R/privateUtilities.R
In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Defines functions
grid.eti
makeLeaveNames
getParentNode
getPFMid
getoffsetPosByIC_old
getoffsetPosByIC
ungappedScore
SWU
checkALLR
getALLRbyBase
getICbyBase
getAlignedICWithoutGap
UngappedAlignmentAA
UngappedAlignment
getIE
addPseudolog2
coloredSymbols
checkSummary
importSVG
colalpha
hex2psrgb
checkInteger
checkInteger <- function(N){
!length(grep("[^[:digit:]]", as.character(N)))
}
#' @importFrom grDevices col2rgb
hex2psrgb<-function(col){
col<-col2rgb(col)
col<-col/255
col<-paste(col,collapse=" ")
col
}
#' @importFrom grDevices col2rgb rgb
colalpha <- function(col, alpha){
col<-col2rgb(col)
rgb(t(col), alpha = round(alpha*255), maxColorValue = 255)
}
#' @importFrom grDevices svg dev.off
#' @importFrom grid convertHeight stringHeight grid.text gpar polygonGrob
#' @importFrom utils install.packages
importSVG <- function(font, color, ch, fontface="bold", envir=.globals){
run_grImport2 <- TRUE
if(exists("tmp_motifStack_grImport2", envir = .globals)){
run_grImport2 <- get("tmp_motifStack_grImport2", envir = .globals)
}
if(capabilities("cairo") && !requireNamespace("grImport2", quietly = TRUE) &&
run_grImport2){
## install grImport2
install.packages("grImport2", repos = "https://cloud.r-project.org",
quiet = TRUE)
}
if(capabilities("cairo") && requireNamespace("grImport2", quietly = TRUE) &&
run_grImport2){
psfilename<-tempfile(fileext = ".svg")
if(requireNamespace("Cairo")) FUN = Cairo::CairoSVG else FUN = svg
FUN(psfilename, width = 1, height = 1, bg = NA, pointsize=72, family = font)
h <- convertHeight(stringHeight(ch), unitTo = "points", valueOnly = TRUE)
grid.text(ch, gp = gpar(fontsize=floor(1.05*72*(72/h)),
fontfamily=font, col=color, fontface=fontface))
dev.off()
x <- tryCatch(grImport2::readPicture(psfilename), error=function(.e){
message(.e, "Will try grImport")
assign("tmp_motifStack_grImport2", FALSE, envir=.globals)
NULL
})
unlink(psfilename)
if(length(x)){
assign("pictureGrob", grImport2::pictureGrob, envir=envir)
assign("tmp_motifStack_grImport2", TRUE, envir=.globals)
return(x)
}
}
checkGhost <- function(){
# get ghostscript path
gscmd <- Sys.getenv("R_GSCMD")
if(is.null(gscmd) || !nzchar(gscmd)) {
if(.Platform$OS.type=="windows"){
poss <- Sys.which(c("gswin64c.exe",
"gswin32c.exe"))
poss <- poss[nzchar(poss)]
return(length(poss)>0)
}else{
gscmd <- "gs"
}
}
suppressWarnings(rc <- system(paste(shQuote(gscmd), "-help > /dev/null")))
return(rc == 0)
}
if(checkGhost() && !requireNamespace("grImport", quietly = TRUE)){
## install grImport
install.packages("grImport", repos = "https://cloud.r-project.org",
quiet = TRUE)
}
if(checkGhost() && requireNamespace("grImport", quietly = TRUE)){
motifStack_private_fontsize <- 18
ps<-paste("%!PS\n/",font,
" findfont\n",motifStack_private_fontsize,
" scalefont\n",
hex2psrgb(color),
" setrgbcolor\nsetfont\nnewpath\n0 0 moveto\n(",
ch,") show",sep="")
psfilename<-tempfile()
psfilename <- gsub("\\", "/", psfilename, fixed=TRUE)
# step1 create a ps file
cat(ps,file=paste(psfilename,".ps",sep=""))
# step2 convert it by grImport::PostScriptTrace
grImport::PostScriptTrace(paste(psfilename,".ps",sep=""),
paste(psfilename,".xml",sep=""))
# step3 read by grImport::readPicture
x<-grImport::readPicture(paste(psfilename,".xml",sep=""))
unlink(c(paste(psfilename,".ps",sep=""),
paste("capture",basename(psfilename),".ps",sep=""),
paste(psfilename,".xml",sep="")))
assign("pictureGrob", grImport::pictureGrob, envir=envir)
return(x)
}
warning("No import funciton (grImport or grImport2) available.",
"Use predefined fonts.")
assign("pictureGrob", function(picture, x = .5, y = .5,
width = 1, height = 1,
just = "centre", distort = TRUE){
## plot
gl <- gList()
for(i in seq_along(picture)){
gl <- gList(gl, polygonGrob(picture[[i]]$x*width+x,
picture[[i]]$y*height+y,
gp = gpar(fill=picture[[i]]$color,
col=picture[[i]]$color)))
}
return(gl)
}, envir=envir)
letterPolygon <-
list(A=list(list(color="black",
x=c(0.95,0.734703,0.6673312,0.3334011,0.2660293,
0.05,0.3744101,0.6263222,0.95),
y=c(0,0,0.2446256,0.2446256,0,0,1,1,0)),
list(color="white",
x=c(0.5003662,0.5000439,0.4996631,0.4992238,0.4987258,
0.4981692,0.4975541,0.4968804,0.4961481,0.4953572,
0.4945077,0.4945077,0.4937535,0.4929552,0.4921131,
0.491227,0.490297,0.489323,0.4883051,0.4872433,
0.4861375,0.4849878,0.4849878,0.4838015,0.4825858,
0.4813409,0.4800667,0.4787632,0.4774304,0.4760683,
0.474677,0.4732563,0.4718063,0.4718063,0.4704809,
0.4691408,0.467786,0.4664166,0.4650325,0.4636338,
0.4622205,0.4607925,0.4593499,0.4578926,0.4578926,
0.3788039,0.6219284,0.5428397,0.5413751,0.5399105,
0.5384459,0.5369813,0.5355167,0.5340521,0.5325875,
0.5311229,0.5296583,0.5281937,0.5281937,0.5268828,
0.5255867,0.5243051,0.5230382,0.521786,0.5205484,
0.5193255,0.5181172,0.5169235,0.5157445,0.5157445,
0.5145875,0.5134597,0.5123613,0.5112921,0.5102522,
0.5092417,0.5082604,0.5073084,0.5063857,0.5054923,
0.5054923,0.5047819,0.5041155,0.5034931,0.5029146,
0.50238,0.5018893,0.5014426,0.5010399,0.500681,
0.5003662,0.5003662),
y=c(0.8650852,0.8634915,0.8616753,0.8596368,0.8573758,
0.8548925,0.8521868,0.8492587,0.8461082,0.8427354,
0.8391401,0.8391401,0.8353818,0.8315196,0.8275537,
0.8234841,0.8193106,0.8150334,0.8106523,0.8061675,
0.8015789,0.7968866,0.7968866,0.7920979,0.7872202,
0.7822535,0.7771979,0.7720534,0.7668199,0.7614974,
0.756086,0.7505856,0.7449963,0.7449963,0.7395182,
0.7340549,0.7286064,0.7231727,0.7177539,0.7123499,
0.7069607,0.7015864,0.6962268,0.6908821,0.6908821,
0.409192,0.409192,0.6908821,0.6962268,0.7015864,
0.7069607,0.7123499,0.7177539,0.7231727,0.7286064,
0.7340549,0.7395182,0.7449963,0.7449963,0.7505856,
0.756086,0.7614974,0.7668199,0.7720534,0.7771979,
0.7822535,0.7872202,0.7920979,0.7968866,0.7968866,
0.8015789,0.8061675,0.8106523,0.8150334,0.8193106,
0.8234841,0.8275537,0.8315196,0.8353818,0.8391401,
0.8391401,0.8427354,0.8461082,0.8492587,0.8521868,
0.8548925,0.8573758,0.8596368,0.8616753,0.8634915,
0.8650852,0.8650852))
),
B=list(list(color="black",
x=c(0.95,0.949674,0.9486959,0.9470658,0.9447836,
0.9418494,0.9382631,0.9340248,0.9291344,0.923592,
0.9173975,0.9173975,0.910654,0.9034643,0.8958284,
0.8877464,0.8792183,0.870244,0.8608236,0.8509571,
0.8406444,0.8298856,0.8298856,0.8187235,0.8072011,
0.7953184,0.7830753,0.7704719,0.7575081,0.744184,
0.7304995,0.7164547,0.7020496,0.7020496,0.68755,
0.6728789,0.6580362,0.6430219,0.627836,0.6124786,
0.5969495,0.5812488,0.5653765,0.5493327,0.5493327,
0.05,0.05,0.500429,0.5180858,0.5353651,
0.5522669,0.5687912,0.584938,0.6007073,0.6160991,
0.6311134,0.6457502,0.6600095,0.6600095,0.6738656,
0.6872927,0.7002908,0.7128599,0.725,0.7367112,
0.7479933,0.7588465,0.7692707,0.779266,0.779266,
0.7888151,0.7979009,0.8065234,0.8146826,0.8223785,
0.8296111,0.8363804,0.8426864,0.8485291,0.8539085,
0.8539085,0.8589619,0.8634833,0.8674728,0.8709304,
0.8738561,0.8762498,0.8781115,0.8794414,0.8802393,
0.8805052,0.8805052,0.879939,0.8782402,0.875409,
0.8714452,0.8663489,0.8601201,0.8527588,0.844265,
0.8346387,0.8238799,0.8238799,0.8119457,0.7987931,
0.7844223,0.7688332,0.7520257,0.734,0.714756,
0.6942936,0.672613,0.649714,0.649714,0.6783527,
0.7055844,0.731409,0.7558265,0.778837,0.8004404,
0.8206368,0.8394261,0.8568084,0.8727836,0.8727836,
0.8874547,0.9005815,0.912164,0.9222021,0.9306959,
0.9376454,0.9430505,0.9469113,0.9492278,0.95,
0.95),
y=c(0.2853966,0.2703484,0.255745,0.2415864,0.2278725,
0.2146034,0.2017791,0.1893996,0.1774648,0.1659748,
