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plot.R
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plot.R
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plotcircos <- function(x, color, height, plotTypes, units, rotation, gap.width, labeltextchr, poslabelschr, heightlabelschr, marginlabelschr, data.CN){
circos.par("start.degree"=90-rotation, "gap.degree"=gap.width, cell.padding=c(0,0,0,0), track.margin=c(0,0))
circos.genomicInitialize.new(x,plotType=plotTypes,unit=units)
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="outer"){
circos.genomicLabels(data.CN, labels.column=4, connection_height=heightlabelschr, track.margin=c(0.01,marginlabelschr), side="outside")
}
circos.genomicTrackPlotRegion(ylim = c(0, 1),bg.col = color, bg.border = NA, track.height = height)
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="inner"){
circos.genomicLabels(data.CN, labels.column=4, connection_height=heightlabelschr, track.margin=c(0.01,marginlabelschr), side="inside")
}
}
plotcircos.notrack <- function(x, plotTypes, units, rotation, gap.width, data.CN, labeltextchr, poslabelschr, heightlabelschr, marginlabelschr){
circos.par("start.degree"=90-rotation, "gap.degree"=gap.width, cell.padding=c(0,0,0,0), track.margin=c(0,0))
circos.genomicInitialize.new(x,plotType=plotTypes,unit=units)
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="inner"){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = heightlabelschr, track.margin = c(0.01,marginlabelschr), side = "inside")
}
}
plotcircos.font <- function(x, color, height, plotTypes, units, rotation, gap.width, cexLabel, labeltextchr, poslabelschr, heightlabelschr, marginlabelschr, data.CN){
circos.par("start.degree"=90-rotation, "gap.degree"=gap.width, cell.padding=c(0,0,0,0), track.margin=c(0,0))
circos.genomicInitialize.new.font(x, plotType=plotTypes, unit=units, cexlabel=cexLabel)
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="outer"){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = heightlabelschr, track.margin = c(0.01,marginlabelschr), side = "outside")
}
circos.genomicTrackPlotRegion(ylim = c(0, 1),bg.col = color, bg.border = NA, track.height = height)
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="inner"){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = heightlabelschr, track.margin = c(0.01,marginlabelschr), side = "inside")
}
}
plotcircos.notrack.font <- function(x, plotTypes, units, rotation, gap.width, cexLabel, data.CN, labeltextchr, poslabelschr, heightlabelschr, marginlabelschr){
circos.par("start.degree"=90-rotation, "gap.degree"=gap.width, cell.padding=c(0,0,0,0), track.margin=c(0,0))
circos.genomicInitialize.new.font(x, plotType=plotTypes, unit=units, cexlabel=cexLabel)
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="inner"){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = heightlabelschr, track.margin = c(0.01,marginlabelschr), side = "inside")
}
}
plotcircos.cyto <- function(x, height, plotTypes, units, rotation, gap.width, labeltextchr, poslabelschr, heightlabelschr, marginlabelschr, data.CN){
circos.par("start.degree"=90-rotation, "gap.degree"=gap.width, cell.padding=c(0,0,0,0), track.margin=c(0,0))
circos.genomicInitialize.new(x, plotType = plotTypes, unit=units)
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="outer"){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = heightlabelschr, track.margin = c(0.01,marginlabelschr), side = "outside")
}
circos.genomicTrackPlotRegion(x, ylim = c(0, 1), bg.border = NA,
track.height = height, panel.fun = function(region, value, ...){
col = cytoband.col(value[[2]])
circos.genomicRect(region, value, ybottom = 0,
ytop = 1, col = col, border = NA, ...)
