-100061", "Trh-F-100060", "Trh-M-100052", "Trh-F-000029",
"Trh-F-000040", "Trh-F-100057", "Trh-F-000002", "Trh-M-100075",
"Trh-F-600087", "Trh-F-100091", "Trh-F-100072", "VGlut-F-200225",
"fru-M-000012", "fru-M-300184", "fru-M-100059", "Trh-F-200008",
"Trh-M-300118")
pv8.a.1 = c("Trh-F-100061", "Trh-F-100060", "Trh-M-100052", "Trh-F-000029",
"Trh-F-000040", "Trh-F-100057", "Trh-F-000002", "Trh-M-100075",
"Trh-F-600087", "Trh-F-100091", "Trh-F-100072", "VGlut-F-200225",
"fru-M-000012", "fru-M-300184", "fru-M-100059", "Trh-F-200008",
"Trh-M-300118")
pv8.b = c("fru-M-600077","fru-M-200410")
pv8.b.1 = c("fru-M-600077","fru-M-200410")
pv8.c.1 =pv8.c= "Trh-M-100010"
pv8.d.1 = "CL150R_JK733SF457"
pv8.d.2 = "CL71R_47G10"
pv8.d=c(pv8.d.1,pv8.d.2)
df[pv8.a,]$anatomy.group = "pv8a"
df[pv8.b,]$anatomy.group = "pv8b"
df[pv8.c,]$anatomy.group = "pv8c"
df[pv8.d,]$anatomy.group = "pv8d"
df[pv8.a.1,]$cell.type = "pv8a1"
df[pv8.b.1,]$cell.type = "pv8b1"
df[pv8.c.1,]$cell.type = "pv8c1"
df[pv8.d.1,]$cell.type = "pv8d1"
df[pv8.d.2,]$cell.type = "pv8d2"
###### PNT PV7 ######
### pv7
pv7 = c("Gad1-F-700084", "VGlut-F-000090","fru-M-400051")
df[unique(pv7),]$pnt = "pv7"
pv7.a = pv7.a.1 = "Gad1-F-700084" # Remove? Badly traced. Soma uncertain.
pv7.b = pv7.b.1 = "fru-M-400051"
pv7.c = pv7.c.1 = "VGlut-F-000090" #dont plot
df[pv7.a,]$anatomy.group = "pv7a"
df[pv7.b,]$anatomy.group = "pv7b"
df[pv7.c,]$anatomy.group = "pv7c"
df[pv7.a.1,]$cell.type = "pv7a1"
df[pv7.b.1,]$cell.type = "pv7b1"
df[pv7.c.1,]$cell.type = "pv7c1"
###### PNT PV11 ######
### pv11
pv11 = "Gad1-F-600202"
df[unique(pv11),]$pnt = "pv11"
pv11.a = pv11.a.1 = "Gad1-F-600202"
df[pv11.a,]$anatomy.group = "pv11a"
df[pv11.a.1,]$cell.type = "pv11a1"
###### PNT PV10 ######
### pv10
pv10 = c("Trh-M-400128","Gad1-F-600210")
df[unique(pv10),]$pnt = "pv10"
pv10.a=c("Trh-M-400128","Gad1-F-600210")
pv10.a.1 = "Trh-M-400128"
pv10.a.2 = "Gad1-F-600210"
df[pv10.a,]$anatomy.group = "pv10a"
df[pv10.a.1,]$cell.type = "pv10a1"
df[pv10.a.2,]$cell.type = "pv10a2"
###### PNT PD7 ######
### pd7
pd7 = c("fru-F-400364", "fru-F-400339")
df[unique(pd7),]$pnt = "pd7"
pd7.a = pd7.a.1 = "fru-F-400364"
pd7.b = pd7.b.1 ="fru-F-400339"
df[pd7.a,]$anatomy.group = "pd7a"
df[pd7.b,]$anatomy.group = "pd7b"
df[pd7.a.1,]$anatomy.group = "pd7a1"
df[pd7.b.1,]$anatomy.group = "pd7b1"
###### PNT PV9 ######
### pv9
pv9 = c("Trh-M-400120","Cha-F-700278","Cha-F-700201", "Trh-M-200030","fru-M-200397","Gad1-F-700184",
"Gad1-F-400411", "Cha-F-100449", "fru-F-100122",
"Gad1-F-200151", "fru-M-900055", "fru-M-700194", "fru-M-400196",
"fru-M-400164", "fru-M-400046", "fru-M-300203", "fru-M-200458",
"fru-M-200074", "fru-M-100103", "Gad1-F-800099", "Gad1-F-200414",
"Gad1-F-100290", "Cha-F-300297", "Cha-F-000303", "Trh-M-100020",
"fru-M-900039", "fru-M-800141", "fru-M-700302", "fru-M-700217",
"fru-M-600099", "fru-M-300235", "fru-M-300147", "fru-M-300088",
"fru-M-200179", "fru-M-200153", "fru-M-000167", "fru-M-000022","fru-M-200380")
df[unique(pv9),]$pnt = "pv9"
pv9.a = pv9.a.1 = c("fru-M-600099","fru-M-200153","fru-M-200074","fru-M-100103", "fru-M-800141","fru-M-400046"
,"fru-M-300235", "fru-M-300203", "fru-M-200179","fru-M-200397")
pv9.b = pv9.b.1 = c("fru-M-400196", "fru-M-900055","fru-M-400164","fru-M-300147","fru-M-700194","fru-M-900039","fru-M-700302","fru-M-700217")
pv9.c.1 = c("Gad1-F-100290","Gad1-F-700184","Gad1-F-400411","Cha-F-000303","Gad1-F-200414","Cha-F-300297")
pv9.c.2=c("Cha-F-100449","Gad1-F-200151")
pv9.c=c(pv9.c.1,pv9.c.2)
pv9.d = pv9.d.1= c("fru-M-000022","fru-M-200458","fru-M-300088","fru-M-000167")
pv9.e = pv9.e.1 = c("Trh-M-200030","Trh-M-400120")
pv9.f = pv9.f.1 = "Trh-M-100020"
pv9.g = pv9.g.1 = c("fru-F-100122","fru-M-200380")
pv9.h = pv9.h.1 = "Gad1-F-800099"
pv9.i = pv9.i.1 = "Cha-F-700278"
pv9.j = pv9.j.1 = "Cha-F-700201"
df[pv9.a,]$anatomy.group = "pv9a"
df[pv9.b,]$anatomy.group = "pv9b"
