R/constants.R
In acorg/acutilsLite: A package for working with CPE databases
Defines functions
coloraa
aa.colors
aa.values
clusters.toFactor
clusters.number
clusters.colour
clusters.subsMatrix
h3_clusters
#' order for matching
#' @export
h3_clade_grouping_heirarchy <- c(
"3C.2A1",
"3C.2A1A",
"3C.2A1B",
"3C.2A2",
"3C.2A",
"3C.3A",
"3C.3"
)
#' order for plotting
#' @export
h3_clade_order <- c(
"3C.3",
"3C.3A",
"3C.2A",
"3C.2A1",
"3C.2A1A",
"3C.2A1B",
"3C.2A2",
"Other",
"Clade missing"
)
#' @export
h3_clusters <- function(){
c(
"HK68",
"EN72",
"VI75",
"TX77",
"BK79",
"SI87",
"BE89",
"BE92",
"WU95",
"SY97",
"FU02",
"CA04",
"WI05",
"PE09",
"SW13",
"HK14"
)
}
#' @export
h3_cluster_colors <- c(
"HK68" = "#a208bd",
"EN72" = "#00ffe1",
"VI75" = "#f9d004",
"TX77" = "#ab4c00",
"BK79" = "#00ff00",
"SI87" = "#0000ff",
"BE89" = "#ff0000",
"BE92" = "#f894f8",
"WU95" = "#37802b",
"SY97" = "#00afff",
"FU02" = "#ffd700",
"CA04" = "green",
"WI05" = "blue",
"PE09" = "purple",
"SW13" = "grey80",
"HK14" = "grey80"
)
#' @export
h3_clade_colors <- c(
"3C.3" = '#7570b3',
"3C.3A" = '#e7298a',
"3C.2A" = '#0B691B',
"3C.2A1" = '#7D2B07',
"3C.2A1A" = '#E2D11F',
"3C.2A1B" = '#F4B329',
"3C.2A2" = '#1FD16E',
"Other" = 'black',
"Clade missing" = 'grey50'
)
#' @export
h3_cluster_subs <- list(
HK68 = c("155T"),
EN72 = c("155Y"),
VI75 = c("189K"),
TX77 = c("158E", "193N"),
BK79 = c("156E"),
SI87 = c("155H", "159Y", "189R"),
BE89 = c("145K"),
BE92 = c("156K"),
WU95 = c("145K"),
SY97 = c("156Q", "158K"),
FU02 = c("156H"),
CA04 = c("145N"),
WI05 = c("193F"),
PE09 = c("158N", "189K")
)
#' @export
clusters.subsMatrix <- function(){
output <- do.call(rbind, lapply(h3_cluster_subs, function(x){
position <- substr(x, 1, 3)
aa <- substr(x, 4, 4)
result <- rep("", 7)
result[match(position, b7_positions)] <- aa
result
}))
colnames(output) <- b7_positions
output
}
#' @export
clusters.colour <- function(clusters){
h3_cluster_colors[as.character(clusters)]
}
#' @export
clusters.number <- function(clusters){
clusters[clusters == "BR07"] <- "WI05"
match(
clusters,
h3_clusters()
)
}
#' @export
clusters.toFactor <- function(clusters, excluded_clusters = NULL){
cluster_levels <- h3_clusters()
factor(clusters, levels = cluster_levels[!cluster_levels %in% excluded_clusters])
}
#' @export
b7_positions <- c(145, 155, 156, 158, 159, 189, 193)
#' @export
accessory_residues <- c(133, 143)
#' @export
h3_2004_variable_positions <- c(
1, 2, 3, 5, 6, 7, 8, 10, 18, 21, 25, 29, 31, 33, 34, 45, 47, 49, 50, 53, 54, 55, 57, 58, 59,
62, 63, 67, 75, 78, 79, 80, 81, 82, 83, 88, 92, 94, 96, 101, 103, 106, 112, 114, 115, 121, 122,
124, 126, 128, 129, 131, 132, 133, 135, 137, 138, 139, 140, 142, 143, 144, 145, 146, 148, 155,
156, 157, 158, 159, 160, 163, 164, 165, 167, 169, 171, 172, 173, 174, 175, 176, 182, 185, 186,
188, 189, 190, 192, 193, 194, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 208, 209, 213,
214, 216, 217, 219, 220, 222, 225, 226, 227, 229, 230, 231, 233, 235, 236, 242, 244, 246, 247,
248, 259, 260, 261, 262, 264, 267, 268, 269, 271, 272, 273, 275, 276, 278, 279, 280, 285, 286,
289, 291, 292, 299, 304, 307, 309, 310, 312, 313, 323, 325, 326
)
siteA <- c(122, 124, 126, 130, 131, 132, 133, 135, 138, 142, 145)
siteB <- c(128, 129, 155, 156, 157, 158, 159, 160, 163, 164, 165, 186, 190, 193, 194, 196, 197, 198)
siteC <- c(44, 45, 46, 47, 48, 50, 51, 53, 54, 273, 275, 278, 279, 280, 294, 297, 299, 300, 304, 305, 307, 308, 309, 310, 311, 312)
siteD <- c(96, 102, 103, 117, 121, 167, 170, 171, 172, 173, 174, 175, 176, 177, 179, 182, 201, 203, 207, 208, 209, 212, 213, 214, 215, 216, 217, 218, 219, 226, 227, 228, 229, 230, 238, 240, 242, 244, 246, 247, 248)
RBS <- c(98, 134, 135, 136, 137, 138, 153, 183, 190, 194, 224, 225, 226, 227, 228)
siteA_Annette <- c(siteA, 137, 140, 143, 144, 146, 150, 152, 168)
siteB_Annette <- c(siteB, 187, 188, 189, 192)
siteC_Annette <- c(siteC, 276)
siteD_Annette <- siteD
siteE_Annette <- c(57, 59, 62, 63, 67, 75, 78, 80, 81, 82, 83, 86, 87, 88, 91, 92, 94, 109, 260, 261, 262, 265)
#' @export
h3_sites <- list(
RBS = RBS,
A = siteA,
B = siteB,
C = siteC,
D = siteD,
A_Annette = siteA_Annette,
B_Annette = siteB_Annette,
C_Annette = siteC_Annette,
D_Annette = siteD_Annette,
E_Annette = siteE_Annette
)
#' @export
aa_characteristics <- tibble::tribble(
~aa, ~character,
"R", "Positive",
"K", "Positive",
"H", "Positive",
"D", "Negative",
"E", "Negative",
"S", "Polar uncharged",
"T", "Polar uncharged",
"N", "Polar uncharged",
"Q", "Polar uncharged",
"C", "Special",
"G", "Special",