xlim = get.cell.meta.data("xlim")
circos.rect(xlim[1], 0, xlim[2], 1, border = "black")
}, cell.padding = c(0, 0, 0, 0))
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="inner"){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = heightlabelschr, track.margin = c(0.01,marginlabelschr), side = "inside")
}
}
plotcircos.cyto.font <- function(x, height, plotTypes, units, rotation, gap.width, cexLabel, labeltextchr, poslabelschr, heightlabelschr, marginlabelschr, data.CN){
circos.par("start.degree"=90-rotation, "gap.degree"=gap.width, cell.padding=c(0,0,0,0), track.margin=c(0,0))
circos.genomicInitialize.new.font(x, plotType=plotTypes, unit=units, cexlabel=cexLabel)
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="outer"){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = heightlabelschr, track.margin = c(0.01,marginlabelschr), side = "outside")
}
circos.genomicTrackPlotRegion(x, ylim = c(0, 1), bg.border = NA,
track.height = height, panel.fun = function(region, value, ...){
col = cytoband.col(value[[2]])
circos.genomicRect(region, value, ybottom = 0,
ytop = 1, col = col, border = NA, ...)
xlim = get.cell.meta.data("xlim")
circos.rect(xlim[1], 0, xlim[2], 1, border = "black")
}, cell.padding = c(0, 0, 0, 0))
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1 && poslabelschr=="inner"){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = heightlabelschr, track.margin = c(0.01,marginlabelschr), side = "inside")
}
}
circos.genomicInitialize.new <-
function (data, sector.names = NULL, major.by = NULL, unit = "", plotType, tickLabelsStartFromZero = TRUE, track.height = 0.05,
...)
{
if(is.factor(data[[1]])){
fa = levels(data[[1]])
}
else {
fa = unique(data[[1]])
}
if(!is.null(sector.names)){
if(length(sector.names) != length(fa)){
stop("length of `sector.names` and length of sectors differ.\n")
}
}
else {
sector.names = fa
}
names(sector.names) = fa
x1 = tapply(data[[2]], data[[1]], min)[fa]
x2 = tapply(data[[3]], data[[1]], max)[fa]
op = circos.par("cell.padding")
ow = circos.par("points.overflow.warning")
circos.par(cell.padding = c(0, 0, 0, 0), points.overflow.warning = FALSE)
circos.initialize(factor(fa, levels = fa), xlim = cbind(x1,
x2), ...)
if(any(plotType %in% c("axis", "labels"))){
circos.genomicTrackPlotRegion(data, ylim = c(0, 1), bg.border = NA,
track.height = track.height, panel.fun = function(region,
value, ...){
sector.index = get.cell.meta.data("sector.index")
xlim = get.cell.meta.data("xlim")
if(tickLabelsStartFromZero){
offset = xlim[1]
if(is.null(major.by)){
xlim = get.cell.meta.data("xlim")
major.by = .default.major.by()
}
major.at = seq(xlim[1], xlim[2], by = major.by)
major.at = c(major.at, major.at[length(major.at)] +
major.by)
if(major.by > 1e+06){
major.tick.labels = paste((major.at - offset)/1e+06,
"MB", sep = "")
}
else if(major.by > 1000){
major.tick.labels = paste((major.at - offset)/1000,
"KB", sep = "")
}
else {
major.tick.labels = paste((major.at - offset),
"bp", sep = "")
}
}
else {
if(is.null(major.by)){
xlim = get.cell.meta.data("xlim")
major.by = .default.major.by()
}
major.at = seq(floor(xlim[1]/major.by) * major.by,
xlim[2], by = major.by)
major.at = c(major.at, major.at[length(major.at)] +
major.by)
if(major.by > 1e+06){
major.tick.labels = paste(major.at/1e+06,
"MB", sep = "")
}
else if(major.by > 1000){
major.tick.labels = paste(major.at/1000,
"KB", sep = "")
}
else {
major.tick.labels = paste(major.at, "bp",
sep = "")
}
}
if(unit==""){ major.tick.labels <- gsub("[mkbp]","",major.tick.labels,ignore.case = T)}
if(all(c("axis", "labels") %in% plotType)){
circos.axis(h = 0, major.at = major.at, labels = major.tick.labels,
labels.cex = 0.49 * par("cex"), labels.facing = "clockwise",
major.tick.percentage = 0.2)
circos.text(mean(xlim), 1.2, labels = sector.names[sector.index],
cex = par("cex")-0.1, adj = c(0.5, -0.1*par("cex")*6-(par("cex")-1)*3), niceFacing = TRUE)
}
else if("labels" %in% plotType){
circos.text(mean(xlim), 0, labels = sector.names[sector.index],
cex = par("cex")-0.1, adj = c(0.5, -0.1*par("cex")*6-(par("cex")-1)*3), niceFacing = TRUE)
}
else if("axis" %in% plotType){
circos.axis(h = 0, major.at = major.at, labels = major.tick.labels,
labels.cex = 0.49 * par("cex"), labels.facing = "clockwise",
major.tick.percentage = 0.2)
}
})
}
circos.par(cell.padding = op, points.overflow.warning = ow)
return(invisible(NULL))
}
circos.genomicInitialize.new.font <-
function (data, sector.names = NULL, major.by = NULL, unit = "", plotType, tickLabelsStartFromZero = TRUE, track.height = 0.05, cexlabel,
...)