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0.009962936,0.007627872,0.005604151,0.003891772,
0.002490734,0.001401038,0.0006226835,0.0001556709,0,0,
0,1,1,0.9998443,0.9993773,0.998599,0.9975093,0.9961082,
0.9943958,0.9923721,0.9900371,0.9873907,0.9844329,
0.9844329,0.9813047,0.9778503,0.9740697,0.9699629,
0.96553,0.9607709,0.9556857,0.9502743,0.9445367,
0.9384729,0.9384729,0.932083,0.9253669,0.9183247,
0.9109563,0.9032617,0.8952409,0.886894,0.8782209,
0.8692216,0.8598962,0.8598962,0.8502446,0.8402669,
0.8299629,0.8193328,0.8083766,0.7970941,0.7854855,
0.7735508,0.7612898,0.7487027,0.7487027,0.7319199,
0.7156709,0.6999555,0.6847739,0.670126,0.6560119,
0.6424314,0.6293847,0.6168718,0.6048925,0.6048925,
0.5936916,0.5832172,0.5734692,0.5644477,0.5561527,
0.5485841,0.541742,0.5356264,0.5302372,0.5255745,
0.5255745,0.5224166,0.5182802,0.5131653,0.5070719,0.5,
0.4919496,0.4829207,0.4729133,0.4619274,0.4499629,
0.4499629,0.437109,0.4234544,0.4089993,0.3937435,
0.3776872,0.3608302,0.3431727,0.3247146,0.3054559,
0.2853966,0.2853966)),
list(color="white",
x=c(0.6256911,0.6253051,0.6241468,0.6222164,0.6195138,
0.6160391,0.6117922,0.6067731,0.6009819,0.5944185,
0.5870829,0.5870829,0.5790867,0.5705415,0.5614471,
0.5518036,0.5416111,0.5308694,0.5195786,0.5077388,
0.4953499,0.4824118,0.4824118,0.3030982,0.3030982,
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0.6127188,0.6166826,0.6199256,0.622448,0.6242498,
0.6253308,0.6256911,0.6256911,NA,0.6951859,
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0.5651535,0.5585643,0.5519066,0.5451802,0.5383851,
0.5315214,0.5245891,0.5175882,0.5175882,0.3030982,
0.3030982,0.5235939,0.5304233,0.537184,0.5438761,
0.5504995,0.5570543,0.5635405,0.5699581,0.576307,
0.5825872,0.5887989,0.5887989,0.595062,0.6011535,
0.6070734,0.6128217,0.6183985,0.6238036,0.6290372,
0.6340991,0.6389895,0.6437083,0.6437083,0.6484099,
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0.6722955,0.6755558,0.6786101,0.6814585,0.6814585,
0.6840667,0.6864004,0.6884595,0.690244,0.6917541,
0.6929895,0.6939504,0.6946368,0.6950486,0.6951859,
0.6951859),
y=c(0.7190511,0.7315715,0.7433358,0.754344,0.764596,
0.7740919,0.7828317,0.7908154,0.798043,0.8045145,
0.8102298,0.8102298,0.8154411,0.8201038,0.8242179,
0.8277835,0.8308006,0.8332691,0.835189,0.8365604,
0.8373832,0.8376575,0.8376575,0.8376575,0.6011861,
0.6011861,0.6014826,0.6023721,0.6038547,0.6059303,
0.608599,0.6118606,0.6157153,0.6201631,0.6252039,
0.6308377,0.6308377,0.6370571,0.6438547,0.6512305,
0.6591846,0.6677168,0.6768273,0.6865159,0.6967828,
0.7076279,0.7190511,0.7190511,NA,0.3039288,
0.3115122,0.3188436,0.3259229,0.3327502,0.3393254,
0.3456486,0.3517198,0.3575389,0.363106,0.3684211,
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0.3917717,0.3958191,0.399659,0.4032913,0.4067161,
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0.1738176,0.1757746,0.1779096,0.1802224,0.1827131,
0.1853818,0.1882283,0.1912528,0.1912528,0.1946256,
0.1982209,0.2020385,0.2060786,0.210341,0.2148258,
0.219533,0.2244626,0.2296145,0.2349889,0.2349889,
0.2406153,0.2465234,0.2527131,0.2591846,0.2659377,
0.2729726,0.2802891,0.2878873,0.2957672,0.3039288,
0.3039288)),
list(color="white",
x=c(0.6951859,0.69504,0.6946025,0.6938732,0.6928522,
0.6915396,0.6899352,0.6880391,0.6858513,0.6833718,
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0.5972069,0.5909438,0.5845091,0.5845091,0.5781258,
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0.576307,0.5825872,0.5887989,0.5887989,0.595062,
0.6011535,0.6070734,0.6128217,0.6183985,0.6238036,
0.6290372,0.6340991,0.6389895,0.6437083,0.6437083,
0.6484099,0.6529056,0.6571954,0.6612793,0.6651573,
0.6688294,0.6722955,0.6755558,0.6786101,0.6814585,
0.6814585,0.6840667,0.6864004,0.6884595,0.690244,
0.6917541,0.6929895,0.6939504,0.6946368,0.6950486,
0.6951859,0.6951859),
y=c(0.3039288,0.3115122,0.3188436,0.3259229,0.3327502,
0.3393254,0.3456486,0.3517198,0.3575389,0.363106,
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0.1946256,0.1982209,0.2020385,0.2060786,0.210341,
0.2148258,0.219533,0.2244626,0.2296145,0.2349889,
0.2349889,0.2406153,0.2465234,0.2527131,0.2591846,
0.2659377,0.2729726,0.2802891,0.2878873,0.2957672,
0.3039288,0.3039288))
),
C=list(list(color="black",
x=c(0.2972527,0.2978297,0.2995604,0.3024451,0.3064835,
0.3116758,0.318022,0.325522,0.3341758,0.3439835,
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0.725,0.725,0.95,0.9447582,0.9392527,
0.9334835,0.9274505,0.9211538,0.9145934,0.9077692,
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0.384937,0.3780726,0.3711787,0.364255,0.3573017,
0.3573017,0.3503929,0.3436027,0.3369311,0.3303781,
0.3239437,0.3176279,0.3114307,0.3053521,0.2993921,
0.2935508,0.2935508,0.2867606,0.2800297,0.273358,
0.2667457,0.2601927,0.253699,0.2472646,0.2408895,
0.2345738,0.2283173,0.2283173,0.2344255,0.240593,
0.2468199,0.253106,0.2594514,0.2658562,0.2723202,
0.2788436,0.2854262,0.2920682,0.2920682,0.2977687,
0.3036027,0.3095701,0.3156709,0.3219051,0.3282728,
0.3347739,0.3414085,0.3481764,0.3550778,0.3550778,
0.3621868,0.3692809,0.3763603,0.3834248,0.3904744,
0.3975093,0.4045293,0.4115345,0.4185248,0.4255004,
0.4255004,1,1,0))
),
W=list(list(color="black",
x=c(0.7960912,0.6143322,0.5674267,0.5659023,0.5642606,
0.5625016,0.5606254,0.5586319,0.5565505,0.5544104,
0.5522117,0.5499544,0.5476384,0.545557,0.5434169,
0.5412182,0.5389609,0.536645,0.5345928,0.5325407,
0.5304886,0.5284365,0.5263844,0.5214007,0.5164169,
0.5114332,0.5064495,0.5014658,0.4962182,0.4910293,
0.485899,0.4808274,0.4758143,0.4737329,0.4715928,
0.4693941,0.4671368,0.4648208,0.4627394,0.4605993,
0.4584007,0.4561433,0.4538274,0.4517752,0.4497231,
0.447671,0.4456189,0.4435668,0.4415733,0.4396971,
0.4379381,0.4362964,0.434772,0.3864007,0.2046417,
0.05,0.2398208,0.3050489,0.306456,0.3077459,
0.3089186,0.3099739,0.3109121,0.3117622,0.3125537,
0.3132866,0.3139609,0.3145765,0.3151336,0.3156319,
0.3160717,0.3164528,0.3167752,0.3186221,0.320645,
0.3228436,0.3252182,0.3277687,0.3301726,0.3326938,
0.3353322,0.3380879,0.3409609,0.3439511,0.3470586,
0.3502834,0.3536254,0.3570847,0.4296417,0.572557,
0.645114,0.6488078,0.6522671,0.6554919,0.6584821,
0.6612378,0.6641107,0.6668664,0.6695049,0.6720261,
0.67443,0.6769805,0.679355,0.6815537,0.6835765,
0.6854235,0.6857166,0.6860098,0.6863029,0.6865961,
0.6868893,0.6872117,0.6875928,0.6880326,0.6885309,
0.6890879,0.6897036,0.6903779,0.6911107,0.6919023,
0.6927524,0.6936906,0.6947459,0.6959186,0.6972085,
0.6986156,0.7601792,0.95,0.7960912),
y=c(0,0,0.1979244,0.2037658,0.2100222,
0.2166938,0.2237806,0.2312824,0.2390808,0.2470571,
0.2552113,0.2635434,0.2720534,0.2809785,0.2899629,
0.2990067,0.3081097,0.3172721,0.3267013,0.3360119,
0.3452039,0.3542772,0.363232,0.384166,0.4054559,
0.4271016,0.449103,0.4714603,0.4488362,0.4266271,
0.4048332,0.3834544,0.3624907,0.353536,0.3444626,
0.3352706,0.32596,0.3165308,0.3073684,0.2982654,
0.2892216,0.2802372,0.2713121,0.2628021,0.25447,
0.2463158,0.2383395,0.2305411,0.2233062,0.216427,
0.2099036,0.2037361,0.1979244,0,0,
1,1,0.4848036,0.4730319,0.4608451,
0.4482431,0.4352261,0.4217939,0.4083024,0.3951075,
0.382209,0.3696071,0.3573017,0.3431282,0.3290734,
0.3151371,0.3013195,0.2876205,0.2984136,0.309444,
0.3207116,0.3322165,0.3439585,0.3545738,0.3656635,
0.3772276,0.3892661,0.4017791,0.4148851,0.4281097,
0.4414529,0.4549148,0.4684952,0.7197924,0.7197924,
0.4684952,0.4551816,0.4419274,0.4287324,0.4155967,
0.4025204,0.3900074,0.3779689,0.3664047,0.355315,