df[pv9.c,]$anatomy.group = "pv9c"
df[pv9.d,]$anatomy.group = "pv9d"
df[pv9.e,]$anatomy.group = "pv9e"
df[pv9.f,]$anatomy.group = "pv9f"
df[pv9.g,]$anatomy.group = "pv9g"
df[pv9.h,]$anatomy.group = "pv9h"
df[pv9.i,]$anatomy.group = "pv9i"
df[pv9.j,]$anatomy.group = "pv9j"
df[pv9.a.1,]$cell.type = "pv9a1"
df[pv9.b.1,]$cell.type = "pv9b1"
df[pv9.c.1,]$cell.type = "pv9c1"
df[pv9.c.2,]$cell.type = "pv9c2"
df[pv9.d.1,]$cell.type = "pv9d1"
df[pv9.e.1,]$cell.type = "pv9e1"
df[pv9.f.1,]$cell.type = "pv9f1"
df[pv9.g.1,]$cell.type = "pv9g1"
df[pv9.h.1,]$cell.type = "pv9h1"
df[pv9.i.1,]$cell.type = "pv9i1"
df[pv9.j.1,]$cell.type = "pv9j1"
###### PNT PV5 ######
### PV5
pv5 = c("Gad1-F-000349","Cha-F-400324","Gad1-F-200177","E0585-F-300073","Gad1-F-900137", "Gad1-F-900098", "Gad1-F-800215", "Gad1-F-700139",
"Gad1-F-500244", "Gad1-F-500180", "Gad1-F-400275", "Gad1-F-300321",
"Gad1-F-300243", "Gad1-F-300163", "Gad1-F-300155", "Gad1-F-200403",
"Gad1-F-200289", "Gad1-F-200232", "Cha-F-100398",
"Cha-F-200402", "Cha-F-500250", "Cha-F-700211", "Cha-F-700258",
"E0585-F-300013", "E0585-F-300033", "E0585-F-300040", "E0585-F-300047",
"E0585-F-300050", "E0585-F-300058", "E0585-F-300063", "E0585-F-300066",
"E0585-F-300071", "E0585-F-400005", "E0585-F-400008",
"E0585-F-400013", "E0585-F-400015", "E0585-F-400018", "E0585-F-400025",
"E0585-F-400028", "E0585-F-500000", "E0585-F-500001", "E0585-F-500010",
"E0585-F-800001", "E0585-F-800004", "Gad1-F-000139", "Gad1-F-000155",
"Gad1-F-000393", "Gad1-F-100091", "Gad1-F-100093", "Gad1-F-100099",
"Gad1-F-100247", "Gad1-F-100357", "Cha-F-300025", "Cha-F-600051",
"Cha-F-500138", "Cha-F-300204", "Cha-F-300241", "Cha-F-200169",
"Cha-F-800045", "Cha-F-200186", "Cha-F-100141", "Cha-F-200204",
"Cha-F-500187", "VGlut-F-400058", "Gad1-F-100023","TH-M-200014",
"Gad1-F-700165", "Gad1-F-600214", "Gad1-F-400335", "Gad1-F-400304",
"Gad1-F-400226", "Gad1-F-400166", "Gad1-F-300298", "Gad1-F-300184",
"Gad1-F-200362", "Gad1-F-200255", "Gad1-F-200220", "Gad1-F-200199",
"Cha-F-000427", "Cha-F-100394", "Cha-F-100457", "Cha-F-600232",
"E0585-F-300020", "E0585-F-300043", "E0585-F-300052", "E0585-F-300064",
"E0585-F-300069", "E0585-F-300070", "E0585-F-400003", "E0585-F-400009",
"E0585-F-400011", "E0585-F-400021", "E0585-F-400029", "E0585-F-500008",
"E0585-F-500009", "E0585-F-700001", "E0585-F-800003", "Gad1-F-000125",
"Gad1-F-000338", "Gad1-F-100211", "Gad1-F-100322", "Cha-F-200082",
"Cha-F-100068", "Cha-F-100083", "Cha-F-400179","E0585-F-700002",
"Gad1-F-900040", "Gad1-F-900052", "Gad1-F-100003", "TH-M-300021", "TH-M-100016", "Cha-F-300342",
"TH-M-000023", "fru-M-200172","E0585-F-400002", "E0585-F-400001","Cha-F-800011","E0585-F-600002","Cha-F-100264",
"Cha-F-100398","Gad1-F-200362","Gad1-F-300312","Gad1-F-200177","120216c0",
"120618c0", "120628c1", "120708c1","Gad1-F-300290",
"120712c1", "130213c0","130214c1","130425c1","120813c0", "130118c0","120619c1", "120710c0", "120914c0", "121130c0", "121212c0",
"121213c0", "121217c0", "121227c2", "130208c1", "130211c3", "130220c1",
"130313c1", "130605c1", "130606c1", "130617c3", "130702c1",
"130703c1", "130704c2", "130710c3", "130711c1", "130712c1", "130717c0",
"130814c0", "130816c2", "131118c3", "131126c3", "131204c0",
"131212c0", "160121c1","Cha-F-700170","Cha-F-400240","Gad1-F-400162","Cha-F-000317")
df[unique(pv5),]$pnt = "pv5"
pv5.a.1 = c("Cha-F-400324","Gad1-F-500180", "Cha-F-200402", "Gad1-F-500244","Cha-F-800011","Gad1-F-100093", "Gad1-F-200403", "Gad1-F-100247", "Gad1-F-400335",
"Gad1-F-000338", "Gad1-F-400226", "Cha-F-000427", "Gad1-F-200289",
"Gad1-F-400275", "Cha-F-500187", "Cha-F-300241", "Gad1-F-300298",
"Gad1-F-100322", "Gad1-F-900137", "Gad1-F-100357",
"120914c0","120813c0","120712c1",
"120628c1","120708c1")
pv5.a.2 = c("Cha-F-100457", "Gad1-F-100091","Gad1-F-300184", "Cha-F-400179", "Gad1-F-400304",
"Gad1-F-200199", "Cha-F-100394", "Gad1-F-600214", "Gad1-F-200220","Cha-F-500138")