{
if(is.factor(data[[1]])){
fa = levels(data[[1]])
}
else {
fa = unique(data[[1]])
}
if(!is.null(sector.names)){
if(length(sector.names) != length(fa)){
stop("length of `sector.names` and length of sectors differ.\n")
}
}
else {
sector.names = fa
}
names(sector.names) = fa
x1 = tapply(data[[2]], data[[1]], min)[fa]
x2 = tapply(data[[3]], data[[1]], max)[fa]
op = circos.par("cell.padding")
ow = circos.par("points.overflow.warning")
circos.par(cell.padding = c(0, 0, 0, 0), points.overflow.warning = FALSE)
circos.initialize(factor(fa, levels = fa), xlim = cbind(x1,
x2), ...)
if(any(plotType %in% c("axis", "labels"))){
circos.genomicTrackPlotRegion(data, ylim = c(0, 1), bg.border = NA,
track.height = track.height, panel.fun = function(region,
value, ...){
sector.index = get.cell.meta.data("sector.index")
xlim = get.cell.meta.data("xlim")
if(tickLabelsStartFromZero){
offset = xlim[1]
if(is.null(major.by)){
xlim = get.cell.meta.data("xlim")
major.by = .default.major.by()
}
major.at = seq(xlim[1], xlim[2], by = major.by)
major.at = c(major.at, major.at[length(major.at)] +
major.by)
if(major.by > 1e+06){
major.tick.labels = paste((major.at - offset)/1e+06,
"MB", sep = "")
}
else if(major.by > 1000){
major.tick.labels = paste((major.at - offset)/1000,
"KB", sep = "")
}
else {
major.tick.labels = paste((major.at - offset),
"bp", sep = "")
}
}
else {
if(is.null(major.by)){
xlim = get.cell.meta.data("xlim")
major.by = .default.major.by()
}
major.at = seq(floor(xlim[1]/major.by) * major.by,
xlim[2], by = major.by)
major.at = c(major.at, major.at[length(major.at)] +
major.by)
if(major.by > 1e+06){
major.tick.labels = paste(major.at/1e+06,
"MB", sep = "")
}
else if(major.by > 1000){
major.tick.labels = paste(major.at/1000,
"KB", sep = "")
}
else {
major.tick.labels = paste(major.at, "bp",
sep = "")
}
}
if(unit==""){ major.tick.labels <- gsub("[mkbp]","",major.tick.labels,ignore.case = T)}
if(all(c("axis", "labels") %in% plotType)){
circos.axis(h = 0, major.at = major.at, labels = major.tick.labels,
labels.cex = 0.49 * cexlabel, labels.facing = "clockwise",
major.tick.percentage = 0.2)
circos.text(mean(xlim), 1.2, labels = sector.names[sector.index],
cex = cexlabel, adj = c(0.5, -0.1*cexlabel*6-(cexlabel-1)*3), niceFacing = TRUE)
}
else if("labels" %in% plotType){
circos.text(mean(xlim), 0, labels = sector.names[sector.index],
cex = cexlabel, adj = c(0.5, -0.1*cexlabel*6-(cexlabel-1)*3), niceFacing = TRUE)
}
else if("axis" %in% plotType){
circos.axis(h = 0, major.at = major.at, labels = major.tick.labels,
labels.cex = 0.49 * cexlabel, labels.facing = "clockwise",
major.tick.percentage = 0.2)
}
})
}
circos.par(cell.padding = op, points.overflow.warning = ow)
return(invisible(NULL))
}
downloadfile = function(name){downloadHandler(
filename = function(){ name },
content = function(file){
chr <- read.csv(name,head=T,as.is=T)
write.csv(chr, file, row.names=FALSE, quote=F)
})
}
updateText = function(x, input, session){if(input[[paste("uploadtrack",x,sep="")]] == 2){
assign(paste("highlightclear",x,sep=""),input[[paste("clearText_button",x,sep="")]])