0.3446998,0.3329281,0.3213343,0.3099185,0.2986805,
0.2876205,0.2884211,0.2908228,0.2948258,0.3004299,
0.3076353,0.3160267,0.325189,0.3351223,0.3458265,
0.3573017,0.3693403,0.3817346,0.3944848,0.4075908,
0.4210526,0.4347517,0.4479763,0.4607265,0.4730022,
0.4848036,1,1,0))
),
X=list(list(color="black",
x=c(0.7229862,0.5010985,0.2784784,0.05,0.3861269,
0.0800244,0.3085028,0.5010985,0.6929618,0.9199756,
0.60655,0.95,0.7229862),
y=c(0,0.3654559,0,0,0.5270571,
1,1,0.6812454,1,1,
0.5270571,0,0))
),
Y=list(list(color="black",
x=c(0.6082651,0.6082651,0.3917349,0.3917349,0.05,
0.2775777,0.498527,0.7224223,0.95,0.6082651),
y=c(0.4121572,0,0,0.4121572,1,
1,0.5804299,1,1,0.4121572))
),
Z=list(list(color="black",
x=c(0.95,0.05,0.05,0.6245956,0.1150809,
0.1150809,0.9148906,0.9148906,0.340295,0.95,
0.95),
y=c(0,0,0.1549296,0.828762,0.828762,
1,1,0.8480356,0.171238,0.171238,
0))
)
)
x <- letterPolygon[[toupper(ch)]]
x <- lapply(x, function(.ele){
if(.ele$color=="black") .ele$color <- color
.ele
})
return(x)
}
checkSummary <- function(x){
if("summary" %in% slotNames(x)){
if(any(is.na(x@summary@xscale))){
x@summary@xscale <- c(0, 72)
}
if(any(is.na(x@summary@yscale))){
x@summary@yscale <- c(72, 0)
}
}
x
}
coloredSymbols <- function(ncha, font, color, rname, alpha,
fontface="bold", envir = .globals){
symbols<-list()
for(i in 1:ncha){
symbols[[i]]<-checkSummary(importSVG(font, color[i], rname[i], fontface))
}
if(!missing(alpha)){
for(i in 1:ncha){
symbols[[paste0(i, "_", alpha)]]<-checkSummary(
importSVG(font, colalpha(color, alpha)[i], rname[i],
fontface, envir = envir))
}
}
symbols
}
addPseudolog2<-function(x){
x <- round(x, digits=6)
ifelse(x < .000001, -20, log2(x)) ## !important -10.
}
## get Information Entropy from matrix
getIE<-function(x){
addPseudolog2(nrow(x))
}
UngappedAlignment<-function(pfms, i, threshold, minimalConsensus=0,
rcpostfix="(RC)", revcomp=TRUE){
if(!is(pfms[[i]], "pfm")){
pcms <- pfms
pfms <- lapply(pfms, pcm2pfm)
}else{
pcms <- NULL
}
res<-getAlignedICWithoutGap(pfms[[i-1]], pfms[[i]], threshold, revcomp)
if(!is.null(pcms)) pfms <- pcms
if(res$max>=minimalConsensus){
if(res$rev){
pfms[[i]]<-matrixReverseComplement(pfms[[i]])
pfms[[i]]@name<-paste(pfms[[i]]@name, rcpostfix, sep="")
}
if(res$offset>0){
pfms[[i]]<-addBlank(pfms[[i]], res$offset, FALSE)
}else{
if(res[1]<0){
pfms[1:(i-1)]<-lapply(pfms[1:(i-1)],function(.ele)
addBlank(.ele, -1*res$offset, FALSE))
}
}
}
pfms
}
UngappedAlignmentAA<-function(pcms, i, threshold, minimalConsensus){
pcm1 <- pcms[[i-1]]
pcm2 <- pcms[[i]]
offset1 <- 0
offset2 <- 0
## trim pcm
trimPCMbyIC <- function(pcm, t){
ic <- getIC(pcm)
w <- rle(ic < t)
offL <- offR <- 0
if(w$values[1]) {
offL <- w$lengths[1]
}
if(w$values[length(w$values)]) {
offR <- w$lengths[length(w$values)]
}
if(offL+1>ncol(pcm@mat)-offR){
return(pcm=NULL, offL=offL, offR=offR)
}
pcm@mat <- pcm@mat[, (offL+1):(ncol(pcm@mat)-offR), drop=FALSE]
list(pcm=pcm, offL=offL, offR=offR)
}
res <- trimPCMbyIC(pcm1, t=threshold)
if(is.null(res$pcm)){
return(pcms)
}
pcm1 <- res$pcm
offset1 <- res$offL
res <- trimPCMbyIC(pcm2, t=threshold)
if(is.null(res$pcm)){
return(pcms)
}
pcm2 <- res$pcm
offset2 <- res$offL
res<-compare2profiles(pcm1, pcm2, method="Smith-Waterman")
if(res$length>=minimalConsensus){
of1 <- offset1 + res$i_start
of2 <- offset2 + res$j_start
if(of1<of2){
pcms[seq.int(i-1)] <- lapply(pcms[seq.int(i-1)], function(.ele){
addBlank(.ele, of2-of1, FALSE)
})
}else{
if(of1>of2){
pcms[[i]] <- addBlank(pcms[[i]], of1-of2, FALSE)
}
}
}
pcms
}
getAlignedICWithoutGap<-function(pfm1, pfm2, threshold, revcomp=TRUE){
if(!is(pfm1, "pfm") | !is(pfm2, "pfm"))
stop("class of pfm1 and pfm2 must be pfm")
offset1<-getoffsetPosByIC(pfm1, pfm2, threshold)
if(revcomp){
pfm3<-matrixReverseComplement(pfm2)
offset2<-getoffsetPosByIC(pfm1, pfm3, threshold)
}else{
offset2<-list(k=0,max=0)
}
offset<-0
rev<-FALSE
if((offset1$max < offset2$max)){
rev<-TRUE
max<-offset2$max
offset<-offset2$k
}else{
max<-offset1$max
offset<-offset1$k
}
list(offset=offset,rev=rev,max=max)
}
getICbyBase<-function(p, pfmj){
re<-rep(0, 5)
re[1:4]<-pfmj * (addPseudolog2(pfmj) - addPseudolog2(p))
re[5]<-sum(re[1:4])
re
}
getALLRbyBase <- function(b, pfmi, pfmj){##return 2x ALLR
sum(pfmj * (addPseudolog2(pfmi) - addPseudolog2(b))) +
sum(pfmi * (addPseudolog2(pfmj) - addPseudolog2(b)))
}
checkALLR <- function(...){
getALLRbyBase(...)>0
}
SWU <- function(pattern, subject, b,
match=1, mismatch=-1,
gap=-1000){## motif length will never longer than 1000
if(!is(pattern, "matrix") || !is(subject, "matrix")){
stop("pattern and subject must be numeric matrix")
}
m <- ncol(pattern)
n <- ncol(subject)
score <- matrix(0, nrow=m+1, ncol=n+1)
point <- matrix("none", nrow=m+1, ncol=n+1)
max_i <- 1
max_j <- 1
max_score <- 0
for(i in 1:m){
for(j in 1:n){
diagonal_score <- 0
left_score <- 0
up_score <- 0
#calculate match score
col1 <- subject[, j]
col2 <- pattern[, i]
#score by KLLR
if(checkALLR(b, col1, col2)){
diagonal_score <- score[i, j] + match
}else{
diagonal_score <- score[i, j] + mismatch
}
#calculate gap scores
up_score <- score[i, j+1] + gap
left_score <- score[i+1, j] + gap
if(diagonal_score <=0 && up_score <=0 && left_score <=0){
score[i+1, j+1] <- 0
point[i+1, j+1] <- "none"
next # terminate this iteration of the loop
}
#choose best score
if(diagonal_score >= up_score){
if(diagonal_score >= left_score){
score[i+1, j+1] <- diagonal_score
point[i+1, j+1] <- "diagonal"
}else{
score[i+1, j+1] <- left_score
point[i+1, j+1] <- "left"
}
}else{
if(up_score > left_score){
score[i+1, j+1] <- up_score
point[i+1, j+1] <- "up"
}else{
score[i+1, j+1] <- left_score
point[i+1, j+1] <- "left"
}
}
#set maximum score
if(score[i+1, j+1] > max_score){
max_i <- i+1
max_j <- j+1
max_score <- score[i+1, j+1]
}
}
}
#trace-back
align1 <- c()
align2 <- c()
i <- max_i
j <- max_j
while(1){
if(point[i, j]=="none"){
break
}
if(point[i, j]=="diagonal"){
align1 <- c(align1, j-1)
align2 <- c(align2, i-1)
i <- i-1
j <- j-1
}else{
if(point[i, j]=="left"){
align1 <- c(align1, j-1)
align2 <- c(align2, 0)
j <- j-1
}else{
if(point[i, j]=="up"){
align1 <- c(align1, 0)
align2 <- c(align2, i-1)
i <- i-1
}
}
}
}
align1 <- rev(align1)
align2 <- rev(align2)
if(length(align1)<1 | length(align2)<1){
k <- 0
}else{
k=align1[1]-align2[1]
}
list(k=k, max=max_score)
}
ungappedScore <- function(query, subject, b, threshold){
if(!is(query, "matrix") || !is(subject, "matrix")){
stop("query and subject must be numeric matrix")
}
m <- ncol(query)
n <- ncol(subject)
score <- matrix(0, nrow=m+1, ncol=n+1)
for(i in 1:m){
for(j in 1:n){
ic1 <- getICbyBase(b, query[, i])[5]
ic2 <- getICbyBase(b, subject[, j])[5]
if(ic1>=threshold && ic2>=threshold){
value <- getICbyBase(b, c(query[, i]+subject[, j])/2)[5]
}else{
value <- 0
}
score[i+1, j+1] <- score[i, j] + value
}
}
score[1:m, 1:n] <- 0
max_score <- max(score)
if(max_score==0){
return(list(k=0, max=0))
}
idx <- which(score==max_score, arr.ind=TRUE)
if(nrow(idx)>1){
idxn <- apply(idx, 1, min)
idx <- idx[which(idxn==min(idxn))[1], , drop=FALSE]
}
max_r <- idx[, "row"]
max_c <- idx[, "col"]
k <- max_r - max_c
list(k=as.numeric(k), max=max_score)
}
getoffsetPosByIC<-function(pfm1, pfm2, threshold){
if(!is(pfm1, "pfm") | !is(pfm2, "pfm"))
stop("class of pfm1 and pfm2 must be pfm")
res <- ungappedScore(pfm1$mat, pfm2$mat, b=pfm1$background, threshold)
res
}
#' @importFrom stats sd cor
getoffsetPosByIC_old<-function(pfm1, pfm2, threshold){
if(!is(pfm1, "pfm") | !is(pfm2, "pfm"))