pv5.a.3 = c("VGlut-F-400058", "Gad1-F-100099","120216c0",
"120619c1","120710c0","130118c0")
pv5.a.4 = c("Gad1-F-700139","Gad1-F-000349","Cha-F-500250","Cha-F-700211")
pv5.a.5 = c("Gad1-F-100091","Cha-F-500138" )
pv5.a.6 ="Gad1-F-300312"
pv5.a= c(pv5.a.1,pv5.a.2,pv5.a.3,pv5.a.4,pv5.a.5,pv5.a.6)
pv5.b.1=c("Gad1-F-000155", "E0585-F-400002", "Cha-F-100083", "Gad1-F-100023",
"E0585-F-300073", "120618c0", "131118c3", "160121c1", "Cha-F-200082",
"Cha-F-300204", "Cha-F-200169", "Cha-F-800045", "Gad1-F-900098",
"Gad1-F-300321")
pv5.b.2 = c("121130c0", "Cha-F-700258", "E0585-F-300063", "130213c0",
"E0585-F-300066","E0585-F-300064","E0585-F-400029","130214c1",
"E0585-F-400003","E0585-F-400021","Cha-F-100264","130425c1")
pv5.b.3 = c("E0585-F-700001", "E0585-F-800004", "E0585-F-400015",
"E0585-F-800001", "E0585-F-500010", "Cha-F-200204", "Cha-F-300342")
pv5.b.4 = c("Cha-F-600232")
pv5.b.5 = c("E0585-F-400001")
pv5.b.6 = c("E0585-F-800003","Gad1-F-900040")
pv5.b=c(pv5.b.2,pv5.b.1,pv5.b.3,pv5.b.4,pv5.b.5,pv5.b.6)
pv5.c.1=c("Cha-F-000317","Gad1-F-200232", "E0585-F-300013", "E0585-F-300033", "E0585-F-300040",
"E0585-F-300047", "E0585-F-300071",
"Gad1-F-000139", "Cha-F-600051",
"E0585-F-300020", "E0585-F-300052",
"E0585-F-300070", "E0585-F-500008",
"Gad1-F-900052", "Gad1-F-100003", "130605c1",
"130702c1","E0585-F-300043", "130703c1","130712c1",
"130717c0","130814c0","130710c3","Cha-F-700170")
pv5.c.2 = c("E0585-F-500009", "Gad1-F-000125", "E0585-F-400009", "Cha-F-100068", "130220c1", "130313c1","130605c1","130704c2","130710c3",
"E0585-F-400018", "Cha-F-100141", "E0585-F-300050", "Gad1-F-300155",
"E0585-F-300058", "121212c0", "130606c1", "Cha-F-300025", "E0585-F-300069", "121213c0")
pv5.c.3 = c("121217c0", "130211c3","121227c2")
pv5.c.4=c("E0585-F-400025", "E0585-F-400005", "E0585-F-400008","E0585-F-400013",
"Gad1-F-200255","E0585-F-400011","130208c1","130711c1","130816c2")
pv5.c.5=c("130617c3","131126c3", "131204c0", "131212c0")
pv5.c=c(pv5.c.2,pv5.c.1,pv5.c.3,pv5.c.4,pv5.c.5)
pv5.d.1 =c("Gad1-F-800215","Gad1-F-300163","E0585-F-600002" )
pv5.d.2 = c("Gad1-F-200362")
pv5.d.3=c("Gad1-F-000393")
pv5.d = c(pv5.d.1,pv5.d.2,pv5.d.3)
pv5.e.1 = c("TH-M-300021","TH-M-200014") #PPL1-a'3
pv5.e.2 = c("TH-M-100016", "TH-M-000023")
pv5.e.3 = "Gad1-F-400166"
pv5.e = c(pv5.e.1,pv5.e.2,pv5.e.3)
pv5.f = pv5.f.1 = c("Gad1-F-300243", "E0585-F-500000", "E0585-F-500001","Gad1-F-400162")
pv5.g.1 = c("Cha-F-100398")
pv5.g.2 = c("Gad1-F-700165")
pv5.g.3 = "Gad1-F-200177"
pv5.g=c(pv5.g.1,pv5.g.2,pv5.g.3) #3E
pv5.h = pv5.h.1 = c("E0585-F-400028","E0585-F-700002")
pv5.i = pv5.i.1 = "fru-M-200172" # check other pnts
pv5.j = pv5.j.1 = "Gad1-F-100211"
pv5.k = pv5.k.1 = c("Gad1-F-300290")
pv5.l = pv5.l.1 = "Cha-F-400240"
df[pv5.a,]$anatomy.group = "pv5a"
df[pv5.b,]$anatomy.group = "pv5b"
df[pv5.c,]$anatomy.group = "pv5c"
df[pv5.d,]$anatomy.group = "pv5d"
df[pv5.e,]$anatomy.group = "pv5e"
df[pv5.f,]$anatomy.group = "pv5f"
df[pv5.g,]$anatomy.group = "pv5g"
df[pv5.h,]$anatomy.group = "pv5h"
df[pv5.i,]$anatomy.group = "pv5i"
df[pv5.j,]$anatomy.group = "pv5j"
df[pv5.k,]$anatomy.group = "pv5k"
df[pv5.l,]$anatomy.group = "pv5l"
df[pv5.a.1,]$cell.type = "pv5a1"
df[pv5.a.2,]$cell.type = "pv5a2"
df[pv5.a.3,]$cell.type = "pv5a3"
df[pv5.a.4,]$cell.type = "pv5a4"
df[pv5.a.5,]$cell.type = "pv5a5"
df[pv5.a.6,]$cell.type = "pv5a6"
df[pv5.b.1,]$cell.type = "pv5b1"
df[pv5.b.2,]$cell.type = "pv5b2"
df[pv5.b.3,]$cell.type = "pv5b3"
df[pv5.b.4,]$cell.type = "pv5b4"
df[pv5.b.5,]$cell.type = "pv5b5"
df[pv5.b.6,]$cell.type = "pv5b6"
df[pv5.c.1,]$cell.type = "pv5c1"
df[pv5.c.2,]$cell.type = "pv5c2"
df[pv5.c.3,]$cell.type = "pv5c3"
df[pv5.c.4,]$cell.type = "pv5c4"
df[pv5.c.5,]$cell.type = "pv5c5"
df[pv5.d.1,]$cell.type = "pv5d1"
df[pv5.d.2,]$cell.type = "pv5d2"
df[pv5.d.3,]$cell.type = "pv5d3"
df[pv5.e.1,]$cell.type = "pv5e1" #PPl1-a'3
df[pv5.e.2,]$cell.type = "pv5e1" #PPl1-a'3?