"P", "Special",
"A", "Hydrophobic",
"V", "Hydrophobic",
"I", "Hydrophobic",
"L", "Hydrophobic",
"M", "Hydrophobic",
"F", "Hydrophobic",
"Y", "Hydrophobic",
"W", "Hydrophobic"
)
#' @export
aa.values <- function(){
c(
c("G","A","S","T"),
c("C","V","I","L","P","F","Y","M","W"),
c("N","Q","H"),
c("D","E"),
c("K","R"),
c("*", "X")
)
}
#' @export
aa.colors <- function(){
aa <- aa.values()
aacols <- as.vector(coloraa(rbind(aa)))
names(aacols) <- aa
aacols
}
#' @export
coloraa <- function(x, alpha = 0.5, simplify = T){
if(is.vector(x)) x <- rbind(x)
if(ncol(x) == 0) return(x)
aacolors <- x
aacolors[] <- ""
aacolors[x %in% c("G","A","S","T") ] <- "orange"
aacolors[x %in% c("C","V","I","L","P","F","Y","M","W") ] <- "green"
aacolors[x %in% c("N","Q","H","Z") ] <- "magenta"
aacolors[x %in% c("D","E","B") ] <- "red"
aacolors[x %in% c("K","R") ] <- "blue"
aacolors[x %in% c("*", "X", "-", ".", "") ] <- "grey50"
if(sum(aacolors == "") > 0){
stop(sprintf("aas '%s' not recognised.", paste(unique(x[aacolors == ""]), collapse = ", ")))
}
aacolors[] <- adjustcolor(aacolors, alpha.f = alpha)
if (simplify){
if (length(aacolors) == 1) return(aacolors[[1]])
}
aacolors
}
#'@export
aacolors_al <- c(
"D" = "#F7CF08",
"E" = "#CD8D00",
"R" = "#B2A1FF",
"H" = "#7571BC",
"K" = "#440FAE",
"N" = "#18E0F7",
"Q" = "#0080FF",
"S" = "#0F52BA",
"T" = "navy",
"C" = "#00F000",
"G" = "#4CBB17",
"P" = "#1A4F30",
"A" = "#EB1919",
"I" = "#F93BBB",
"L" = "#FF2976",
"M" = "#FF5A3D",
"F" = "#C34822",
"W" = "#A30000",
"Y" = "#941651",
"V" = "#681226"
)
#' All known two-letter place name abbreviations
#' @export
place_abvs <- c(
"-A" = "SAUDI-ARABIA",
"-B" = "SUPHAN-BURI",
"-D" = "NORDRHEIN-WESTFALEN",
"-G" = "FRENCH-GUIANA",
"-H" = "SENDI-H",
"-I" = "RHODE-ISLAND",
"-K" = "SA-KAEO",
"-L" = "SRI-LANKA",
"-M" = "PUERTO-MONTT",
"-N" = "SAKON-NAKHON",
"-O" = "DISTRICT-OF-COLUMBIA",
"-P" = "ST-PETERSBURG",
"-S" = "SAN-SEBASTIAN",
"-T" = "SAN-ANTONIO",
"-V" = "MECKLENBURG-VORPO.",
"AA" = "ANNARBOR",
"AB" = "ALABAMA",
"AC" = "AICHI",
"AD" = "ALBANIA",
"AE" = "ALGERIA",
"AF" = "SOUTH-AFRICA",
"AG" = "ARGENTINA",
"AH" = "AUSTRIA",
"AI" = "ASTURIAS",
"AJ" = "SAKAI",
"AK" = "AKITA",
"AL" = "AUSTRALIA",
"AM" = "AMSTERDAM",
"AN" = "ANHUI",
"AO" = "AOMORI",
"AP" = "CHIANGMAI",
"AQ" = "ANG-THONG",
"AR" = "ARIZONA",
"AS" = "ALICESPRINGS",
"AT" = "ATLANTA",
"AU" = "AUCKLAND",
"AV" = "SANTIAGAO",
"AX" = "ALASKA",
"AY" = "AYTTHAYA",
"AZ" = "AYATTHAYA",
"BA" = "BANGKOK",
"BB" = "BILBAO",
"BC" = "BUCHAREST",
"BD" = "BADEN-WURTTEMBERG",
"BE" = "BEIJING",
"BF" = "BALEARES",
"BG" = "BELGIUM",
"BH" = "BELGRADE",
"BI" = "BILTHOVEN",
"BJ" = "BEIIJNG",
"BK" = "BANGKOKI",
"BL" = "BELEM",
"BM" = "BREMEN",
"BN" = "BERLIN",
"BO" = "BARCELONA",
"BP" = "BURIRUM",
"BQ" = "PATTANI",
"BR" = "BRISBANE",
"BS" = "BRASOV",
"BT" = "BAGKOK",
"BU" = "BUSAN",
"BV" = "PHARE",
"BW" = "PHICHIT",
"BX" = "BURIRAM",
"BY" = "BAYERN",
"BZ" = "BRAZIL",
"CA" = "CANBERRA",
"CB" = "CHIBA",
"CC" = "CHRISTCHURCH",
"CD" = "COLLINDALE",
"CE" = "CAEN",
"CF" = "CALIFORNIA",
"CG" = "CHUNGNAM",
"CH" = "CHINA",
"CI" = "CAEN",
"CJ" = "CHEJU",
"CK" = "CHEONBUK",
"CL" = "CHILE",
"CM" = "CHIANGMAI",
"CN" = "CONNECTICUT",
"CO" = "COLORADO",
"CP" = "CLUJ",
"CQ" = "CANARIAS",
"CR" = "CHIANGRAI",
"CS" = "CALARASI",
"CT" = "CHITA",
"CU" = "CHANTABURI",
"CV" = "CARTAGENA",
"CW" = "CHANGWON",
"CZ" = "CZECHOSLOVAKIA",
"DA" = "DAEGU",
"DB" = "NY",
"DC" = "CA",
"DD" = "DUNDIN",
"DE" = "DELFT",
"DF" = "KYUNGGI",
"DG" = "PAU",
"DH" = "MILAN",
"DI" = "SALAMANCA",
"DJ" = "DAEJEON",
"DK" = "DAKAR",
"DL" = "CASABLANCA",
"DM" = "MEKNES",
"DN" = "DENMARK",
"DO" = "MARRAKECH",
"DP" = "AGADIR",
"DQ" = "ATHENS",
"DR" = "SANTANDER",
"DS" = "DESGENETTES",
"DU" = "DUNEDIN",
"DV" = "DEVA",
"DW" = "DARWIN",
"DX" = "TENNESEE",
"DY" = "BRANDYS",
"DZ" = "TRANG",
"EA" = "SIENA",
"EB" = "ANGTHONG",
"EC" = "ECUADOR",
"ED" = "NIEDERSACHSEN",
"EE" = "NEPAL",
"EF" = "KALASIN",
"EG" = "EGYPT",
"EH" = "EHIME",
"EI" = "EINDHOVEN",
"EJ" = "PHITSANULOK",
"EK" = "EKATERINBURG",
"EL" = "EL-SALVADOR",
"EM" = "PRACHUAPKHIRIKKAN",
"EN" = "ENGLAND",
"EO" = "CHACHOENGSAO",
"EP" = "NEW-HAMPSHIRE",
"EQ" = "EQUADOR",
"ER" = "TOMSK",
"ES" = "ENSCHEDE",
"ET" = "EXTREMAD",
"EU" = "EUSKADI",
"EV" = "PONTEVEORA",
"EX" = "EXTREMADURA",
"EY" = "KYOTO",
"EZ" = "EKATEZINBURG",
"FA" = "FATICK",
"FB" = "FUKUI",
"FC" = "FUKUOKA-C",
"FD" = "FES",
"FE" = "FIRENZE",
"FF" = "ANNECY",
"FG" = "MACU",
"FH" = "FOSHAN",
"FI" = "FINLAND",
"FJ" = "FIJI",
"FK" = "FUOKA",
"FL" = "FLORIDA",
"FM" = "SUKHBAATAR",
"FN" = "SAINSHAND",