stop("class of pfm1 and pfm2 must be pfm")
score1<-rep(0, ncol(pfm1@mat))
score2<-rep(0, ncol(pfm2@mat))
value1<-rep(0, ncol(pfm1@mat))
value2<-rep(0, ncol(pfm2@mat))
for(i in 1:ncol(pfm1@mat)){
J<-ifelse(ncol(pfm1@mat)+1-i>ncol(pfm2@mat),
ncol(pfm2@mat),ncol(pfm1@mat)+1-i)
for(j in 1:J){
ic1<-getICbyBase(pfm1@background, pfm1@mat[,i+j-1])
ic2<-getICbyBase(pfm2@background, pfm2@mat[,j])
#ic3<-getALLRbyBase(pfm1@background, pfm1@mat[,i+j-1], pfm2@mat[,j])
ic3 <- getICbyBase(pfm1@background,
(pfm1@mat[,i+j-1]+pfm2@mat[,j])/2)
if(sd(pfm1@mat[,i+j-1])==0 || sd(pfm2@mat[,j])==0){
corr <- 0
}else{
corr <- cor(pfm1@mat[,i+j-1], pfm2@mat[,j], method="spearman")
}
if(ic1[5]>threshold & ic2[5]>threshold){
#a<-ic1[1:4]>mean(ic1[1:4])
#b<-ic2[1:4]>mean(ic2[1:4])
#if(ic3>0) score1[i]<-score1[i]+1
#if(ic3>0.25) {
#if(any(a&b)){
if(corr>0){
score1[i]<-score1[i]+1
value1[i] <- value1[i]+ic3[5]
}
}
}
}
for(i in 1:ncol(pfm2@mat)){
J<-ifelse(ncol(pfm2@mat)+1-i>ncol(pfm1@mat),
ncol(pfm1@mat),ncol(pfm2@mat)+1-i)
for(j in 1:J){
ic2<-getICbyBase(pfm2@background, pfm2@mat[,i+j-1])
ic1<-getICbyBase(pfm1@background, pfm1@mat[,j])
#ic3<-getALLRbyBase(pfm1@background, pfm1@mat[,j], pfm2@mat[,i+j-1])
ic3 <- getICbyBase(pfm1@background,
(pfm2@mat[,i+j-1]+pfm1@mat[,j])/2)
if(sd(pfm1@mat[,j])==0 || sd(pfm2@mat[,i+j-1])==0){
corr <- 0
}else{
corr <- cor(pfm1@mat[,j], pfm2@mat[,i+j-1], method="spearman")
}
if(ic1[5]>threshold & ic2[5]>threshold){
#a<-ic1[1:4]>mean(ic1[1:4])
#b<-ic2[1:4]>mean(ic2[1:4])
#if(ic3>0) score2[i]<-score2[i]+1
#if(ic3>0.25) {
#if(any(a&b)){
if(corr>0){
score2[i]<-score2[i]+1
value2[i] <- value2[i]+ic3[5]
}
}
}
}
k1<-match(max(score1),score1)
k2<-match(max(score2),score2)
sc <- (score1[k1] < score2[k2]) || ((score1[k1] == score2[k2]) &&
(value1[k1] < value2[k2]))
k <- ifelse(sc, -1*(k2-1), (k1-1))
max <- ifelse(sc, score2[k2], score1[k1])
val <- ifelse(sc, value2[k2], value1[k1])
list(k=k,max=max,val=val)
}
setClass("Rect",
representation(x="numeric", y="numeric",
width="numeric", height="numeric"),
prototype=prototype(x=0, y=0, width=0, height=0)
)
setGeneric("isContainedIn", function(a, b) standardGeneric("isContainedIn"))
setMethod("isContainedIn", signature(a="Rect", b="Rect"), function(a, b){
a@x >= b@x && a@y >= b@y &&
a@x+a@width <= b@x+b@width && a@y+a@height <= b@y+b@height
})
setClass("pos",
representation(box="Rect", beta="numeric", sig="pfm",
freq="numeric", norm="numeric")
)
getPFMid <- function(pfms, nodename, rcpostfix="(RC)"){
pfmNames <- as.character(unlist(lapply(pfms, function(.ele) .ele@name)))
pfmNames <- gsub(rcpostfix,"",pfmNames, fixed=TRUE)
which(pfmNames==nodename)
}
getParentNode <- function(nodelist, nodename){
for(i in 1:length(nodelist)){
currNode <- nodelist[[i]]
if(currNode@left==nodename) return(c(currNode@parent, "left"))
if(currNode@right==nodename) return(c(currNode@parent, "right"))
}
NULL
}
makeLeaveNames <- function(ch){
gsub(".", "_", make.names(ch), fixed=TRUE)
}
#' @importFrom graphics par
#' @importFrom grid stringWidth stringHeight grid.rect gpar grid.text
grid.eti <- function(x, y, label, clabel, boxes=FALSE,
coul = rep(1, length(x)),
bg = "white", draw=TRUE){
if (length(label) == 0)
return(invisible())
if (is.null(label))
return(invisible())
if (any(label == ""))
return(invisible())
cex0 <- par("cex") * clabel
plot <- gList()
for (i in seq_along(x)) {
cha <- as.character(label[i])
cha <- paste(" ", cha, " ", sep = "")
x1 <- x[i]
y1 <- y[i]
xh <- cex0*stringWidth(cha)
yh <- cex0*stringHeight(cha) * 1.66666666667
if (boxes) {
plot <- gList(plot,
rectGrob(x=x1, y=y1, width=xh, height=yh,
gp=gpar(fill = bg, col = coul[i]),
default.units = "native"))
}
plot <- gList(plot,
textGrob(x=x1, y=y1, label=cha,
gp=gpar(cex = cex0, col = coul[i]),
default.units = "native"))
}
if(draw){
suppressWarnings(grid.draw(plot))
}else{
plot
}
}
jianhong/motifStack documentation built on Jan. 31, 2024, 5:03 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions grid.eti makeLeaveNames getParentNode getPFMid getoffsetPosByIC_old getoffsetPosByIC ungappedScore SWU checkALLR getALLRbyBase getICbyBase getAlignedICWithoutGap UngappedAlignmentAA UngappedAlignment getIE addPseudolog2 coloredSymbols checkSummary importSVG colalpha hex2psrgb checkInteger
checkInteger <- function(N){
!length(grep("[^[:digit:]]", as.character(N)))
}
#' @importFrom grDevices col2rgb
hex2psrgb<-function(col){
col<-col2rgb(col)
col<-col/255
col<-paste(col,collapse=" ")
col
}
#' @importFrom grDevices col2rgb rgb
colalpha <- function(col, alpha){
col<-col2rgb(col)
rgb(t(col), alpha = round(alpha*255), maxColorValue = 255)
}
#' @importFrom grDevices svg dev.off
#' @importFrom grid convertHeight stringHeight grid.text gpar polygonGrob
#' @importFrom utils install.packages
importSVG <- function(font, color, ch, fontface="bold", envir=.globals){
run_grImport2 <- TRUE
if(exists("tmp_motifStack_grImport2", envir = .globals)){
run_grImport2 <- get("tmp_motifStack_grImport2", envir = .globals)
}
if(capabilities("cairo") && !requireNamespace("grImport2", quietly = TRUE) &&
run_grImport2){
## install grImport2
install.packages("grImport2", repos = "https://cloud.r-project.org",
quiet = TRUE)
}
if(capabilities("cairo") && requireNamespace("grImport2", quietly = TRUE) &&
run_grImport2){
psfilename<-tempfile(fileext = ".svg")
if(requireNamespace("Cairo")) FUN = Cairo::CairoSVG else FUN = svg
FUN(psfilename, width = 1, height = 1, bg = NA, pointsize=72, family = font)
h <- convertHeight(stringHeight(ch), unitTo = "points", valueOnly = TRUE)
grid.text(ch, gp = gpar(fontsize=floor(1.05*72*(72/h)),
fontfamily=font, col=color, fontface=fontface))
dev.off()
x <- tryCatch(grImport2::readPicture(psfilename), error=function(.e){
message(.e, "Will try grImport")
assign("tmp_motifStack_grImport2", FALSE, envir=.globals)
NULL
})
unlink(psfilename)
if(length(x)){
assign("pictureGrob", grImport2::pictureGrob, envir=envir)
assign("tmp_motifStack_grImport2", TRUE, envir=.globals)
return(x)
}
}
checkGhost <- function(){
# get ghostscript path
gscmd <- Sys.getenv("R_GSCMD")
if(is.null(gscmd) || !nzchar(gscmd)) {
if(.Platform$OS.type=="windows"){
poss <- Sys.which(c("gswin64c.exe",
"gswin32c.exe"))
poss <- poss[nzchar(poss)]
return(length(poss)>0)
}else{
gscmd <- "gs"
}
}
suppressWarnings(rc <- system(paste(shQuote(gscmd), "-help > /dev/null")))
return(rc == 0)
}
if(checkGhost() && !requireNamespace("grImport", quietly = TRUE)){
## install grImport
install.packages("grImport", repos = "https://cloud.r-project.org",
quiet = TRUE)
}
if(checkGhost() && requireNamespace("grImport", quietly = TRUE)){
motifStack_private_fontsize <- 18
ps<-paste("%!PS\n/",font,
" findfont\n",motifStack_private_fontsize,
" scalefont\n",
hex2psrgb(color),
" setrgbcolor\nsetfont\nnewpath\n0 0 moveto\n(",
ch,") show",sep="")
psfilename<-tempfile()
psfilename <- gsub("\\", "/", psfilename, fixed=TRUE)
# step1 create a ps file
cat(ps,file=paste(psfilename,".ps",sep=""))
# step2 convert it by grImport::PostScriptTrace
grImport::PostScriptTrace(paste(psfilename,".ps",sep=""),
paste(psfilename,".xml",sep=""))
# step3 read by grImport::readPicture
x<-grImport::readPicture(paste(psfilename,".xml",sep=""))
unlink(c(paste(psfilename,".ps",sep=""),
paste("capture",basename(psfilename),".ps",sep=""),
paste(psfilename,".xml",sep="")))
assign("pictureGrob", grImport::pictureGrob, envir=envir)
return(x)
}
warning("No import funciton (grImport or grImport2) available.",
"Use predefined fonts.")