df[pv5.e.3,]$cell.type = "pv5e1" #PPl1-a'3?
df[pv5.f.1,]$cell.type = "pv5f1"
df[pv5.g.1,]$cell.type = "pv5g1"
df[pv5.g.2,]$cell.type = "pv5g2"
df[pv5.g.3,]$cell.type = "pv5g3"
df[pv5.h.1,]$cell.type = "pv5h1"
df[pv5.i.1,]$cell.type = "pv5i1"
df[pv5.j.1,]$cell.type = "pv5j1"
df[pv5.k.1,]$cell.type = "pv5k1"
df[pv5.l.1,]$cell.type = "pv5l1"
###### PNT PV3 ######
### pv3
pv3 = c("Cha-F-000110","Gad1-F-700071", "Gad1-F-300161", "5HT1A-M-300003", "Gad1-F-500252","Cha-F-700277","CL123R_70G02", "Cha-F-000350","Gad1-F-600301","Gad1-F-000101")
df[unique(pv3),]$pnt = "pv3"
pv3.a.1 = c("Gad1-F-300161","Gad1-F-000101","CL123R_70G02")
pv3.a.2 = c("Gad1-F-600301")
pv3.a=c(pv3.a.1,pv3.a.2)
pv3.b = pv3.b.1 = "Gad1-F-500252" #maybe pv2?
pv3.c = pv3.c.1 = c("Cha-F-000350")
pv3.d = pv3.d.1 = c("Cha-F-700277","Cha-F-100320")
pv3.e = pv3.e.1 = "5HT1A-M-300003"
pv3.f = pv3.f.1 = "Gad1-F-700071"
pv3.g = pv3.g.1 = "Cha-F-000110" #maybe pv2?
df[pv3.a,]$anatomy.group = "pv3a"
df[pv3.b,]$anatomy.group = "pv3b"
df[pv3.c,]$anatomy.group = "pv3c"
df[pv3.d,]$anatomy.group = "pv3d"
df[pv3.e,]$anatomy.group = "pv3e"
df[pv3.f,]$anatomy.group = "pv3f"
df[pv3.g,]$anatomy.group = "pv3g"
df[pv3.a.1,]$cell.type = "pv3a1"
df[pv3.a.2,]$cell.type = "pv3a2"
df[pv3.b.1,]$cell.type = "pv3b1"
df[pv3.c.1,]$cell.type = "pv3c1"
df[pv3.d.1,]$cell.type = "pv3d1"
df[pv3.e.1,]$cell.type = "pv3e1"
df[pv3.f.1,]$cell.type = "pv3f1"
df[pv3.g.1,]$cell.type = "pv3g1"
###### PNT PV4 ######
### pv4
pv4 = c("Gad1-F-000381","Gad1-F-500038","Cha-F-800134","VGlut-F-500323","Cha-F-500303",
"fru-F-400011","VGlut-F-500046","CL100R_26C12","CL98R_26G09",
"Gad1-F-000201", "fru-F-400180", "Cha-F-000507",
"Cha-F-600243", "Cha-F-300221", "Cha-F-100221", "VGlut-F-400084",
"5HT1A-F-300030", "fru-M-500368", "5HT1A-F-300034", "Cha-F-300186",
"Cha-F-100456", "fru-F-400219", "Cha-F-400318", "VGlut-F-500444",
"VGlut-F-700430", "Gad1-F-500281", "Cha-F-900046", "VGlut-F-600752",
"Cha-F-500234", "fru-F-500177", "fru-F-500479","Cha-F-200186",
"Gad1-F-100345", "VGlut-F-500399", "VGlut-F-500442", "VGlut-F-800068",
"VGlut-F-500445", "Cha-F-100028", "VGlut-F-400240",
"fru-F-100052","140207c0","CL97R_26C12","CL29GR_JRC_IS23354-000.swc",
"Cha-F-600209", "E0585-F-300056", "fru-M-200351",
"Cha-F-200398", "Cha-F-100412","CL29CR_30H02","CL29CR_14B11",
"Gad1-F-500023", "VGlut-F-700436", "Cha-F-500298","fru-M-200253", "Gad1-F-500178" ,
"Gad1-F-200395", "Cha-F-100278", "VGlut-F-300393", "Gad1-F-100338","Gad1-F-100132",
"VGlut-F-600090", "Gad1-F-500338", "Gad1-F-600125", "Gad1-F-500171","Cha-F-700255",
"Gad1-F-600205", "VGlut-F-400394","Gad1-F-700108", "Cha-F-600269", "Cha-F-000485",
"Cha-F-600207", "VGlut-F-500411", "VGlut-F-700602", "Gad1-F-300148",
"VGlut-F-600764", "VGlut-F-300574", "VGlut-F-500243", "VGlut-F-500399",
"VGlut-F-700084", "VGlut-F-600311", "VGlut-F-600030",
"Gad1-F-400027", "VGlut-F-700503", "VGlut-F-700280", "VGlut-F-800064",
"VGlut-F-700342", "Gad1-F-700258", "Gad1-F-100178", "VGlut-F-700001", "Gad1-F-100154",
"VGlut-F-600075", "Cha-F-300212", "VGlut-F-700260", "Cha-F-400138", "Gad1-F-200322",
"VGlut-F-200590", "Gad1-F-400124", "VGlut-F-000390",
"Gad1-F-600252","VGlut-F-400195","Cha-F-600226","140211c0","Gad1-F-300135",
"130703c0", "130408c0", "130411c2", "140117c2","130312c1",
"130619c0", "130625c0", "130724c0", "130826c0", "130627c0",
"130829c0", "130911c0", "130912c0", "130912c1", "130923c0", "130925c2",
"140206c2", "140212c0","130821c0","131212c1", "130829c1", "130205c2",
"130219c0", "130704c1", "130911c2", "130913c0",
"Gad1-F-900064", "Cha-F-000395", "Cha-F-600226", "Cha-F-800106",