if(get(paste("highlightclear",x,sep="")) == 0) return(NULL)
isolate({updateTextInput(session, paste("hltData",x,sep=""), label = ",", value = "")})
}
}
.default.major.by = function(sector.index = get.cell.meta.data("sector.index"),
track.index = get.cell.meta.data("track.index")){
d = circos.par("major.by.degree")
cell.start.degre = get.cell.meta.data("cell.start.degree", sector.index, track.index)
tm = reverse.circlize(c(cell.start.degre, cell.start.degre-d), rep(get.cell.meta.data("cell.bottom.radius", sector.index = sector.index, track.index = track.index), 2))
major.by = abs(tm[1, 1] - tm[2, 1])
digits = as.numeric(gsub("^.*e([+-]\\d+)$", "\\1", sprintf("%e", major.by)))
major.by = round(major.by, digits = -1*digits)
return(major.by)
}
get_most_inside_radius = function() {
tracks = get.all.track.index()
if(length(tracks) == 0) {
1
}else{
n = length(tracks)
get.cell.meta.data("cell.bottom.radius", track.index = tracks[n]) - get.cell.meta.data("track.margin", track.index = tracks[n])[1] - circos.par("track.margin")[2]
}
}
plotfig <- function(input, output, trackindx, data.L, data.L1, data.L2, data.C, data.T, data.N, data.CN, hltTrack.List, hltdata.List, heightSize, widthSize, colorChr, heightChr, gap.width, cexlabel, unitChr, outAxis, labelChr, fontSize, trackChr, datatypeChr, transparencyHlt, legendtext, labeltext, poslabels, heightlabels, marginlabels, fillareaTrack, borderareaTrack, selreaTrack, addlegend, poslegend, transparencyhltLinks, labeltextchr, poslabelschr, heightlabelschr, marginlabelschr, transparencyTrack, transparencyLinks, marginLinks, selcolorLinks, barBoundary, coldir1Track, coldir2Track, colrectTrack, colorTrack, colformatLinks, colorLinks, gracolinks, linksTrack, typeTrack, coltypeTk, colorcusTrack, rectTrack, rectcolTrack, rectcoldisTrack, rectcoldiscusTrack, borderTrack, innergapTrack, gridsborderTrack, colgridsborderTrack, directionTrack, colorlineTrack, symbolTrack, pointsizeTrack, baselineTrack, heightTrack, colhmapTrack, heatmapcols, heatmapcol, lineshmapTrack, heightlinesTrack, marginlinesTrack, marginTrack , bgcolTrack){
## *** The highlight regions ***
if(!is.null(data.L)){
highlightLinks <<- input$highlightLinks
hltdataLinks <<- input$hltDataLinks
hltregion1.export <<- NULL
hltregion2.export <<- NULL
if(highlightLinks==1 && nchar(hltdataLinks)!=0){
tmpL <- matrix(strsplit(hltdataLinks, "\n")[[1]])
colnamesL <- c("chr","start","end","color")
datL <- matrix(0, length(tmpL), length(colnamesL))
colnames(datL) <- colnamesL
for(l in 1:length(tmpL)){
rowL <- strsplit(tmpL[l], ",")[[1]]
if(length(rowL)==4){
datL[l,] <- rowL
}
}
datL.ht <- as.data.frame(t(datL),stringsAsFactors=F)
datL.ht1 <- unlist(lapply(datL.ht,function(x){
all(x==0)
})
)
output$errorinfo3 <- renderPrint({
if(input$linksTrack && !is.null(input$linksFile) && input$highlightLinks==1 && nchar(input$hltDataLinks)>0){
validate(
need(all(datL.ht1==FALSE), "Error: Data to highlight genomic regions should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color.")