"FO" = "FLORENCE",
"FP" = "CAMBODIA",
"FQ" = "HOLLAND",
"FR" = "FRANCE",
"FS" = "FUKUSHIMA",
"FT" = "DUBAI",
"FU" = "FUJIAN",
"FV" = "GANSUCHENGGUAN",
"FW" = "HONDURAS",
"FX" = "KALININGRAD",
"FY" = "ASTRAKHAN",
"FZ" = "FUZHOU",
"GA" = "GUAM",
"GB" = "GENOA",
"GC" = "GREECE",
"GD" = "GUANGDONG",
"GE" = "GENEVA",
"GF" = "GUILDFORD",
"GG" = "GEORGIA",
"GH" = "GIRONA",
"GI" = "GIFU",
"GJ" = "GUADALAJARA",
"GK" = "GOTEBURG",
"GL" = "GUALDALAGARA",
"GM" = "GUMMA",
"GN" = "GRANADA",
"GO" = "GOTENBORG",
"GP" = "GIFU-C",
"GQ" = "GALICIA",
"GR" = "GRONINGEN",
"GS" = "GANSU",
"GT" = "GOTEBORG",
"GU" = "GUIZHOU",
"GV" = "SEGOVIA",
"GW" = "GUNMA",
"GX" = "GUANGXI",
"GY" = "GERMANY",
"GZ" = "GUANGZHOU",
"HA" = "HAWAII",
"HB" = "HARBIN",
"HC" = "SACHSEN",
"HD" = "HOKKAIDO",
"HE" = "HEBEI",
"HF" = "HIROSHIMA",
"HG" = "HUNGARY",
"HH" = "SHIZUOKA",
"HI" = "HUBEI",
"HJ" = "HYOGO",
"HK" = "HONGKONG",
"HL" = "HIME",
"HM" = "HENAN",
"HN" = "HUNAN",
"HO" = "HOUSTON",
"HP" = "HONG-KONGK",
"HQ" = "HAINAN",
"HS" = "HIROSHIMA-C",
"HT" = "HAMAMATU-C",
"HU" = "HUNTINGTON",
"HV" = "HANNOVER",
"HW" = "NAKHON-SAWAN",
"HX" = "SHAANXI",
"HY" = "CHANTHABURI",
"HZ" = "SHIZUOKA-C",
"IA" = "IASI",
"IB" = "IBARAKI",
"IC" = "INCHEON",
"ID" = "INDONESIA",
"IE" = "ICELAND",
"IF" = "IRAN",
"IH" = "IDAHO",
"II" = "INDIA",
"IJ" = "BEIJINGXUANWU",
"IK" = "ISHIKAWA",
"IL" = "ILLINOIS",
"IM" = "SHIMANE",
"IN" = "INDIANA",
"IO" = "SOLOMON-ISLANDS",
"IP" = "MURMANSK",
"IQ" = "STPETERSBURG",
"IR" = "IRELAND",
"IS" = "ISRAEL",
"IT" = "ITALY",
"IU" = "ISTANBUL",
"IV" = "INVERNESS",
"IW" = "IWATE",
"IX" = "BEIJINXUANWU",
"IY" = "CHAIYAPUM",
"IZ" = "HAMBURG",
"JA" = "JIANGXI",
"JB" = "BRANDENBURG",
"JC" = "BURSA",
"JD" = "EDIRNE",
"JE" = "ANTALYA",
"JF" = "KHOVD",
"JG" = "NEWYORK",
"JH" = "JHB",
"JI" = "JILIN",
"JJ" = "JEJU",
"JK" = "NOVGOROD",
"JL" = "TURKEY",
"JM" = "SUDAN",
"JN" = "AFGHANISTAN",
"JO" = "JOHANNESBURG",
"JP" = "JAPAN",
"JQ" = "NIGERIA",
"JR" = "KENTUCKY",
"JS" = "JIANGSU",
"JT" = "TALCAHUANO",
"JU" = "UTAH",
"JV" = "MASSACHUSETTS",
"JW" = "KANSAS",
"JX" = "JIANGXIDONGHU",
"JY" = "MONTANA",
"JZ" = "IOWA",
"KA" = "KASAULI",
"KB" = "KAGAWA",
"KC" = "KOCHI",
"KD" = "KANAGAWA",
"KE" = "KUMAMOTO-C",
"KF" = "KUM",
"KG" = "KAGOSHIMA",
"KH" = "KHABAROVSK",
"KI" = "KYONGGI",
"KJ" = "KWANGJU",
"KK" = "KYONGBUK",
"KL" = "KHON-KAEN",
"KM" = "KUMAMOTO",
"KN" = "KANGWON",
"KO" = "KOBE",
"KP" = "NAKHON-PATHOM",
"KQ" = "KAMPHAENG-PHET",
"KR" = "KOREA",
"KS" = "KAWASAKI",
"KT" = "KYOTO-C",
"KU" = "KITAKYUSYU",
"KV" = "KANCHANABURI",
"KW" = "KWANGJIN",
"KX" = "KYUNGNAM",
"KY" = "KITAKYUSHU",
"KZ" = "KYONGNAM",
"LA" = "LAUSANNE",
"LB" = "LOPBURI",
"LC" = "LOP-BURI",
"LD" = "LYON-TRS",
"LE" = "LENINGRAD",
"LF" = "LOBBURI",
"LG" = "LIAONING",
"LH" = "LYON-CHU",
"LI" = "LINNKOPING",
"LJ" = "LAMPANG",
"LK" = "LAMOANG",
"LL" = "CASTILLA",
"LM" = "LIMOGES",
"LN" = "LEON",
"LO" = "LOSANGELES",
"LP" = "LIPETZK",
"LQ" = "LOEI",
"LR" = "LA-REUNION",
"LS" = "LISBON",
"LT" = "LATVIA",
"LU" = "LOUISIANA",
"LV" = "SLOVENIA",
"LW" = "SCHLESWIG-HOLSTEIN",
"LX" = "LEICESTERSHIRE",
"LY" = "LYON",
"LZ" = "LINCOLN",
"MA" = "MADRID",
"MB" = "MOROCCO",
"MC" = "MICHIGAN",
"MD" = "MAD",
"ME" = "MEMPHIS",
"MF" = "CLERMONTFERRAND",
"MG" = "MIYAGI",
"MH" = "MAE-HONG-SORN",
"MI" = "MISSISSIPPI",
"MJ" = "MIE",
"MK" = "MIYAZAKI",
"ML" = "MALY",
"MM" = "MALMO",
"MN" = "MAE-HONG-SON",
"MO" = "MISSOURI",
"MP" = "MONTPELLIER",
"MQ" = "MACAU",
"MR" = "MADAGASCAR",
"MS" = "MINNESOTA",
"MT" = "SAMUT-SAKHON",
"MU" = "SAMUT-PRAKAN",
"MV" = "MONGOLIA",
"MW" = "MOSCOW",
"MX" = "MEXICO",
"MY" = "MAYOCLINIC",
"MZ" = "MASSACHUSETS",
"NA" = "NANCHANG",
"NB" = "NEBRASKA",
"NC" = "NEWCASTLE",
"ND" = "NORTH-DAKOTA",
"NE" = "NICE",
"NF" = "NRW",
"NG" = "NIIGATA",
"NH" = "NARA",
"NI" = "NIJMEGEN",
"NJ" = "NEW-JERSEY",
"NK" = "NAGANO",
"NL" = "NETHERLANDS",
"NM" = "NAGOYA",
"NN" = "NINGBO",
"NO" = "NORTH-CAROLINA",
"NP" = "NIGATA",
"NQ" = "NAPAL",
"NR" = "NOVOSIBIRSK",
"NS" = "NAGASAKI",
"NT" = "NIIGATA-C",
"NU" = "NONTHABURI",
"NV" = "NEVADA",
"NW" = "NEW-CALEDONIA",
"NX" = "NINGXIA",
"NY" = "NEW-YORK",
"NZ" = "NAKHON-RATCHASIMA",
"OA" = "OSAKA-C",
"OB" = "NOVY-BYDZOV",
"OC" = "OTAGA",
"OD" = "NORDRHEIN",
"OE" = "ORENSE",
"OF" = "OREL",
"OG" = "OREGON",
"OH" = "OHIO",
"OI" = "OITA",
"OJ" = "BOLIVIA",
"OK" = "OKLAHOMA",
"OL" = "CHOIBALSAN",
"OM" = "OMSK",
"ON" = "OKINAWA",
"OO" = "NAKONNAYOK",
"OP" = "GUADELOUPE",
"OQ" = "CHONGQING",
"OR" = "ORADEA",
"OS" = "OSLO",
"OT" = "OTAGO",
"OU" = "OUJDA",
"OV" = "OVIEDO",
"OW" = "NORWAY",
"OX" = "MAINE",