"Gad1-F-000274", "Gad1-F-100154", "VGlut-F-500419",
"VGlut-F-800074", "VGlut-F-500253", "VGlut-F-900028", "Trh-F-000048","Gad1-F-600205")
df[unique(pv4),]$pnt = "pv4"
pv4.a.1 = c("130826c0", "130829c0", "130925c2", "130821c0", "130911c0",
"130829c1","Cha-F-100412", "Cha-F-900046", "Cha-F-700255","130205c2", "Gad1-F-100338")
pv4.a.2 = c("Cha-F-100221", "Gad1-F-500178", "5HT1A-F-300030", "5HT1A-F-300034","Gad1-F-600205", "Cha-F-300221", "Gad1-F-200395","Gad1-F-600205")
pv4.a.3 = c("Cha-F-100456", "Cha-F-300186", "Gad1-F-500281", "Gad1-F-100345","Gad1-F-000201","fru-F-400180",
"130913c0","130912c0", "130911c2")
pv4.a.4=c("VGlut-F-500253","VGlut-F-600752", "VGlut-F-600090", "VGlut-F-700430", "VGlut-F-700436","130724c0","130219c0","130703c0")
pv4.a.5 = c("Cha-F-500234","fru-M-500368","130625c0","130619c0",
"fru-F-500177","fru-F-400219","fru-F-500479","fru-F-400011","Gad1-F-000381")
pv4.a.6 = c("Gad1-F-100132")
pv4.a.7 = c("Gad1-F-700108","130627c0","Cha-F-600207")
pv4.a.8 = c("Gad1-F-400124","Cha-F-800134","Gad1-F-500038")
pv4.a.9 = c("130408c0","130411c2","130704c1")
pv4.a.10 = c("VGlut-F-300393","Cha-F-500303","Cha-F-600226")
pv4.a.11 = "Gad1-F-600252"
pv4.a= c(pv4.a.1,pv4.a.2,pv4.a.3,pv4.a.4,pv4.a.5,pv4.a.6,pv4.a.7,pv4.a.8,pv4.a.9,pv4.a.10)
pv4.b.1 = c("VGlut-F-500411","VGlut-F-700602","Gad1-F-300148", "VGlut-F-600764","VGlut-F-300574", "VGlut-F-500243","VGlut-F-500399", "VGlut-F-700084","140117c2")
pv4.b.2 = c("Gad1-F-100154","131212c1","E0585-F-300056","VGlut-F-500444","140207c0", "VGlut-F-400084", "Gad1-F-100154","Cha-F-100028","Gad1-F-200322","140211c0","140206c2")
pv4.b.3 = c("Gad1-F-300135")
pv4.b= c(pv4.b.1,pv4.b.2,pv4.b.3)
pv4.c.1 = c("VGlut-F-500046","VGlut-F-600030","Gad1-F-400027","VGlut-F-700503",
"VGlut-F-400240","VGlut-F-700280","VGlut-F-800064","VGlut-F-700342",
"Gad1-F-000274","VGlut-F-500419")
pv4.c.2=c("VGlut-F-400195" ,"VGlut-F-800074", "VGlut-F-900028" ,
"fru-M-200253","Gad1-F-100178","Gad1-F-700258")
pv4.c.3 = "VGlut-F-600311"
pv4.c.4= "VGlut-F-500445"
pv4.c.5 = "VGlut-F-500442"
pv4.c.6 = "Cha-F-600243"
pv4.c=c(pv4.c.1,pv4.c.2,pv4.c.3,pv4.c.4,pv4.c.5,pv4.c.6)
pv4.d.1 =c("Cha-F-600269", "Cha-F-000485", "Gad1-F-500338", "Cha-F-200398",
"130923c0","Cha-F-000507","140212c0")
pv4.d.2 =c("Gad1-F-500171","Gad1-F-500023","Cha-F-100278","Cha-F-800106","VGlut-F-500323")
pv4.d.3 ="Gad1-F-600125"
pv4.d.4 ="VGlut-F-400394"
pv4.d.5 ="Cha-F-600209"
pv4.d.6 =c("130912c1")
pv4.d = c(pv4.d.1,pv4.d.2,pv4.d.3,pv4.d.4,pv4.d.5,pv4.d.6)
pv4.e.1 = c("VGlut-F-700001","VGlut-F-600075","Cha-F-300212","VGlut-F-700260")
pv4.e.2 = c("Cha-F-400138","VGlut-F-200590","Trh-F-000048")
pv4.e.3 =c("Cha-F-500298")
pv4.e.4=c("CL100R_26C12")
pv4.e = c(pv4.e.1,pv4.e.2,pv4.e.3,pv4.e.4)
pv4.f = pv4.f.1 = c("130312c1","Cha-F-400318")
pv4.g.1 = c("VGlut-F-800068")
pv4.g.2=c("fru-M-200351","VGlut-F-000390")
pv4.g=c(pv4.g.1,pv4.g.2)
pv4.h = pv4.h.1 = "fru-F-100052"
pv4.i = pv4.i.1 = c("Cha-F-200186","CL29CR_30H02","CL29CR_14B11")
pv4.j = pv4.j.1 = "Gad1-F-900064"
pv4.k.1 = "Cha-F-000395"
pv4.k.2 = "CL29FR_IS24835"
pv4.k=c(pv4.k.1,pv4.k.2)
pv4.l = pv4.l.1 = "CL98R_26G09"
pv4.m = pv4.m.1 = "CL97R_26C12"
pv4.n = pv4.n.1 = "CL29GR_JRC_IS23354-000.swc"
df[pv4.a,]$anatomy.group = "pv4a"
df[pv4.b,]$anatomy.group = "pv4b"
df[pv4.c,]$anatomy.group = "pv4c"
df[pv4.d,]$anatomy.group = "pv4d"
df[pv4.e,]$anatomy.group = "pv4e"
df[pv4.f,]$anatomy.group = "pv4f"
df[pv4.g,]$anatomy.group = "pv4g"
df[pv4.h,]$anatomy.group = "pv4h"
df[pv4.i,]$anatomy.group = "pv4i"
df[pv4.j,]$anatomy.group = "pv4j"
df[pv4.k,]$anatomy.group = "pv4k"