assign("pictureGrob", function(picture, x = .5, y = .5,
width = 1, height = 1,
just = "centre", distort = TRUE){
## plot
gl <- gList()
for(i in seq_along(picture)){
gl <- gList(gl, polygonGrob(picture[[i]]$x*width+x,
picture[[i]]$y*height+y,
gp = gpar(fill=picture[[i]]$color,
col=picture[[i]]$color)))
}
return(gl)
}, envir=envir)
letterPolygon <-
list(A=list(list(color="black",
x=c(0.95,0.734703,0.6673312,0.3334011,0.2660293,
0.05,0.3744101,0.6263222,0.95),
y=c(0,0,0.2446256,0.2446256,0,0,1,1,0)),
list(color="white",
x=c(0.5003662,0.5000439,0.4996631,0.4992238,0.4987258,
0.4981692,0.4975541,0.4968804,0.4961481,0.4953572,
0.4945077,0.4945077,0.4937535,0.4929552,0.4921131,
0.491227,0.490297,0.489323,0.4883051,0.4872433,
0.4861375,0.4849878,0.4849878,0.4838015,0.4825858,
0.4813409,0.4800667,0.4787632,0.4774304,0.4760683,
0.474677,0.4732563,0.4718063,0.4718063,0.4704809,
0.4691408,0.467786,0.4664166,0.4650325,0.4636338,
0.4622205,0.4607925,0.4593499,0.4578926,0.4578926,
0.3788039,0.6219284,0.5428397,0.5413751,0.5399105,
0.5384459,0.5369813,0.5355167,0.5340521,0.5325875,
0.5311229,0.5296583,0.5281937,0.5281937,0.5268828,
0.5255867,0.5243051,0.5230382,0.521786,0.5205484,
0.5193255,0.5181172,0.5169235,0.5157445,0.5157445,
0.5145875,0.5134597,0.5123613,0.5112921,0.5102522,
0.5092417,0.5082604,0.5073084,0.5063857,0.5054923,
0.5054923,0.5047819,0.5041155,0.5034931,0.5029146,
0.50238,0.5018893,0.5014426,0.5010399,0.500681,
0.5003662,0.5003662),
y=c(0.8650852,0.8634915,0.8616753,0.8596368,0.8573758,
0.8548925,0.8521868,0.8492587,0.8461082,0.8427354,
0.8391401,0.8391401,0.8353818,0.8315196,0.8275537,
0.8234841,0.8193106,0.8150334,0.8106523,0.8061675,
0.8015789,0.7968866,0.7968866,0.7920979,0.7872202,
0.7822535,0.7771979,0.7720534,0.7668199,0.7614974,
0.756086,0.7505856,0.7449963,0.7449963,0.7395182,
0.7340549,0.7286064,0.7231727,0.7177539,0.7123499,
0.7069607,0.7015864,0.6962268,0.6908821,0.6908821,
0.409192,0.409192,0.6908821,0.6962268,0.7015864,
0.7069607,0.7123499,0.7177539,0.7231727,0.7286064,
0.7340549,0.7395182,0.7449963,0.7449963,0.7505856,
0.756086,0.7614974,0.7668199,0.7720534,0.7771979,
0.7822535,0.7872202,0.7920979,0.7968866,0.7968866,
0.8015789,0.8061675,0.8106523,0.8150334,0.8193106,
0.8234841,0.8275537,0.8315196,0.8353818,0.8391401,
0.8391401,0.8427354,0.8461082,0.8492587,0.8521868,
0.8548925,0.8573758,0.8596368,0.8616753,0.8634915,
0.8650852,0.8650852))
),
B=list(list(color="black",
x=c(0.95,0.949674,0.9486959,0.9470658,0.9447836,
0.9418494,0.9382631,0.9340248,0.9291344,0.923592,
0.9173975,0.9173975,0.910654,0.9034643,0.8958284,
0.8877464,0.8792183,0.870244,0.8608236,0.8509571,
0.8406444,0.8298856,0.8298856,0.8187235,0.8072011,
0.7953184,0.7830753,0.7704719,0.7575081,0.744184,
0.7304995,0.7164547,0.7020496,0.7020496,0.68755,
0.6728789,0.6580362,0.6430219,0.627836,0.6124786,
0.5969495,0.5812488,0.5653765,0.5493327,0.5493327,
0.05,0.05,0.500429,0.5180858,0.5353651,
0.5522669,0.5687912,0.584938,0.6007073,0.6160991,
0.6311134,0.6457502,0.6600095,0.6600095,0.6738656,
0.6872927,0.7002908,0.7128599,0.725,0.7367112,
0.7479933,0.7588465,0.7692707,0.779266,0.779266,
0.7888151,0.7979009,0.8065234,0.8146826,0.8223785,
0.8296111,0.8363804,0.8426864,0.8485291,0.8539085,
0.8539085,0.8589619,0.8634833,0.8674728,0.8709304,
0.8738561,0.8762498,0.8781115,0.8794414,0.8802393,
0.8805052,0.8805052,0.879939,0.8782402,0.875409,
0.8714452,0.8663489,0.8601201,0.8527588,0.844265,
0.8346387,0.8238799,0.8238799,0.8119457,0.7987931,
0.7844223,0.7688332,0.7520257,0.734,0.714756,
0.6942936,0.672613,0.649714,0.649714,0.6783527,
0.7055844,0.731409,0.7558265,0.778837,0.8004404,
0.8206368,0.8394261,0.8568084,0.8727836,0.8727836,
0.8874547,0.9005815,0.912164,0.9222021,0.9306959,
0.9376454,0.9430505,0.9469113,0.9492278,0.95,
0.95),
y=c(0.2853966,0.2703484,0.255745,0.2415864,0.2278725,
0.2146034,0.2017791,0.1893996,0.1774648,0.1659748,
0.1549296,0.1549296,0.1442995,0.1340549,0.1241957,
0.114722,0.1056338,0.09693106,0.08861379,0.08068199,
0.07313566,0.0659748,0.0659748,0.05933284,0.0530467,
0.04711638,0.04154188,0.0363232,0.03146034,0.0269533,
0.02280208,0.01900667,0.01556709,0.01556709,0.01260934,
0.009962936,0.007627872,0.005604151,0.003891772,
0.002490734,0.001401038,0.0006226835,0.0001556709,0,0,
0,1,1,0.9998443,0.9993773,0.998599,0.9975093,0.9961082,
0.9943958,0.9923721,0.9900371,0.9873907,0.9844329,
0.9844329,0.9813047,0.9778503,0.9740697,0.9699629,
0.96553,0.9607709,0.9556857,0.9502743,0.9445367,
0.9384729,0.9384729,0.932083,0.9253669,0.9183247,
0.9109563,0.9032617,0.8952409,0.886894,0.8782209,
0.8692216,0.8598962,0.8598962,0.8502446,0.8402669,
0.8299629,0.8193328,0.8083766,0.7970941,0.7854855,
0.7735508,0.7612898,0.7487027,0.7487027,0.7319199,
0.7156709,0.6999555,0.6847739,0.670126,0.6560119,
0.6424314,0.6293847,0.6168718,0.6048925,0.6048925,
0.5936916,0.5832172,0.5734692,0.5644477,0.5561527,
0.5485841,0.541742,0.5356264,0.5302372,0.5255745,
0.5255745,0.5224166,0.5182802,0.5131653,0.5070719,0.5,
0.4919496,0.4829207,0.4729133,0.4619274,0.4499629,
0.4499629,0.437109,0.4234544,0.4089993,0.3937435,
0.3776872,0.3608302,0.3431727,0.3247146,0.3054559,
0.2853966,0.2853966)),
list(color="white",
x=c(0.6256911,0.6253051,0.6241468,0.6222164,0.6195138,
0.6160391,0.6117922,0.6067731,0.6009819,0.5944185,
0.5870829,0.5870829,0.5790867,0.5705415,0.5614471,
0.5518036,0.5416111,0.5308694,0.5195786,0.5077388,
0.4953499,0.4824118,0.4824118,0.3030982,0.3030982,
0.4841277,0.4976921,0.5105872,0.5228132,0.5343699,
0.5452574,0.5554757,0.5650248,0.5739047,0.5821153,
0.5896568,0.5896568,0.5965033,0.6026292,0.6080343,
0.6127188,0.6166826,0.6199256,0.622448,0.6242498,
0.6253308,0.6256911,0.6256911,NA,0.6951859,
0.69504,0.6946025,0.6938732,0.6928522,0.6915396,
0.6899352,0.6880391,0.6858513,0.6833718,0.6806006,
0.6806006,0.6775806,0.6743546,0.6709228,0.667285,
0.6634414,0.6593918,0.6551363,0.6506749,0.6460076,
0.6411344,0.6411344,0.636244,0.6311821,0.6259485,
0.6205434,0.6149666,0.6092183,0.6032984,0.5972069,
0.5909438,0.5845091,0.5845091,0.5781258,0.571674,
0.5651535,0.5585643,0.5519066,0.5451802,0.5383851,
0.5315214,0.5245891,0.5175882,0.5175882,0.3030982,
0.3030982,0.5235939,0.5304233,0.537184,0.5438761,
0.5504995,0.5570543,0.5635405,0.5699581,0.576307,