"OY" = "OKAYAMA",
"OZ" = "RUSSIA",
"PA" = "PARIS",
"PB" = "PARMA",
"PC" = "PORT-CHALMERS",
"PD" = "POLAND",
"PE" = "PERTH",
"PF" = "PHATTHALUNG",
"PG" = "PERUGIA",
"PH" = "PHILIPPINES",
"PI" = "POITIERS",
"PJ" = "PRAJIANBURI",
"PK" = "PHUKET",
"PL" = "PILSEN",
"PM" = "PANAMA",
"PN" = "PUSAN",
"PO" = "PUERTO-RICO",
"PP" = "PRACHUAP-KHIRI-KHAN",
"PQ" = "PATHUMTHANI",
"PR" = "PRAGUE",
"PS" = "PENNSYLVANIA",
"PT" = "PATHUM-THANI",
"PU" = "PERU",
"PV" = "PHILLIPINES",
"PW" = "PRACHINBURI",
"PX" = "PHETCHABUN",
"PY" = "PARAGUAY",
"PZ" = "PRABCHINBURI",
"QA" = "QUANZHOU",
"QB" = "BANGLADESH",
"QC" = "CORDOBA",
"QD" = "ARKANSAS",
"QE" = "MARTINIQUE",
"QF" = "COLOMBIA",
"QG" = "JAMAICA",
"QH" = "POL",
"QI" = "KIEV",
"QJ" = "ODESSA",
"QK" = "PALENCIA",
"QL" = "NOUACKCHOTT",
"QM" = "HESSEN",
"QN" = "GERONA",
"QO" = "MAURITIUS",
"QP" = "FUKUOKAC",
"QQ" = "CONGQING",
"QR" = "GIFUC",
"QS" = "HIROSHIMAC",
"QT" = "QINGDAO",
"QU" = "QUEENSLAND",
"QV" = "KUMAMOTOC",
"QW" = "NIIGATAC",
"QX" = "SENDAIH",
"QY" = "MARSEILLE",
"QZ" = "BORDEAUX",
"RA" = "ROME",
"RB" = "ROI-ET",
"RC" = "PRACHINMURI",
"RD" = "ROTTERDAM",
"RE" = "REUNION",
"RF" = "RABAT",
"RG" = "ARAGON",
"RH" = "RHEINLAND-PFALZ",
"RI" = "SORIA",
"RJ" = "RIO-DE-JANEIRO",
"RK" = "SAMUTPRAKHAN",
"RL" = "BRATISLAVA",
"RM" = "ROMANIA",
"RN" = "SURIN",
"RO" = "ROMA",
"RP" = "PRACHUAPKHIRIKHAN",
"RQ" = "ROSTOV-ON-DON",
"RR" = "SARABURI",
"RS" = "BURGOS",
"RT" = "RATCHABURI",
"RU" = "RU",
"RV" = "ARVAIKHEER",
"RW" = "NARATHIWAT",
"RX" = "ROSTOVDON",
"RY" = "KRASNOYARSK",
"RZ" = "TRABZON",
"SA" = "SOUTH-AUSTRALIA",
"SB" = "SAGA",
"SC" = "SOUTH-CAROLINA",
"SD" = "SHANGDONG",
"SE" = "SENDAI",
"SF" = "SOFIA",
"SG" = "SHIGA",
"SH" = "SHANGHAI",
"SI" = "SICHUAN",
"SJ" = "SPAIN",
"SK" = "ST.-ETIENNE",
"SL" = "SCOTLAND",
"SM" = "SAMARA",
"SN" = "ST-ETIENNE",
"SO" = "SOUTH-DAKOTA",
"SP" = "SINGAPORE",
"SQ" = "SACHSEN-ANHALT",
"SR" = "SAPPORO",
"SS" = "ST.-PETERSBURG",
"ST" = "STOCKHOLM",
"SU" = "SEOUL",
"SV" = "SHANTOU",
"SW" = "SW",
"SX" = "SOPHIA",
"SY" = "SYDNEY",
"SZ" = "SANTIAGO",
"TA" = "TAIWAN",
"TB" = "THURINGEN",
"TC" = "TOCHIGI",
"TD" = "TRENTO",
"TE" = "TEXAS",
"TF" = "TARRAGONA",
"TG" = "TONGA",
"TH" = "THESSALONIKI",
"TI" = "TILBURG",
"TJ" = "TIANJIN",
"TK" = "TAK",
"TL" = "THAILAND",
"TM" = "TASMANIA",
"TN" = "TOULON",
"TO" = "TOULOUSE",
"TP" = "TOYAMA",
"TQ" = "TOKUSHIMA",
"TR" = "TEHRAN",
"TS" = "TRIESTE",
"TT" = "TOTTORI",
"TU" = "TULA",
"TV" = "TOWNSVILLE",
"TW" = "TENNESSEE",
"TX" = "TX",
"TY" = "TOKYO",
"TZ" = "TANGER",
"UA" = "U.K.",
"UB" = "UTTARADIT",
"UC" = "UD",
"UD" = "UDORN",
"UE" = "UBON-RATCHATHANI",
"UF" = "UBONRATCHATHANI",
"UG" = "URUAGUAY",
"UH" = "SUPHANBURI",
"UI" = "UNITED-KINGDOM",
"UJ" = "UTHAI-THANI",
"UK" = "UK",
"UL" = "ULSAN",
"UM" = "UMEA",
"UN" = "UNITEDKINGDOM",
"UO" = "SUKHOTHAI",
"UP" = "SAMUTPRAKAN",
"UQ" = "UMEA",
"UR" = "URUGUAY",
"US" = "USSR/RUSSIA",
"UT" = "UTRECHT",
"UU" = "ULAN-UDE",
"UV" = "SUCEAVA",
"UW" = "ULAANBAATAR",
"UX" = "BENELUX",
"UY" = "GUYANE",
"UZ" = "UKRAINE",
"VA" = "VALENCIA",
"VB" = "VINA-DEL-MAR",
"VC" = "COSTARICA",
"VD" = "VALLADOLID",
"VE" = "VIETNAM",
"VF" = "COOK-ISLAND",
"VG" = "VIRGINIA",
"VH" = "JEONBUK",
"VI" = "VICTORIA",
"VJ" = "GUATEMALA",
"VK" = "SLOVAKIA",
"VL" = "VOLGOGRAD",
"VM" = "VLADIMIR",
"VN" = "VIENNA",
"VO" = "VORONEZH",
"VP" = "KENYA",
"VQ" = "SING",
"VR" = "STAVROPOL",
"VT" = "VERMONT",
"VV" = "AVILA",
"VY" = "IVORY-COAST",
"VZ" = "VENEZUELA",
"WA" = "WASHINGTON",
"WB" = "WY--",
"WE" = "WELLINGTON",
"WG" = "GWANGJU",
"WH" = "WUZHOU",
"WK" = "WAIKATO",
"WM" = "WAKAYAMA",
"WN" = "WISCONSIN",
"WO" = "GANGWON",
"WR" = "WARSAW",
"WS" = "WEST-VIRGINIA",
"WU" = "WUHAN",
"WV" = "WESTVIRGINIA",
"WW" = "NEWMARKET",
"WX" = "NEW-MEXICO",
"WY" = "WYOMING",
"WZ" = "SWITZERLAND",
"XI" = "XINJIANGCHANGJI",
"XJ" = "XINJIANG-HUTUBI",
"XM" = "XIAMEN",
"XN" = "XINJIANGHUTUBI",
"XX" = "CX-ROUSSE",
"YA" = "YAMAGA",
"YB" = "YUNAN",
"YD" = "BYDGOSZCZ",
"YE" = "GYEONGNAM",
"YG" = "YAMAGUCHI",
"YI" = "YAMANESHI",
"YK" = "YOKOSUKA",
"YL" = "MARYLAND",
"YM" = "YAMANASHI",
"YN" = "KYUNGBUK",
"YO" = "YOKOHAMA",
"YR" = "YARYSLAVL",
"YS" = "YAROSLAVL",
"YT" = "YAMAGATA",
"YU" = "YUNNAN",
"YY" = "NAKHONNAYOK",
"YZ" = "YUNGNAM",
"ZA" = "ZAMBIA",
"ZB" = "AZERBAIJAN",
"ZE" = "ZAGREB",
"ZG" = "ZARAGOSSA",
"ZH" = "ZHEJIANG",
"ZI" = "IZMIR",
"ZL" = "ZLIN",
"ZM" = "ZAMORA",
"ZN" = "RYAZAN",
"ZR" = "ZARAGOZA",
"ZU" = "SHIZUOKAC",
"ZX" = "CHUNGBUK",
"ZY" = "SAITAMA",
"OT" = "GOETEBORG"
)
acorg/acutilsLite documentation built on Feb. 19, 2021, 4:56 p.m.