df[pv4.l,]$anatomy.group = "pv4l"
df[pv4.m,]$anatomy.group = "pv4m"
df[pv4.n,]$anatomy.group = "pv4n"
df[pv4.a.1,]$cell.type = "pv4a1"
df[pv4.a.2,]$cell.type = "pv4a2"
df[pv4.a.3,]$cell.type = "pv4a3"
df[pv4.a.4,]$cell.type = "pv4a4"
df[pv4.a.5,]$cell.type = "pv4a5"
df[pv4.a.6,]$cell.type = "pv4a6"
df[pv4.a.7,]$cell.type = "pv4a7"
df[pv4.a.8,]$cell.type = "pv4a8"
df[pv4.a.9,]$cell.type = "pv4a9"
df[pv4.a.10,]$cell.type = "pv4a10"
df[pv4.b.1,]$cell.type = "pv4b1"
df[pv4.b.2,]$cell.type = "pv4b2"
df[pv4.c.1,]$cell.type = "pv4c1"
df[pv4.c.2,]$cell.type = "pv4c2"
df[pv4.c.3,]$cell.type = "pv4c3"
df[pv4.c.4,]$cell.type = "pv4c4"
df[pv4.c.5,]$cell.type = "pv4c5"
df[pv4.c.6,]$cell.type = "pv4c6"
df[pv4.d.1,]$cell.type = "pv4d1"
df[pv4.d.2,]$cell.type = "pv4d2"
df[pv4.d.3,]$cell.type = "pv4d3"
df[pv4.d.4,]$cell.type = "pv4d4"
df[pv4.d.5,]$cell.type = "pv4d5"
df[pv4.d.6,]$cell.type = "pv4d6"
df[pv4.e.1,]$cell.type = "pv4e1"
df[pv4.e.2,]$cell.type = "pv4e2"
df[pv4.e.3,]$cell.type = "pv4e3"
df[pv4.f.1,]$cell.type = "pv4f1"
df[pv4.g.1,]$cell.type = "pv4g1"
df[pv4.g.2,]$cell.type = "pv4g2"
df[pv4.h.1,]$cell.type = "pv4h1"
df[pv4.i.1,]$cell.type = "pv4i1"
df[pv4.j.1,]$cell.type = "pv4j1"
df[pv4.k.1,]$cell.type = "pv4k1"
df[pv4.k.2,]$cell.type = "pv4k2"
df[pv4.l.1,]$cell.type = "pv4l1"
df[pv4.m.1,]$cell.type = "pv4m1"
df[pv4.n.1,]$cell.type = "pv4n1"
###### PNT PV2 ######
### PV2
pv2 = c("Gad1-F-600088","Gad1-F-800194","Gad1-F-500328","Gad1-F-400232",
"Gad1-F-100074","CL52R_11E08","CL123R_70G02","CL133R_39D07",
"5HT1A-M-100027", "Gad1-F-800092", "Gad1-F-700138", "Cha-F-000086",
"Cha-F-300168", "Cha-F-400222", "Cha-F-000242", "Trh-F-500222",
"Gad1-F-800126", "Gad1-F-500266", "Cha-F-200448","Cha-F-600097",
"Trh-M-500183","5HT1A-M-200001","5HT1A-F-100028","131030c0",
"131031c1","CL135R_10A11", "131028c0","ICL151B_IS24671", "131122c1")
df[unique(pv2),]$pnt = "pv2"
pv2.a.1 = c("5HT1A-M-200001", "Cha-F-300168", "5HT1A-F-100028",
"131028c0", "131030c0")
pv2.a.2 = c("Gad1-F-400232", "Cha-F-000242")
pv2.a.3 = c("Cha-F-400222","5HT1A-M-100027")
pv2.a.4 = "Gad1-F-600088"
pv2.a.5 = "Gad1-F-800194"
pv2.a=c(pv2.a.1,pv2.a.2,pv2.a.3,pv2.a.4)
pv2.b = c("Gad1-F-800092","Gad1-F-100074","CL133R_39D07","131122c1")
pv2.b.1 = c("Gad1-F-800092")
pv2.b.2 = "Gad1-F-100074"
pv2.b.3 ="CL133R_39D07"
pv2.b=c(pv2.b.1,pv2.b.2,pv2.b.3)
pv2.c.1 = c("Gad1-F-700138","131031c1")
pv2.c.2 = c("140613c0","131118c1")
pv2.c=c(pv2.c.1,pv2.c.2)
pv2.d = pv2.d.1 = "Gad1-F-500328"
pv2.e = pv2.e.1 = "Cha-F-000086"
pv2.f = pv2.f.1 = "ICL151B_IS24671"
pv2.g = pv2.g.1 = c("Gad1-F-500266", "Cha-F-200448")
pv2.h = pv2.h.1 = "Gad1-F-800126"# Could be its own tract
pv2.i = pv2.i.1 = "Cha-F-600097"
pv2.j = pv2.j.1 = "CL52R_11E08"
pv2.k = pv2.k.1 = "CL135R_10A11"
df[pv2.a,]$anatomy.group = "pv2a"
df[pv2.b,]$anatomy.group = "pv2b"
df[pv2.c,]$anatomy.group = "pv2c"
df[pv2.d,]$anatomy.group = "pv2d"
df[pv2.e,]$anatomy.group = "pv2e"
df[pv2.f,]$anatomy.group = "pv2f"
df[pv2.g,]$anatomy.group = "pv2g"#dont use for plotting
df[pv2.h,]$anatomy.group = "pv2h"
df[pv2.i,]$anatomy.group = "pv2i"
df[pv2.j,]$anatomy.group = "pv2j"
df[pv2.k,]$anatomy.group = "pv2k"
df[pv2.a.1,]$cell.type = "pv2a1"
df[pv2.a.2,]$cell.type = "pv2a2"
df[pv2.a.3,]$cell.type = "pv2a3"
df[pv2.a.4,]$cell.type = "pv2a4"
df[pv2.a.5,]$cell.type = "pv2a5"
df[pv2.b.1,]$cell.type = "pv2b1"
df[pv2.b.2,]$cell.type = "pv2b2"
df[pv2.c.1,]$cell.type = "pv2c1"
df[pv2.c.2,]$cell.type = "pv2c2"
df[pv2.d.1,]$cell.type = "pv2d1"
df[pv2.e.1,]$cell.type = "pv2e1"
df[pv2.f.1,]$cell.type = "pv2f1"