0.5825872,0.5887989,0.5887989,0.595062,0.6011535,
0.6070734,0.6128217,0.6183985,0.6238036,0.6290372,
0.6340991,0.6389895,0.6437083,0.6437083,0.6484099,
0.6529056,0.6571954,0.6612793,0.6651573,0.6688294,
0.6722955,0.6755558,0.6786101,0.6814585,0.6814585,
0.6840667,0.6864004,0.6884595,0.690244,0.6917541,
0.6929895,0.6939504,0.6946368,0.6950486,0.6951859,
0.6951859),
y=c(0.7190511,0.7315715,0.7433358,0.754344,0.764596,
0.7740919,0.7828317,0.7908154,0.798043,0.8045145,
0.8102298,0.8102298,0.8154411,0.8201038,0.8242179,
0.8277835,0.8308006,0.8332691,0.835189,0.8365604,
0.8373832,0.8376575,0.8376575,0.8376575,0.6011861,
0.6011861,0.6014826,0.6023721,0.6038547,0.6059303,
0.608599,0.6118606,0.6157153,0.6201631,0.6252039,
0.6308377,0.6308377,0.6370571,0.6438547,0.6512305,
0.6591846,0.6677168,0.6768273,0.6865159,0.6967828,
0.7076279,0.7190511,0.7190511,NA,0.3039288,
0.3115122,0.3188436,0.3259229,0.3327502,0.3393254,
0.3456486,0.3517198,0.3575389,0.363106,0.3684211,
0.3684211,0.3735063,0.378384,0.3830541,0.3875167,
0.3917717,0.3958191,0.399659,0.4032913,0.4067161,
0.4099333,0.4099333,0.4130986,0.4160712,0.418851,
0.4214381,0.4238325,0.4260341,0.428043,0.4298592,
0.4314826,0.4329133,0.4329133,0.4341809,0.435315,
0.4363158,0.4371831,0.437917,0.4385174,0.4389844,
0.439318,0.4395182,0.4395849,0.4395849,0.4395849,
0.1623425,0.1623425,0.1624092,0.1626093,0.1629429,
0.1634099,0.1640104,0.1647443,0.1656116,0.1666123,
0.1677465,0.1690141,0.1690141,0.1704374,0.1720385,
0.1738176,0.1757746,0.1779096,0.1802224,0.1827131,
0.1853818,0.1882283,0.1912528,0.1912528,0.1946256,
0.1982209,0.2020385,0.2060786,0.210341,0.2148258,
0.219533,0.2244626,0.2296145,0.2349889,0.2349889,
0.2406153,0.2465234,0.2527131,0.2591846,0.2659377,
0.2729726,0.2802891,0.2878873,0.2957672,0.3039288,
0.3039288)),
list(color="white",
x=c(0.6951859,0.69504,0.6946025,0.6938732,0.6928522,
0.6915396,0.6899352,0.6880391,0.6858513,0.6833718,
0.6806006,0.6806006,0.6775806,0.6743546,0.6709228,
0.667285,0.6634414,0.6593918,0.6551363,0.6506749,
0.6460076,0.6411344,0.6411344,0.636244,0.6311821,
0.6259485,0.6205434,0.6149666,0.6092183,0.6032984,
0.5972069,0.5909438,0.5845091,0.5845091,0.5781258,
0.571674,0.5651535,0.5585643,0.5519066,0.5451802,
0.5383851,0.5315214,0.5245891,0.5175882,0.5175882,
0.3030982,0.3030982,0.5235939,0.5304233,0.537184,
0.5438761,0.5504995,0.5570543,0.5635405,0.5699581,
0.576307,0.5825872,0.5887989,0.5887989,0.595062,
0.6011535,0.6070734,0.6128217,0.6183985,0.6238036,
0.6290372,0.6340991,0.6389895,0.6437083,0.6437083,
0.6484099,0.6529056,0.6571954,0.6612793,0.6651573,
0.6688294,0.6722955,0.6755558,0.6786101,0.6814585,
0.6814585,0.6840667,0.6864004,0.6884595,0.690244,
0.6917541,0.6929895,0.6939504,0.6946368,0.6950486,
0.6951859,0.6951859),
y=c(0.3039288,0.3115122,0.3188436,0.3259229,0.3327502,
0.3393254,0.3456486,0.3517198,0.3575389,0.363106,
0.3684211,0.3684211,0.3735063,0.378384,0.3830541,
0.3875167,0.3917717,0.3958191,0.399659,0.4032913,
0.4067161,0.4099333,0.4099333,0.4130986,0.4160712,
0.418851,0.4214381,0.4238325,0.4260341,0.428043,
0.4298592,0.4314826,0.4329133,0.4329133,0.4341809,
0.435315,0.4363158,0.4371831,0.437917,0.4385174,
0.4389844,0.439318,0.4395182,0.4395849,0.4395849,
0.4395849,0.1623425,0.1623425,0.1624092,0.1626093,
0.1629429,0.1634099,0.1640104,0.1647443,0.1656116,
0.1666123,0.1677465,0.1690141,0.1690141,0.1704374,
0.1720385,0.1738176,0.1757746,0.1779096,0.1802224,
0.1827131,0.1853818,0.1882283,0.1912528,0.1912528,
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0.2148258,0.219533,0.2244626,0.2296145,0.2349889,
0.2349889,0.2406153,0.2465234,0.2527131,0.2591846,
0.2659377,0.2729726,0.2802891,0.2878873,0.2957672,
0.3039288,0.3039288))
),
C=list(list(color="black",
x=c(0.2972527,0.2978297,0.2995604,0.3024451,0.3064835,
0.3116758,0.318022,0.325522,0.3341758,0.3439835,
0.3549451,0.3549451,0.3670522,0.3802967,0.3946786,
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0.5048544,0.5271978,0.5271978,0.5345495,0.5417692,
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0.6067143,0.6124835,0.6181209,0.6236264,0.629,
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0.725,0.725,0.95,0.9447582,0.9392527,
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0.9006813,0.8933297,0.8857143,0.8857143,0.8779835,
0.869956,0.8616319,0.853011,0.8440934,0.8348791,
0.8253681,0.8155604,0.805456,0.7950549,0.7950549,
0.7845137,0.7736593,0.7624918,0.751011,0.739217,
0.7271099,0.7146896,0.701956,0.6889093,0.6755495,
0.6755495,0.6620247,0.6481538,0.6339368,0.6193736,
0.6044643,0.5892088,0.5736071,0.5576593,0.5413654,
0.5247253,0.5247253,0.5000247,0.476033,0.45275,
0.4301758,0.4083104,0.3871538,0.366706,0.346967,
0.3279368,0.3096154,0.3096154,0.2919698,0.274967,
0.2586071,0.2428901,0.2278159,0.2133846,0.1995962,
0.1864505,0.1739478,0.1620879,0.1620879,0.1508544,
0.1402308,0.130217,0.1208132,0.1120192,0.1038352,
0.096261,0.0892967,0.0829423,0.0771978,0.0771978,
0.0720302,0.0674066,0.0633269,0.0597912,0.0567995,
0.0543516,0.0524478,0.0510879,0.050272,0.05,
0.05,0.0502802,0.0511209,0.052522,0.0544835,
0.0570055,0.0600879,0.0637308,0.0679341,0.0726978,
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0.5304886,0.5284365,0.5263844,0.5214007,0.5164169,
0.5114332,0.5064495,0.5014658,0.4962182,0.4910293,
0.485899,0.4808274,0.4758143,0.4737329,0.4715928,
0.4693941,0.4671368,0.4648208,0.4627394,0.4605993,
0.4584007,0.4561433,0.4538274,0.4517752,0.4497231,
0.447671,0.4456189,0.4435668,0.4415733,0.4396971,
0.4379381,0.4362964,0.434772,0.3864007,0.2046417,
0.05,0.2398208,0.3050489,0.306456,0.3077459,
0.3089186,0.3099739,0.3109121,0.3117622,0.3125537,
0.3132866,0.3139609,0.3145765,0.3151336,0.3156319,
0.3160717,0.3164528,0.3167752,0.3186221,0.320645,
0.3228436,0.3252182,0.3277687,0.3301726,0.3326938,
0.3353322,0.3380879,0.3409609,0.3439511,0.3470586,
0.3502834,0.3536254,0.3570847,0.4296417,0.572557,
0.645114,0.6488078,0.6522671,0.6554919,0.6584821,
0.6612378,0.6641107,0.6668664,0.6695049,0.6720261,
0.67443,0.6769805,0.679355,0.6815537,0.6835765,
0.6854235,0.6857166,0.6860098,0.6863029,0.6865961,
0.6868893,0.6872117,0.6875928,0.6880326,0.6885309,
0.6890879,0.6897036,0.6903779,0.6911107,0.6919023,