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Defines functions coloraa aa.colors aa.values clusters.toFactor clusters.number clusters.colour clusters.subsMatrix h3_clusters
#' order for matching
#' @export
h3_clade_grouping_heirarchy <- c(
"3C.2A1",
"3C.2A1A",
"3C.2A1B",
"3C.2A2",
"3C.2A",
"3C.3A",
"3C.3"
)
#' order for plotting
#' @export
h3_clade_order <- c(
"3C.3",
"3C.3A",
"3C.2A",
"3C.2A1",
"3C.2A1A",
"3C.2A1B",
"3C.2A2",
"Other",
"Clade missing"
)
#' @export
h3_clusters <- function(){
c(
"HK68",
"EN72",
"VI75",
"TX77",
"BK79",
"SI87",
"BE89",
"BE92",
"WU95",
"SY97",
"FU02",
"CA04",
"WI05",
"PE09",
"SW13",
"HK14"
)
}
#' @export
h3_cluster_colors <- c(
"HK68" = "#a208bd",
"EN72" = "#00ffe1",
"VI75" = "#f9d004",
"TX77" = "#ab4c00",
"BK79" = "#00ff00",
"SI87" = "#0000ff",
"BE89" = "#ff0000",
"BE92" = "#f894f8",
"WU95" = "#37802b",
"SY97" = "#00afff",
"FU02" = "#ffd700",
"CA04" = "green",
"WI05" = "blue",
"PE09" = "purple",
"SW13" = "grey80",
"HK14" = "grey80"
)
#' @export
h3_clade_colors <- c(
"3C.3" = '#7570b3',
"3C.3A" = '#e7298a',
"3C.2A" = '#0B691B',
"3C.2A1" = '#7D2B07',
"3C.2A1A" = '#E2D11F',
"3C.2A1B" = '#F4B329',
"3C.2A2" = '#1FD16E',
"Other" = 'black',
"Clade missing" = 'grey50'
)
#' @export
h3_cluster_subs <- list(
HK68 = c("155T"),
EN72 = c("155Y"),
VI75 = c("189K"),
TX77 = c("158E", "193N"),
BK79 = c("156E"),
SI87 = c("155H", "159Y", "189R"),
BE89 = c("145K"),
BE92 = c("156K"),
WU95 = c("145K"),
SY97 = c("156Q", "158K"),
FU02 = c("156H"),
CA04 = c("145N"),
WI05 = c("193F"),
PE09 = c("158N", "189K")
)
#' @export
clusters.subsMatrix <- function(){
output <- do.call(rbind, lapply(h3_cluster_subs, function(x){
position <- substr(x, 1, 3)
aa <- substr(x, 4, 4)
result <- rep("", 7)
result[match(position, b7_positions)] <- aa
result
}))
colnames(output) <- b7_positions
output
}
#' @export
clusters.colour <- function(clusters){
h3_cluster_colors[as.character(clusters)]
}
#' @export
clusters.number <- function(clusters){
clusters[clusters == "BR07"] <- "WI05"
match(
clusters,
h3_clusters()
)
}
#' @export
clusters.toFactor <- function(clusters, excluded_clusters = NULL){
cluster_levels <- h3_clusters()
factor(clusters, levels = cluster_levels[!cluster_levels %in% excluded_clusters])
}
#' @export
b7_positions <- c(145, 155, 156, 158, 159, 189, 193)
#' @export
accessory_residues <- c(133, 143)
#' @export
h3_2004_variable_positions <- c(
1, 2, 3, 5, 6, 7, 8, 10, 18, 21, 25, 29, 31, 33, 34, 45, 47, 49, 50, 53, 54, 55, 57, 58, 59,
62, 63, 67, 75, 78, 79, 80, 81, 82, 83, 88, 92, 94, 96, 101, 103, 106, 112, 114, 115, 121, 122,
124, 126, 128, 129, 131, 132, 133, 135, 137, 138, 139, 140, 142, 143, 144, 145, 146, 148, 155,
156, 157, 158, 159, 160, 163, 164, 165, 167, 169, 171, 172, 173, 174, 175, 176, 182, 185, 186,
188, 189, 190, 192, 193, 194, 196, 197, 198, 199, 201, 202, 203, 204, 205, 207, 208, 209, 213,
214, 216, 217, 219, 220, 222, 225, 226, 227, 229, 230, 231, 233, 235, 236, 242, 244, 246, 247,
248, 259, 260, 261, 262, 264, 267, 268, 269, 271, 272, 273, 275, 276, 278, 279, 280, 285, 286,
289, 291, 292, 299, 304, 307, 309, 310, 312, 313, 323, 325, 326
)
siteA <- c(122, 124, 126, 130, 131, 132, 133, 135, 138, 142, 145)
siteB <- c(128, 129, 155, 156, 157, 158, 159, 160, 163, 164, 165, 186, 190, 193, 194, 196, 197, 198)
siteC <- c(44, 45, 46, 47, 48, 50, 51, 53, 54, 273, 275, 278, 279, 280, 294, 297, 299, 300, 304, 305, 307, 308, 309, 310, 311, 312)
siteD <- c(96, 102, 103, 117, 121, 167, 170, 171, 172, 173, 174, 175, 176, 177, 179, 182, 201, 203, 207, 208, 209, 212, 213, 214, 215, 216, 217, 218, 219, 226, 227, 228, 229, 230, 238, 240, 242, 244, 246, 247, 248)
RBS <- c(98, 134, 135, 136, 137, 138, 153, 183, 190, 194, 224, 225, 226, 227, 228)
siteA_Annette <- c(siteA, 137, 140, 143, 144, 146, 150, 152, 168)
siteB_Annette <- c(siteB, 187, 188, 189, 192)
siteC_Annette <- c(siteC, 276)
siteD_Annette <- siteD
siteE_Annette <- c(57, 59, 62, 63, 67, 75, 78, 80, 81, 82, 83, 86, 87, 88, 91, 92, 94, 109, 260, 261, 262, 265)
#' @export
h3_sites <- list(
RBS = RBS,
A = siteA,
B = siteB,
C = siteC,
D = siteD,
A_Annette = siteA_Annette,
B_Annette = siteB_Annette,
C_Annette = siteC_Annette,
D_Annette = siteD_Annette,
E_Annette = siteE_Annette
)
#' @export
aa_characteristics <- tibble::tribble(
~aa, ~character,
"R", "Positive",
"K", "Positive",
"H", "Positive",
"D", "Negative",
"E", "Negative",
"S", "Polar uncharged",
"T", "Polar uncharged",
"N", "Polar uncharged",
"Q", "Polar uncharged",
"C", "Special",
"G", "Special",
"P", "Special",