df[pv2.g.1,]$cell.type = "pv2g1"
df[pv2.h.1,]$cell.type = "pv2h1"
df[pv2.i.1,]$cell.type = "pv2i1"
df[pv2.j.1,]$cell.type = "pv2j1"
df[pv2.k.1,]$cell.type = "pv2k1"
###### PNT PV1 ######
### PV1
pv1 = c("TH-M-200033", "TH-M-200079", "TH-M-300048", "TH-M-000013", "CL143R_MB583B",
"TH-M-000042", "TH-M-000071", "Trh-M-000025", "Cha-F-000461",
"TH-F-000011", "TH-F-000012", "TH-M-200035","Gad1-F-500004",
"Gad1-F-500089","TH-F-300078","Gad1-F-500325","Cha-F-000278","Cha-F-500094",
"Cha-F-000310", "fru-F-000126", "fru-M-800060", "TH-M-000030","fru-F-000125")
df[unique(pv1),]$pnt = "pv1"
pv1.a.1 = c("Gad1-F-500004","TH-M-200079","TH-M-300048","TH-M-000042","TH-M-200033","TH-M-200035")
pv1.a.2 = c( "Cha-F-000310","Cha-F-000461","TH-F-000012","TH-M-000013","TH-M-000030")
pv1.a.3 = "Cha-F-000310"
pv1.a=c(pv1.a.1,pv1.a.2,pv1.a.3)
pv1.b = c("TH-M-000071","TH-F-300078","Gad1-F-500089","TH-F-000011","Trh-M-000025")
pv1.b.1 = "TH-M-000071"
pv1.b.2 = "TH-F-300078"
pv1.b.3 = "Gad1-F-500089"
pv1.b.4 = "TH-F-000011"
pv1.b.5 = "Trh-M-000025"
pv1.c = pv1.c.1 = "Cha-F-000278" # Could be its own tract?
pv1.d = pv1.d.1 = "Cha-F-500094" # Could be its own tract?
pv1.e = pv1.e.1 = "Gad1-F-500325"
pv1.f = pv1.f.1 = "fru-F-000126" # Could be its own tract?
pv1.g = pv1.g.1 = "fru-M-800060" # Could be its own tract?
pv1.h = pv1.h.1 = "fru-F-000125" # Could be its own tract?
pv1.i = pv1.i.1 = "CL143R_MB583B"
df[pv1.a,]$anatomy.group = "pv1a"
df[pv1.b,]$anatomy.group = "pv1b"
df[pv1.c,]$anatomy.group = "pv1c"
df[pv1.d,]$anatomy.group = "pv1d"
df[pv1.e,]$anatomy.group = "pv1e"
df[pv1.f,]$anatomy.group = "pv1f"
df[pv1.g,]$anatomy.group = "pv1g"
df[pv1.h,]$anatomy.group = "pv1h"
df[pv1.i,]$anatomy.group = "pv1i"
df[pv1.a.1,]$cell.type = "pv1a1"
df[pv1.a.2,]$cell.type = "pv1a2"
df[pv1.a.3,]$cell.type = "pv1a3"
df[pv1.b.1,]$cell.type = "pv1b1"
df[pv1.b.2,]$cell.type = "pv1b2"
df[pv1.b.3,]$cell.type = "pv1b3"
df[pv1.b.4,]$cell.type = "pv1b4"
df[pv1.b.5,]$cell.type = "pv1b5"
df[pv1.c.1,]$cell.type = "pv1c1"
df[pv1.d.1,]$cell.type = "pv1d1"
df[pv1.e.1,]$cell.type = "pv1e1"
df[pv1.f.1,]$cell.type = "pv1f1"
df[pv1.g.1,]$cell.type = "pv1g1"
df[pv1.h.1,]$cell.type = "pv1h1"
df[pv1.i.1,]$cell.type = "pv1i1"
###### PNT PD6 ######
pd6 = c("Trh-F-000061", "Trh-M-600117", "Trh-M-600108", "Trh-M-200113",
"Trh-M-200014", "Trh-M-700039","Gad1-F-200110", "fru-M-500259", "VGlut-F-900053", "VGlut-F-000454",
"Cha-F-500087", "Cha-F-600179", "VGlut-F-000336", "fru-F-000130",
"VGlut-F-300515","fru-M-500095")
df[unique(pd6),]$pnt = "pd6"
pd6a = c("fru-M-500259", "VGlut-F-900053","VGlut-F-000454","Cha-F-500087", "Cha-F-600179",
"VGlut-F-000336", "fru-F-000130", "VGlut-F-300515","Gad1-F-200110")
pd6.a.1 = c("fru-M-500259", "VGlut-F-900053","VGlut-F-000454","Cha-F-500087", "Cha-F-600179",
"VGlut-F-000336", "fru-F-000130", "VGlut-F-300515")
pd6.a.2 = "Gad1-F-200110"
pd6.a = c( pd6.a.1, pd6.a.2)
pd6.b = pd6.b.1 = c("Trh-M-700039","Trh-F-000061", "Trh-M-600108", "Trh-M-200113")
pd6.c = pd6.c.1 = "Trh-M-600117"
pd6.d = pd6.d.1 = "Trh-M-200014"
pd6.e = pd6.e.1 = "fru-M-500095"
df[pd6.a,]$anatomy.group = "pd6a"
df[pd6.b,]$anatomy.group = "pd6b"
df[pd6.c,]$anatomy.group = "pd6c"
df[pd6.d,]$anatomy.group = "pd6d"
df[pd6.e,]$anatomy.group = "pd6e"
df[pd6.a.1,]$cell.type = "pd6a1"
df[pd6.a.2,]$cell.type = "pd6a2"
df[pd6.b.1,]$cell.type = "pd6b1"
df[pd6.c.1,]$cell.type = "pd6c1"
df[pd6.d.1,]$cell.type = "pd6d1"
df[pd6.e.1,]$cell.type = "pd6e1"
###### PNT PD5 ######
### pd5
pd5 = c("Gad1-F-100015")
df[unique(pd5),]$pnt = "pd5"
pd5.a = pd5.a.1 = c("Gad1-F-100015") # New tract?