0.6927524,0.6936906,0.6947459,0.6959186,0.6972085,
0.6986156,0.7601792,0.95,0.7960912),
y=c(0,0,0.1979244,0.2037658,0.2100222,
0.2166938,0.2237806,0.2312824,0.2390808,0.2470571,
0.2552113,0.2635434,0.2720534,0.2809785,0.2899629,
0.2990067,0.3081097,0.3172721,0.3267013,0.3360119,
0.3452039,0.3542772,0.363232,0.384166,0.4054559,
0.4271016,0.449103,0.4714603,0.4488362,0.4266271,
0.4048332,0.3834544,0.3624907,0.353536,0.3444626,
0.3352706,0.32596,0.3165308,0.3073684,0.2982654,
0.2892216,0.2802372,0.2713121,0.2628021,0.25447,
0.2463158,0.2383395,0.2305411,0.2233062,0.216427,
0.2099036,0.2037361,0.1979244,0,0,
1,1,0.4848036,0.4730319,0.4608451,
0.4482431,0.4352261,0.4217939,0.4083024,0.3951075,
0.382209,0.3696071,0.3573017,0.3431282,0.3290734,
0.3151371,0.3013195,0.2876205,0.2984136,0.309444,
0.3207116,0.3322165,0.3439585,0.3545738,0.3656635,
0.3772276,0.3892661,0.4017791,0.4148851,0.4281097,
0.4414529,0.4549148,0.4684952,0.7197924,0.7197924,
0.4684952,0.4551816,0.4419274,0.4287324,0.4155967,
0.4025204,0.3900074,0.3779689,0.3664047,0.355315,
0.3446998,0.3329281,0.3213343,0.3099185,0.2986805,
0.2876205,0.2884211,0.2908228,0.2948258,0.3004299,
0.3076353,0.3160267,0.325189,0.3351223,0.3458265,
0.3573017,0.3693403,0.3817346,0.3944848,0.4075908,
0.4210526,0.4347517,0.4479763,0.4607265,0.4730022,
0.4848036,1,1,0))
),
X=list(list(color="black",
x=c(0.7229862,0.5010985,0.2784784,0.05,0.3861269,
0.0800244,0.3085028,0.5010985,0.6929618,0.9199756,
0.60655,0.95,0.7229862),
y=c(0,0.3654559,0,0,0.5270571,
1,1,0.6812454,1,1,
0.5270571,0,0))
),
Y=list(list(color="black",
x=c(0.6082651,0.6082651,0.3917349,0.3917349,0.05,
0.2775777,0.498527,0.7224223,0.95,0.6082651),
y=c(0.4121572,0,0,0.4121572,1,
1,0.5804299,1,1,0.4121572))
),
Z=list(list(color="black",
x=c(0.95,0.05,0.05,0.6245956,0.1150809,
0.1150809,0.9148906,0.9148906,0.340295,0.95,
0.95),
y=c(0,0,0.1549296,0.828762,0.828762,
1,1,0.8480356,0.171238,0.171238,
0))
)
)
x <- letterPolygon[[toupper(ch)]]
x <- lapply(x, function(.ele){
if(.ele$color=="black") .ele$color <- color
.ele
})
return(x)
}
checkSummary <- function(x){
if("summary" %in% slotNames(x)){
if(any(is.na(x@summary@xscale))){
x@summary@xscale <- c(0, 72)
}
if(any(is.na(x@summary@yscale))){
x@summary@yscale <- c(72, 0)
}
}
x
}
coloredSymbols <- function(ncha, font, color, rname, alpha,
fontface="bold", envir = .globals){
symbols<-list()
for(i in 1:ncha){
symbols[[i]]<-checkSummary(importSVG(font, color[i], rname[i], fontface))
}
if(!missing(alpha)){
for(i in 1:ncha){
symbols[[paste0(i, "_", alpha)]]<-checkSummary(
importSVG(font, colalpha(color, alpha)[i], rname[i],
fontface, envir = envir))
}
}
symbols
}
addPseudolog2<-function(x){
x <- round(x, digits=6)
ifelse(x < .000001, -20, log2(x)) ## !important -10.
}
## get Information Entropy from matrix
getIE<-function(x){
addPseudolog2(nrow(x))
}
UngappedAlignment<-function(pfms, i, threshold, minimalConsensus=0,
rcpostfix="(RC)", revcomp=TRUE){
if(!is(pfms[[i]], "pfm")){
pcms <- pfms
pfms <- lapply(pfms, pcm2pfm)
}else{
pcms <- NULL
}
res<-getAlignedICWithoutGap(pfms[[i-1]], pfms[[i]], threshold, revcomp)
if(!is.null(pcms)) pfms <- pcms
if(res$max>=minimalConsensus){
if(res$rev){
pfms[[i]]<-matrixReverseComplement(pfms[[i]])
pfms[[i]]@name<-paste(pfms[[i]]@name, rcpostfix, sep="")
}
if(res$offset>0){
pfms[[i]]<-addBlank(pfms[[i]], res$offset, FALSE)
}else{
if(res[1]<0){
pfms[1:(i-1)]<-lapply(pfms[1:(i-1)],function(.ele)
addBlank(.ele, -1*res$offset, FALSE))
}
}
}
pfms
}
UngappedAlignmentAA<-function(pcms, i, threshold, minimalConsensus){
pcm1 <- pcms[[i-1]]
pcm2 <- pcms[[i]]
offset1 <- 0
offset2 <- 0
## trim pcm
trimPCMbyIC <- function(pcm, t){
ic <- getIC(pcm)
w <- rle(ic < t)
offL <- offR <- 0
if(w$values[1]) {
offL <- w$lengths[1]
}
if(w$values[length(w$values)]) {
offR <- w$lengths[length(w$values)]
}
if(offL+1>ncol(pcm@mat)-offR){
return(pcm=NULL, offL=offL, offR=offR)
}
pcm@mat <- pcm@mat[, (offL+1):(ncol(pcm@mat)-offR), drop=FALSE]
list(pcm=pcm, offL=offL, offR=offR)
}
res <- trimPCMbyIC(pcm1, t=threshold)
if(is.null(res$pcm)){
return(pcms)
}
pcm1 <- res$pcm
offset1 <- res$offL
res <- trimPCMbyIC(pcm2, t=threshold)
if(is.null(res$pcm)){
return(pcms)
}
pcm2 <- res$pcm
offset2 <- res$offL
res<-compare2profiles(pcm1, pcm2, method="Smith-Waterman")
if(res$length>=minimalConsensus){
of1 <- offset1 + res$i_start
of2 <- offset2 + res$j_start
if(of1<of2){
pcms[seq.int(i-1)] <- lapply(pcms[seq.int(i-1)], function(.ele){
addBlank(.ele, of2-of1, FALSE)
})
}else{
if(of1>of2){
pcms[[i]] <- addBlank(pcms[[i]], of1-of2, FALSE)
}
}
}
pcms
}
getAlignedICWithoutGap<-function(pfm1, pfm2, threshold, revcomp=TRUE){
if(!is(pfm1, "pfm") | !is(pfm2, "pfm"))
stop("class of pfm1 and pfm2 must be pfm")
offset1<-getoffsetPosByIC(pfm1, pfm2, threshold)
if(revcomp){
pfm3<-matrixReverseComplement(pfm2)
offset2<-getoffsetPosByIC(pfm1, pfm3, threshold)
}else{
offset2<-list(k=0,max=0)
}
offset<-0
rev<-FALSE
if((offset1$max < offset2$max)){
rev<-TRUE
max<-offset2$max
offset<-offset2$k
}else{
max<-offset1$max
offset<-offset1$k
}
list(offset=offset,rev=rev,max=max)
}
getICbyBase<-function(p, pfmj){
re<-rep(0, 5)
re[1:4]<-pfmj * (addPseudolog2(pfmj) - addPseudolog2(p))
re[5]<-sum(re[1:4])
re
}
getALLRbyBase <- function(b, pfmi, pfmj){##return 2x ALLR
sum(pfmj * (addPseudolog2(pfmi) - addPseudolog2(b))) +
sum(pfmi * (addPseudolog2(pfmj) - addPseudolog2(b)))
}
checkALLR <- function(...){
getALLRbyBase(...)>0
}
SWU <- function(pattern, subject, b,
match=1, mismatch=-1,
gap=-1000){## motif length will never longer than 1000
if(!is(pattern, "matrix") || !is(subject, "matrix")){
stop("pattern and subject must be numeric matrix")
}
m <- ncol(pattern)
n <- ncol(subject)
score <- matrix(0, nrow=m+1, ncol=n+1)
point <- matrix("none", nrow=m+1, ncol=n+1)
max_i <- 1
max_j <- 1
max_score <- 0
for(i in 1:m){
for(j in 1:n){
diagonal_score <- 0
left_score <- 0
up_score <- 0
#calculate match score
col1 <- subject[, j]
col2 <- pattern[, i]
#score by KLLR
if(checkALLR(b, col1, col2)){
diagonal_score <- score[i, j] + match
}else{
diagonal_score <- score[i, j] + mismatch
}
#calculate gap scores
up_score <- score[i, j+1] + gap
left_score <- score[i+1, j] + gap