"A", "Hydrophobic",
"V", "Hydrophobic",
"I", "Hydrophobic",
"L", "Hydrophobic",
"M", "Hydrophobic",
"F", "Hydrophobic",
"Y", "Hydrophobic",
"W", "Hydrophobic"
)
#' @export
aa.values <- function(){
c(
c("G","A","S","T"),
c("C","V","I","L","P","F","Y","M","W"),
c("N","Q","H"),
c("D","E"),
c("K","R"),
c("*", "X")
)
}
#' @export
aa.colors <- function(){
aa <- aa.values()
aacols <- as.vector(coloraa(rbind(aa)))
names(aacols) <- aa
aacols
}
#' @export
coloraa <- function(x, alpha = 0.5, simplify = T){
if(is.vector(x)) x <- rbind(x)
if(ncol(x) == 0) return(x)
aacolors <- x
aacolors[] <- ""
aacolors[x %in% c("G","A","S","T") ] <- "orange"
aacolors[x %in% c("C","V","I","L","P","F","Y","M","W") ] <- "green"
aacolors[x %in% c("N","Q","H","Z") ] <- "magenta"
aacolors[x %in% c("D","E","B") ] <- "red"
aacolors[x %in% c("K","R") ] <- "blue"
aacolors[x %in% c("*", "X", "-", ".", "") ] <- "grey50"
if(sum(aacolors == "") > 0){
stop(sprintf("aas '%s' not recognised.", paste(unique(x[aacolors == ""]), collapse = ", ")))
}
aacolors[] <- adjustcolor(aacolors, alpha.f = alpha)
if (simplify){
if (length(aacolors) == 1) return(aacolors[[1]])
}
aacolors
}
#'@export
aacolors_al <- c(
"D" = "#F7CF08",
"E" = "#CD8D00",
"R" = "#B2A1FF",
"H" = "#7571BC",
"K" = "#440FAE",
"N" = "#18E0F7",
"Q" = "#0080FF",
"S" = "#0F52BA",
"T" = "navy",
"C" = "#00F000",
"G" = "#4CBB17",
"P" = "#1A4F30",
"A" = "#EB1919",
"I" = "#F93BBB",
"L" = "#FF2976",
"M" = "#FF5A3D",
"F" = "#C34822",
"W" = "#A30000",
"Y" = "#941651",
"V" = "#681226"
)
#' All known two-letter place name abbreviations
#' @export
place_abvs <- c(
"-A" = "SAUDI-ARABIA",
"-B" = "SUPHAN-BURI",
"-D" = "NORDRHEIN-WESTFALEN",
"-G" = "FRENCH-GUIANA",
"-H" = "SENDI-H",
"-I" = "RHODE-ISLAND",
"-K" = "SA-KAEO",
"-L" = "SRI-LANKA",
"-M" = "PUERTO-MONTT",
"-N" = "SAKON-NAKHON",
"-O" = "DISTRICT-OF-COLUMBIA",
"-P" = "ST-PETERSBURG",
"-S" = "SAN-SEBASTIAN",
"-T" = "SAN-ANTONIO",
"-V" = "MECKLENBURG-VORPO.",
"AA" = "ANNARBOR",
"AB" = "ALABAMA",
"AC" = "AICHI",
"AD" = "ALBANIA",
"AE" = "ALGERIA",
"AF" = "SOUTH-AFRICA",
"AG" = "ARGENTINA",
"AH" = "AUSTRIA",
"AI" = "ASTURIAS",
"AJ" = "SAKAI",
"AK" = "AKITA",
"AL" = "AUSTRALIA",
"AM" = "AMSTERDAM",
"AN" = "ANHUI",
"AO" = "AOMORI",
"AP" = "CHIANGMAI",
"AQ" = "ANG-THONG",
"AR" = "ARIZONA",
"AS" = "ALICESPRINGS",
"AT" = "ATLANTA",
"AU" = "AUCKLAND",
"AV" = "SANTIAGAO",
"AX" = "ALASKA",
"AY" = "AYTTHAYA",
"AZ" = "AYATTHAYA",
"BA" = "BANGKOK",
"BB" = "BILBAO",
"BC" = "BUCHAREST",
"BD" = "BADEN-WURTTEMBERG",
"BE" = "BEIJING",
"BF" = "BALEARES",
"BG" = "BELGIUM",
"BH" = "BELGRADE",
"BI" = "BILTHOVEN",
"BJ" = "BEIIJNG",
"BK" = "BANGKOKI",
"BL" = "BELEM",
"BM" = "BREMEN",
"BN" = "BERLIN",
"BO" = "BARCELONA",
"BP" = "BURIRUM",
"BQ" = "PATTANI",
"BR" = "BRISBANE",
"BS" = "BRASOV",
"BT" = "BAGKOK",
"BU" = "BUSAN",
"BV" = "PHARE",
"BW" = "PHICHIT",
"BX" = "BURIRAM",
"BY" = "BAYERN",
"BZ" = "BRAZIL",
"CA" = "CANBERRA",
"CB" = "CHIBA",
"CC" = "CHRISTCHURCH",
"CD" = "COLLINDALE",
"CE" = "CAEN",
"CF" = "CALIFORNIA",
"CG" = "CHUNGNAM",
"CH" = "CHINA",
"CI" = "CAEN",
"CJ" = "CHEJU",
"CK" = "CHEONBUK",
"CL" = "CHILE",
"CM" = "CHIANGMAI",
"CN" = "CONNECTICUT",
"CO" = "COLORADO",
"CP" = "CLUJ",
"CQ" = "CANARIAS",
"CR" = "CHIANGRAI",
"CS" = "CALARASI",
"CT" = "CHITA",
"CU" = "CHANTABURI",
"CV" = "CARTAGENA",
"CW" = "CHANGWON",
"CZ" = "CZECHOSLOVAKIA",
"DA" = "DAEGU",
"DB" = "NY",
"DC" = "CA",
"DD" = "DUNDIN",
"DE" = "DELFT",
"DF" = "KYUNGGI",
"DG" = "PAU",
"DH" = "MILAN",
"DI" = "SALAMANCA",
"DJ" = "DAEJEON",
"DK" = "DAKAR",
"DL" = "CASABLANCA",
"DM" = "MEKNES",
"DN" = "DENMARK",
"DO" = "MARRAKECH",
"DP" = "AGADIR",
"DQ" = "ATHENS",
"DR" = "SANTANDER",
"DS" = "DESGENETTES",
"DU" = "DUNEDIN",
"DV" = "DEVA",
"DW" = "DARWIN",
"DX" = "TENNESEE",
"DY" = "BRANDYS",
"DZ" = "TRANG",
"EA" = "SIENA",
"EB" = "ANGTHONG",
"EC" = "ECUADOR",
"ED" = "NIEDERSACHSEN",
"EE" = "NEPAL",
"EF" = "KALASIN",
"EG" = "EGYPT",
"EH" = "EHIME",
"EI" = "EINDHOVEN",
"EJ" = "PHITSANULOK",
"EK" = "EKATERINBURG",
"EL" = "EL-SALVADOR",
"EM" = "PRACHUAPKHIRIKKAN",
"EN" = "ENGLAND",
"EO" = "CHACHOENGSAO",
"EP" = "NEW-HAMPSHIRE",
"EQ" = "EQUADOR",
"ER" = "TOMSK",
"ES" = "ENSCHEDE",
"ET" = "EXTREMAD",
"EU" = "EUSKADI",
"EV" = "PONTEVEORA",
"EX" = "EXTREMADURA",
"EY" = "KYOTO",
"EZ" = "EKATEZINBURG",
"FA" = "FATICK",
"FB" = "FUKUI",
"FC" = "FUKUOKA-C",
"FD" = "FES",
"FE" = "FIRENZE",
"FF" = "ANNECY",
"FG" = "MACU",
"FH" = "FOSHAN",
"FI" = "FINLAND",
"FJ" = "FIJI",
"FK" = "FUOKA",
"FL" = "FLORIDA",
"FM" = "SUKHBAATAR",
"FN" = "SAINSHAND",