df[pd5.a,]$anatomy.group = "pd5a"
df[pd5.a.1,]$cell.type = "pd5a1"
###### PNT PD4 ######
### pd4
pd4 = c("Cha-F-000413", "Cha-F-500201", "Cha-F-700283","Gad1-F-000285",
"Gad1-F-100218","Gad1-F-100025", "fru-F-000092",
"VGlut-F-300425", "VGlut-F-100282", "fru-F-000098","Cha-F-400309",
"fru-M-000015", "Cha-F-000005","fru-M-500020",
"Cha-F-000007", "Cha-F-000531", "Cha-F-300350", "fru-F-300195",
"VGlut-F-300438", "VGlut-F-100068","Gad1-F-900054","fru-M-000077")
df[unique(pd4),]$pnt = "pd4"
pd4.a.1 = c("Cha-F-000413","VGlut-F-300425","VGlut-F-100068")
pd4.a.2 = "VGlut-F-100282"
pd4.a.3 = c("fru-F-000098","fru-M-000077")
pd4.a.4 = "VGlut-F-300438"
pd4.a.5 = c("fru-F-000092")
pd4.a=c(pd4.a.1,pd4.a.2,pd4.a.3,pd4.a.4,pd4.a.5)
pd4.b= pd4.b.1 = c("fru-M-000015", "Cha-F-500201", "Cha-F-000531")
pd4.c = c("Cha-F-700283","fru-F-300195")
pd4.c.1 = "Cha-F-700283"
pd4.c.2 = "fru-F-300195"
pd4.d = pd4.d.1 = c("Cha-F-000005","Gad1-F-900054","Cha-F-000007") # "Cha-F-000007" duplicated
pd4.e = pd4.e.1 = c("Gad1-F-000285", "Gad1-F-100218","Gad1-F-100025")
pd4.f = pd4.f.1 = "Cha-F-300350"
pd4.g = pd4.g.1 = "fru-M-500020"
pd4.h = pd4.h.1 = "Cha-F-400309"
pd4.i = pd4.i.1 = "fru-F-000092"
df[pd4.a,]$anatomy.group = "pd4a"
df[pd4.b,]$anatomy.group = "pd4b"
df[pd4.c,]$anatomy.group = "pd4c"
df[pd4.d,]$anatomy.group = "pd4d"
df[pd4.e,]$anatomy.group = "pd4e"
df[pd4.f,]$anatomy.group = "pd4f"
df[pd4.g,]$anatomy.group = "pd4g"
df[pd4.h,]$anatomy.group = "pd4h"
df[pd4.i,]$anatomy.group = "pd4i"
df[pd4.a.1,]$cell.type = "pd4a1"
df[pd4.a.2,]$cell.type = "pd4a2"
df[pd4.a.3,]$cell.type = "pd4a3"
df[pd4.a.4,]$cell.type = "pd4a4"
df[pd4.a.5,]$cell.type = "pd4a5"
df[pd4.b.1,]$cell.type = "pd4b1"
df[pd4.c.1,]$cell.type = "pd4c1"
df[pd4.c.2,]$cell.type = "pd4c2"
df[pd4.d.1,]$cell.type = "pd4d1"
df[pd4.e.1,]$cell.type = "pd4e1"
df[pd4.f.1,]$cell.type = "pd4f1"
df[pd4.g.1,]$cell.type = "pd4g1"
df[pd4.h.1,]$cell.type = "pd4h1"
df[pd4.i.1,]$cell.type = "pd4i1"
###### PNT PD3 ######
### PD3
pd3 = c("Cha-F-100103","Cha-F-400165","Cha-F-500011","Gad1-F-100168", "Gad1-F-200150","Gad1-F-400320","CL153R_IS24693")
df[unique(pd3),]$pnt = "pd3"
pd3.a.1 = c("Cha-F-400165","Cha-F-500011")#116, new tract! LHd2 neuroblast.
pd3.a.2 = c("Gad1-F-100168", "Gad1-F-200150")
pd3.a=c(pd3.a.1,pd3.a.2)
pd3.b = pd3.b.1 = "Cha-F-100103" # correct attribution
pd3.c = pd3.c.1 = "Gad1-F-400320" # correct attribution
pd3.d = pd3.d.1 = "CL153R_IS24693"
df[pd3.a,]$anatomy.group = "pd3a"
df[pd3.b,]$anatomy.group = "pd3b"
df[pd3.c,]$anatomy.group = "pd3c"
df[pd3.d,]$anatomy.group = "pd3d"
df[pd3.a.1,]$cell.type = "pd3a1"
df[pd3.a.2,]$cell.type = "pd3a2"
df[pd3.b.1,]$cell.type = "pd3b1"