if(diagonal_score <=0 && up_score <=0 && left_score <=0){
score[i+1, j+1] <- 0
point[i+1, j+1] <- "none"
next # terminate this iteration of the loop
}
#choose best score
if(diagonal_score >= up_score){
if(diagonal_score >= left_score){
score[i+1, j+1] <- diagonal_score
point[i+1, j+1] <- "diagonal"
}else{
score[i+1, j+1] <- left_score
point[i+1, j+1] <- "left"
}
}else{
if(up_score > left_score){
score[i+1, j+1] <- up_score
point[i+1, j+1] <- "up"
}else{
score[i+1, j+1] <- left_score
point[i+1, j+1] <- "left"
}
}
#set maximum score
if(score[i+1, j+1] > max_score){
max_i <- i+1
max_j <- j+1
max_score <- score[i+1, j+1]
}
}
}
#trace-back
align1 <- c()
align2 <- c()
i <- max_i
j <- max_j
while(1){
if(point[i, j]=="none"){
break
}
if(point[i, j]=="diagonal"){
align1 <- c(align1, j-1)
align2 <- c(align2, i-1)
i <- i-1
j <- j-1
}else{
if(point[i, j]=="left"){
align1 <- c(align1, j-1)
align2 <- c(align2, 0)
j <- j-1
}else{
if(point[i, j]=="up"){
align1 <- c(align1, 0)
align2 <- c(align2, i-1)
i <- i-1
}
}
}
}
align1 <- rev(align1)
align2 <- rev(align2)
if(length(align1)<1 | length(align2)<1){
k <- 0
}else{
k=align1[1]-align2[1]
}
list(k=k, max=max_score)
}
ungappedScore <- function(query, subject, b, threshold){
if(!is(query, "matrix") || !is(subject, "matrix")){
stop("query and subject must be numeric matrix")
}
m <- ncol(query)
n <- ncol(subject)
score <- matrix(0, nrow=m+1, ncol=n+1)
for(i in 1:m){
for(j in 1:n){
ic1 <- getICbyBase(b, query[, i])[5]
ic2 <- getICbyBase(b, subject[, j])[5]
if(ic1>=threshold && ic2>=threshold){
value <- getICbyBase(b, c(query[, i]+subject[, j])/2)[5]
}else{
value <- 0
}
score[i+1, j+1] <- score[i, j] + value
}
}
score[1:m, 1:n] <- 0
max_score <- max(score)
if(max_score==0){
return(list(k=0, max=0))
}
idx <- which(score==max_score, arr.ind=TRUE)
if(nrow(idx)>1){
idxn <- apply(idx, 1, min)
idx <- idx[which(idxn==min(idxn))[1], , drop=FALSE]
}
max_r <- idx[, "row"]
max_c <- idx[, "col"]
k <- max_r - max_c
list(k=as.numeric(k), max=max_score)
}
getoffsetPosByIC<-function(pfm1, pfm2, threshold){
if(!is(pfm1, "pfm") | !is(pfm2, "pfm"))
stop("class of pfm1 and pfm2 must be pfm")
res <- ungappedScore(pfm1$mat, pfm2$mat, b=pfm1$background, threshold)
res
}
#' @importFrom stats sd cor
getoffsetPosByIC_old<-function(pfm1, pfm2, threshold){
if(!is(pfm1, "pfm") | !is(pfm2, "pfm"))
stop("class of pfm1 and pfm2 must be pfm")
score1<-rep(0, ncol(pfm1@mat))
score2<-rep(0, ncol(pfm2@mat))
value1<-rep(0, ncol(pfm1@mat))
value2<-rep(0, ncol(pfm2@mat))
for(i in 1:ncol(pfm1@mat)){
J<-ifelse(ncol(pfm1@mat)+1-i>ncol(pfm2@mat),
ncol(pfm2@mat),ncol(pfm1@mat)+1-i)
for(j in 1:J){
ic1<-getICbyBase(pfm1@background, pfm1@mat[,i+j-1])
ic2<-getICbyBase(pfm2@background, pfm2@mat[,j])
#ic3<-getALLRbyBase(pfm1@background, pfm1@mat[,i+j-1], pfm2@mat[,j])
ic3 <- getICbyBase(pfm1@background,
(pfm1@mat[,i+j-1]+pfm2@mat[,j])/2)
if(sd(pfm1@mat[,i+j-1])==0 || sd(pfm2@mat[,j])==0){
corr <- 0
}else{
corr <- cor(pfm1@mat[,i+j-1], pfm2@mat[,j], method="spearman")
}
if(ic1[5]>threshold & ic2[5]>threshold){
#a<-ic1[1:4]>mean(ic1[1:4])
#b<-ic2[1:4]>mean(ic2[1:4])
#if(ic3>0) score1[i]<-score1[i]+1
#if(ic3>0.25) {
#if(any(a&b)){
if(corr>0){
score1[i]<-score1[i]+1
value1[i] <- value1[i]+ic3[5]
}
}
}
}
for(i in 1:ncol(pfm2@mat)){
J<-ifelse(ncol(pfm2@mat)+1-i>ncol(pfm1@mat),
ncol(pfm1@mat),ncol(pfm2@mat)+1-i)
for(j in 1:J){
ic2<-getICbyBase(pfm2@background, pfm2@mat[,i+j-1])
ic1<-getICbyBase(pfm1@background, pfm1@mat[,j])
#ic3<-getALLRbyBase(pfm1@background, pfm1@mat[,j], pfm2@mat[,i+j-1])
ic3 <- getICbyBase(pfm1@background,
(pfm2@mat[,i+j-1]+pfm1@mat[,j])/2)
if(sd(pfm1@mat[,j])==0 || sd(pfm2@mat[,i+j-1])==0){
corr <- 0
}else{
corr <- cor(pfm1@mat[,j], pfm2@mat[,i+j-1], method="spearman")
}
if(ic1[5]>threshold & ic2[5]>threshold){
#a<-ic1[1:4]>mean(ic1[1:4])
#b<-ic2[1:4]>mean(ic2[1:4])
#if(ic3>0) score2[i]<-score2[i]+1
#if(ic3>0.25) {
#if(any(a&b)){
if(corr>0){
score2[i]<-score2[i]+1
value2[i] <- value2[i]+ic3[5]
}
}
}
}
k1<-match(max(score1),score1)
k2<-match(max(score2),score2)
sc <- (score1[k1] < score2[k2]) || ((score1[k1] == score2[k2]) &&
(value1[k1] < value2[k2]))
k <- ifelse(sc, -1*(k2-1), (k1-1))
max <- ifelse(sc, score2[k2], score1[k1])
val <- ifelse(sc, value2[k2], value1[k1])
list(k=k,max=max,val=val)
}
setClass("Rect",
representation(x="numeric", y="numeric",
width="numeric", height="numeric"),
prototype=prototype(x=0, y=0, width=0, height=0)
)
setGeneric("isContainedIn", function(a, b) standardGeneric("isContainedIn"))
setMethod("isContainedIn", signature(a="Rect", b="Rect"), function(a, b){
a@x >= b@x && a@y >= b@y &&
a@x+a@width <= b@x+b@width && a@y+a@height <= b@y+b@height
})
setClass("pos",
representation(box="Rect", beta="numeric", sig="pfm",
freq="numeric", norm="numeric")
)
getPFMid <- function(pfms, nodename, rcpostfix="(RC)"){
pfmNames <- as.character(unlist(lapply(pfms, function(.ele) .ele@name)))
pfmNames <- gsub(rcpostfix,"",pfmNames, fixed=TRUE)
which(pfmNames==nodename)
}
getParentNode <- function(nodelist, nodename){
for(i in 1:length(nodelist)){
currNode <- nodelist[[i]]
if(currNode@left==nodename) return(c(currNode@parent, "left"))
if(currNode@right==nodename) return(c(currNode@parent, "right"))
}
NULL
}
makeLeaveNames <- function(ch){
gsub(".", "_", make.names(ch), fixed=TRUE)
}
#' @importFrom graphics par
#' @importFrom grid stringWidth stringHeight grid.rect gpar grid.text
grid.eti <- function(x, y, label, clabel, boxes=FALSE,
coul = rep(1, length(x)),
bg = "white", draw=TRUE){
if (length(label) == 0)
return(invisible())
if (is.null(label))
return(invisible())
if (any(label == ""))
return(invisible())
cex0 <- par("cex") * clabel
plot <- gList()
for (i in seq_along(x)) {
cha <- as.character(label[i])
cha <- paste(" ", cha, " ", sep = "")
x1 <- x[i]
y1 <- y[i]
xh <- cex0*stringWidth(cha)
yh <- cex0*stringHeight(cha) * 1.66666666667
if (boxes) {
plot <- gList(plot,
rectGrob(x=x1, y=y1, width=xh, height=yh,
gp=gpar(fill = bg, col = coul[i]),
default.units = "native"))
}
plot <- gList(plot,
textGrob(x=x1, y=y1, label=cha,
gp=gpar(cex = cex0, col = coul[i]),
default.units = "native"))
}
if(draw){
suppressWarnings(grid.draw(plot))
}else{
plot
}
}
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