"FO" = "FLORENCE",
"FP" = "CAMBODIA",
"FQ" = "HOLLAND",
"FR" = "FRANCE",
"FS" = "FUKUSHIMA",
"FT" = "DUBAI",
"FU" = "FUJIAN",
"FV" = "GANSUCHENGGUAN",
"FW" = "HONDURAS",
"FX" = "KALININGRAD",
"FY" = "ASTRAKHAN",
"FZ" = "FUZHOU",
"GA" = "GUAM",
"GB" = "GENOA",
"GC" = "GREECE",
"GD" = "GUANGDONG",
"GE" = "GENEVA",
"GF" = "GUILDFORD",
"GG" = "GEORGIA",
"GH" = "GIRONA",
"GI" = "GIFU",
"GJ" = "GUADALAJARA",
"GK" = "GOTEBURG",
"GL" = "GUALDALAGARA",
"GM" = "GUMMA",
"GN" = "GRANADA",
"GO" = "GOTENBORG",
"GP" = "GIFU-C",
"GQ" = "GALICIA",
"GR" = "GRONINGEN",
"GS" = "GANSU",
"GT" = "GOTEBORG",
"GU" = "GUIZHOU",
"GV" = "SEGOVIA",
"GW" = "GUNMA",
"GX" = "GUANGXI",
"GY" = "GERMANY",
"GZ" = "GUANGZHOU",
"HA" = "HAWAII",
"HB" = "HARBIN",
"HC" = "SACHSEN",
"HD" = "HOKKAIDO",
"HE" = "HEBEI",
"HF" = "HIROSHIMA",
"HG" = "HUNGARY",
"HH" = "SHIZUOKA",
"HI" = "HUBEI",
"HJ" = "HYOGO",
"HK" = "HONGKONG",
"HL" = "HIME",
"HM" = "HENAN",
"HN" = "HUNAN",
"HO" = "HOUSTON",
"HP" = "HONG-KONGK",
"HQ" = "HAINAN",
"HS" = "HIROSHIMA-C",
"HT" = "HAMAMATU-C",
"HU" = "HUNTINGTON",
"HV" = "HANNOVER",
"HW" = "NAKHON-SAWAN",
"HX" = "SHAANXI",
"HY" = "CHANTHABURI",
"HZ" = "SHIZUOKA-C",
"IA" = "IASI",
"IB" = "IBARAKI",
"IC" = "INCHEON",
"ID" = "INDONESIA",
"IE" = "ICELAND",
"IF" = "IRAN",
"IH" = "IDAHO",
"II" = "INDIA",
"IJ" = "BEIJINGXUANWU",
"IK" = "ISHIKAWA",
"IL" = "ILLINOIS",
"IM" = "SHIMANE",
"IN" = "INDIANA",
"IO" = "SOLOMON-ISLANDS",
"IP" = "MURMANSK",
"IQ" = "STPETERSBURG",
"IR" = "IRELAND",
"IS" = "ISRAEL",
"IT" = "ITALY",
"IU" = "ISTANBUL",
"IV" = "INVERNESS",
"IW" = "IWATE",
"IX" = "BEIJINXUANWU",
"IY" = "CHAIYAPUM",
"IZ" = "HAMBURG",
"JA" = "JIANGXI",
"JB" = "BRANDENBURG",
"JC" = "BURSA",
"JD" = "EDIRNE",
"JE" = "ANTALYA",
"JF" = "KHOVD",
"JG" = "NEWYORK",
"JH" = "JHB",
"JI" = "JILIN",
"JJ" = "JEJU",
"JK" = "NOVGOROD",
"JL" = "TURKEY",
"JM" = "SUDAN",
"JN" = "AFGHANISTAN",
"JO" = "JOHANNESBURG",
"JP" = "JAPAN",
"JQ" = "NIGERIA",
"JR" = "KENTUCKY",
"JS" = "JIANGSU",
"JT" = "TALCAHUANO",
"JU" = "UTAH",
"JV" = "MASSACHUSETTS",
"JW" = "KANSAS",
"JX" = "JIANGXIDONGHU",
"JY" = "MONTANA",
"JZ" = "IOWA",
"KA" = "KASAULI",
"KB" = "KAGAWA",
"KC" = "KOCHI",
"KD" = "KANAGAWA",
"KE" = "KUMAMOTO-C",
"KF" = "KUM",
"KG" = "KAGOSHIMA",
"KH" = "KHABAROVSK",
"KI" = "KYONGGI",
"KJ" = "KWANGJU",
"KK" = "KYONGBUK",
"KL" = "KHON-KAEN",
"KM" = "KUMAMOTO",
"KN" = "KANGWON",
"KO" = "KOBE",
"KP" = "NAKHON-PATHOM",
"KQ" = "KAMPHAENG-PHET",
"KR" = "KOREA",
"KS" = "KAWASAKI",
"KT" = "KYOTO-C",
"KU" = "KITAKYUSYU",
"KV" = "KANCHANABURI",
"KW" = "KWANGJIN",
"KX" = "KYUNGNAM",
"KY" = "KITAKYUSHU",
"KZ" = "KYONGNAM",
"LA" = "LAUSANNE",
"LB" = "LOPBURI",
"LC" = "LOP-BURI",
"LD" = "LYON-TRS",
"LE" = "LENINGRAD",
"LF" = "LOBBURI",
"LG" = "LIAONING",
"LH" = "LYON-CHU",
"LI" = "LINNKOPING",
"LJ" = "LAMPANG",
"LK" = "LAMOANG",
"LL" = "CASTILLA",
"LM" = "LIMOGES",
"LN" = "LEON",
"LO" = "LOSANGELES",
"LP" = "LIPETZK",
"LQ" = "LOEI",
"LR" = "LA-REUNION",
"LS" = "LISBON",
"LT" = "LATVIA",
"LU" = "LOUISIANA",
"LV" = "SLOVENIA",
"LW" = "SCHLESWIG-HOLSTEIN",
"LX" = "LEICESTERSHIRE",
"LY" = "LYON",
"LZ" = "LINCOLN",
"MA" = "MADRID",
"MB" = "MOROCCO",
"MC" = "MICHIGAN",
"MD" = "MAD",
"ME" = "MEMPHIS",
"MF" = "CLERMONTFERRAND",
"MG" = "MIYAGI",
"MH" = "MAE-HONG-SORN",
"MI" = "MISSISSIPPI",
"MJ" = "MIE",
"MK" = "MIYAZAKI",
"ML" = "MALY",
"MM" = "MALMO",
"MN" = "MAE-HONG-SON",
"MO" = "MISSOURI",
"MP" = "MONTPELLIER",
"MQ" = "MACAU",
"MR" = "MADAGASCAR",
"MS" = "MINNESOTA",
"MT" = "SAMUT-SAKHON",
"MU" = "SAMUT-PRAKAN",
"MV" = "MONGOLIA",
"MW" = "MOSCOW",
"MX" = "MEXICO",
"MY" = "MAYOCLINIC",
"MZ" = "MASSACHUSETS",
"NA" = "NANCHANG",
"NB" = "NEBRASKA",
"NC" = "NEWCASTLE",
"ND" = "NORTH-DAKOTA",
"NE" = "NICE",
"NF" = "NRW",
"NG" = "NIIGATA",
"NH" = "NARA",
"NI" = "NIJMEGEN",
"NJ" = "NEW-JERSEY",
"NK" = "NAGANO",
"NL" = "NETHERLANDS",
"NM" = "NAGOYA",
"NN" = "NINGBO",
"NO" = "NORTH-CAROLINA",
"NP" = "NIGATA",
"NQ" = "NAPAL",
"NR" = "NOVOSIBIRSK",
"NS" = "NAGASAKI",
"NT" = "NIIGATA-C",
"NU" = "NONTHABURI",
"NV" = "NEVADA",
"NW" = "NEW-CALEDONIA",
"NX" = "NINGXIA",
"NY" = "NEW-YORK",
"NZ" = "NAKHON-RATCHASIMA",
"OA" = "OSAKA-C",
"OB" = "NOVY-BYDZOV",
"OC" = "OTAGA",
"OD" = "NORDRHEIN",
"OE" = "ORENSE",
"OF" = "OREL",
"OG" = "OREGON",
"OH" = "OHIO",
"OI" = "OITA",
"OJ" = "BOLIVIA",
"OK" = "OKLAHOMA",
"OL" = "CHOIBALSAN",
"OM" = "OMSK",
"ON" = "OKINAWA",
"OO" = "NAKONNAYOK",
"OP" = "GUADELOUPE",
"OQ" = "CHONGQING",
"OR" = "ORADEA",
"OS" = "OSLO",
"OT" = "OTAGO",
"OU" = "OUJDA",
"OV" = "OVIEDO",
"OW" = "NORWAY",
"OX" = "MAINE",
"OY" = "OKAYAMA",
"OZ" = "RUSSIA",
"PA" = "PARIS",
"PB" = "PARMA",
"PC" = "PORT-CHALMERS",
"PD" = "POLAND",
"PE" = "PERTH",
"PF" = "PHATTHALUNG",
"PG" = "PERUGIA",
"PH" = "PHILIPPINES",
"PI" = "POITIERS",
"PJ" = "PRAJIANBURI",
"PK" = "PHUKET",
"PL" = "PILSEN",
"PM" = "PANAMA",
"PN" = "PUSAN",
"PO" = "PUERTO-RICO",
"PP" = "PRACHUAP-KHIRI-KHAN",
"PQ" = "PATHUMTHANI",
"PR" = "PRAGUE",
"PS" = "PENNSYLVANIA",
"PT" = "PATHUM-THANI",
"PU" = "PERU",
"PV" = "PHILLIPINES",
"PW" = "PRACHINBURI",
"PX" = "PHETCHABUN",
"PY" = "PARAGUAY",
"PZ" = "PRABCHINBURI",
"QA" = "QUANZHOU",
"QB" = "BANGLADESH",
"QC" = "CORDOBA",
"QD" = "ARKANSAS",
"QE" = "MARTINIQUE",
"QF" = "COLOMBIA",
"QG" = "JAMAICA",
"QH" = "POL",
"QI" = "KIEV",
"QJ" = "ODESSA",
"QK" = "PALENCIA",
"QL" = "NOUACKCHOTT",
"QM" = "HESSEN",
"QN" = "GERONA",
"QO" = "MAURITIUS",
"QP" = "FUKUOKAC",
"QQ" = "CONGQING",
"QR" = "GIFUC",
"QS" = "HIROSHIMAC",
"QT" = "QINGDAO",
"QU" = "QUEENSLAND",
"QV" = "KUMAMOTOC",
"QW" = "NIIGATAC",
"QX" = "SENDAIH",
"QY" = "MARSEILLE",
"QZ" = "BORDEAUX",
"RA" = "ROME",
"RB" = "ROI-ET",
"RC" = "PRACHINMURI",
"RD" = "ROTTERDAM",
"RE" = "REUNION",
"RF" = "RABAT",
"RG" = "ARAGON",
"RH" = "RHEINLAND-PFALZ",
"RI" = "SORIA",
"RJ" = "RIO-DE-JANEIRO",
"RK" = "SAMUTPRAKHAN",
"RL" = "BRATISLAVA",
"RM" = "ROMANIA",
"RN" = "SURIN",
"RO" = "ROMA",
"RP" = "PRACHUAPKHIRIKHAN",
"RQ" = "ROSTOV-ON-DON",
"RR" = "SARABURI",
"RS" = "BURGOS",
"RT" = "RATCHABURI",
"RU" = "RU",
"RV" = "ARVAIKHEER",
"RW" = "NARATHIWAT",
"RX" = "ROSTOVDON",
"RY" = "KRASNOYARSK",
"RZ" = "TRABZON",
"SA" = "SOUTH-AUSTRALIA",
"SB" = "SAGA",
"SC" = "SOUTH-CAROLINA",
"SD" = "SHANGDONG",
"SE" = "SENDAI",
"SF" = "SOFIA",
"SG" = "SHIGA",
"SH" = "SHANGHAI",
"SI" = "SICHUAN",
"SJ" = "SPAIN",
"SK" = "ST.-ETIENNE",
"SL" = "SCOTLAND",
"SM" = "SAMARA",
"SN" = "ST-ETIENNE",
"SO" = "SOUTH-DAKOTA",
"SP" = "SINGAPORE",
"SQ" = "SACHSEN-ANHALT",
"SR" = "SAPPORO",
"SS" = "ST.-PETERSBURG",
"ST" = "STOCKHOLM",
"SU" = "SEOUL",
"SV" = "SHANTOU",
"SW" = "SW",
"SX" = "SOPHIA",
"SY" = "SYDNEY",
"SZ" = "SANTIAGO",
"TA" = "TAIWAN",
"TB" = "THURINGEN",
"TC" = "TOCHIGI",
"TD" = "TRENTO",
"TE" = "TEXAS",
"TF" = "TARRAGONA",
"TG" = "TONGA",
"TH" = "THESSALONIKI",
"TI" = "TILBURG",
"TJ" = "TIANJIN",
"TK" = "TAK",
"TL" = "THAILAND",
"TM" = "TASMANIA",
"TN" = "TOULON",
"TO" = "TOULOUSE",
"TP" = "TOYAMA",
"TQ" = "TOKUSHIMA",
"TR" = "TEHRAN",
"TS" = "TRIESTE",
"TT" = "TOTTORI",
"TU" = "TULA",
"TV" = "TOWNSVILLE",
"TW" = "TENNESSEE",
"TX" = "TX",
"TY" = "TOKYO",
"TZ" = "TANGER",
"UA" = "U.K.",
"UB" = "UTTARADIT",
"UC" = "UD",
"UD" = "UDORN",
"UE" = "UBON-RATCHATHANI",
"UF" = "UBONRATCHATHANI",
"UG" = "URUAGUAY",
"UH" = "SUPHANBURI",
"UI" = "UNITED-KINGDOM",
"UJ" = "UTHAI-THANI",
"UK" = "UK",
"UL" = "ULSAN",
"UM" = "UMEA",
"UN" = "UNITEDKINGDOM",
"UO" = "SUKHOTHAI",
"UP" = "SAMUTPRAKAN",
"UQ" = "UMEA",
"UR" = "URUGUAY",
"US" = "USSR/RUSSIA",
"UT" = "UTRECHT",
"UU" = "ULAN-UDE",
"UV" = "SUCEAVA",
"UW" = "ULAANBAATAR",
"UX" = "BENELUX",
"UY" = "GUYANE",
"UZ" = "UKRAINE",
"VA" = "VALENCIA",
"VB" = "VINA-DEL-MAR",
"VC" = "COSTARICA",
"VD" = "VALLADOLID",
"VE" = "VIETNAM",
"VF" = "COOK-ISLAND",
"VG" = "VIRGINIA",
"VH" = "JEONBUK",
"VI" = "VICTORIA",
"VJ" = "GUATEMALA",
"VK" = "SLOVAKIA",
"VL" = "VOLGOGRAD",
"VM" = "VLADIMIR",
"VN" = "VIENNA",
"VO" = "VORONEZH",
"VP" = "KENYA",
"VQ" = "SING",
"VR" = "STAVROPOL",
"VT" = "VERMONT",
"VV" = "AVILA",
"VY" = "IVORY-COAST",
"VZ" = "VENEZUELA",
"WA" = "WASHINGTON",
"WB" = "WY--",
"WE" = "WELLINGTON",
"WG" = "GWANGJU",
"WH" = "WUZHOU",
"WK" = "WAIKATO",
"WM" = "WAKAYAMA",
"WN" = "WISCONSIN",
"WO" = "GANGWON",
"WR" = "WARSAW",
"WS" = "WEST-VIRGINIA",
"WU" = "WUHAN",
"WV" = "WESTVIRGINIA",
"WW" = "NEWMARKET",
"WX" = "NEW-MEXICO",
"WY" = "WYOMING",
"WZ" = "SWITZERLAND",
"XI" = "XINJIANGCHANGJI",
"XJ" = "XINJIANG-HUTUBI",
"XM" = "XIAMEN",
"XN" = "XINJIANGHUTUBI",
"XX" = "CX-ROUSSE",
"YA" = "YAMAGA",
"YB" = "YUNAN",
"YD" = "BYDGOSZCZ",
"YE" = "GYEONGNAM",
"YG" = "YAMAGUCHI",
"YI" = "YAMANESHI",
"YK" = "YOKOSUKA",
"YL" = "MARYLAND",
"YM" = "YAMANASHI",
"YN" = "KYUNGBUK",
"YO" = "YOKOHAMA",
"YR" = "YARYSLAVL",
"YS" = "YAROSLAVL",
"YT" = "YAMAGATA",
"YU" = "YUNNAN",
"YY" = "NAKHONNAYOK",
"YZ" = "YUNGNAM",
"ZA" = "ZAMBIA",
"ZB" = "AZERBAIJAN",
"ZE" = "ZAGREB",
"ZG" = "ZARAGOSSA",
"ZH" = "ZHEJIANG",
"ZI" = "IZMIR",
"ZL" = "ZLIN",
"ZM" = "ZAMORA",
"ZN" = "RYAZAN",
"ZR" = "ZARAGOZA",
"ZU" = "SHIZUOKAC",
"ZX" = "CHUNGBUK",
"ZY" = "SAITAMA",
"OT" = "GOETEBORG"
)
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