)
}
})
outputOptions(output, "errorinfo3", suspendWhenHidden = FALSE)
datL <- data.frame(datL,stringsAsFactors=F)
datL$start <- as.numeric(datL$start)
datL$end <- as.numeric(datL$end)
datL$color <- datL$color
queryL <- GRanges(seqnames = datL$chr,ranges=IRanges(start=datL$start,end=datL$end),seqinfo=NULL)
subj1 <- GRanges(seqnames = data.L1[,1],ranges=IRanges(start=data.L1[,2],end=data.L1[,3]),seqinfo=NULL)
subj2 <- GRanges(seqnames = data.L2[,1],ranges=IRanges(start=data.L2[,2],end=data.L2[,3]),seqinfo=NULL)
indx1 <<- findOverlaps(queryL,subj1)
indx1 <<- data.frame(indx1,stringsAsFactors=F)
indx1$queryHits <- as.numeric(indx1$queryHits)
indx1$subjectHits <- as.numeric(indx1$subjectHits)
hltregion1 <- data.L1[indx1$subjectHits,]
data.LL1 <- data.L1
hltregion1$color <- datL$color[indx1[,1]]
indx2 <<- findOverlaps(queryL,subj2)
indx2 <<- data.frame(indx2,stringsAsFactors=F)
indx2$queryHits <- as.numeric(indx2$queryHits)
indx2$subjectHits <- as.numeric(indx2$subjectHits)
hltregion2 <- data.L2[indx2$subjectHits,]
data.LL2 <- data.L2
hltregion2$color <- datL$color[indx2[,1]]
hltregion1.export <<- hltregion1
hltregion2.export <<- hltregion2
}
}
output$circosfigure <- renderPlot({
withProgress(message='Making plots',value = 0,{
data.C[,2] <- as.numeric(data.C[,2])
data.C[,3] <- as.numeric(data.C[,3])
circos.clear()
colorChr <- gsub('\\"',"",colorChr)
colorChr <- gsub("0x","#", colorChr)
repnumcol <- round(length(unique(data.C[,1]))/length(colorChr))+1
colorChr <- rep(colorChr, repnumcol)[1:length(unique(data.C[,1]))]
## *** The gap width ***
repnumgap <- round(length(unique(data.C[,1]))/length(gap.width))+1
gap.width <- rep(gap.width, repnumgap)[1:length(unique(data.C[,1]))]
gap.width <- as.numeric(gap.width)
rotation <- gap.width[length(gap.width)]/2
if(fontSize=="custom"){
if(length(legendtext)!=0 && addlegend==1 && poslegend==1){
par(oma=c(0,0,0,0),mar = c(9,0.5,1,9.5),xpd=TRUE,cex=cexlabel-0.1)
}else{
par(mar = c(0.6,0.6,0.6,0.6),cex=cexlabel-0.1)
}
}else{
if(length(legendtext)!=0 && addlegend==1 && poslegend==1){
par(oma=c(0,0,0,0),mar = c(9,0.5,1,9.5),xpd=TRUE,cex=as.numeric(fontSize)-0.05)
}else{
par(mar = c(0.6,0.6,0.6,0.6),cex=as.numeric(fontSize)-0.05)
}
}
if(outAxis == 1){
plotTypes <- unique(c(labelChr,"axis"))
}else{
plotTypes <- NULL
}
if(datatypeChr=="general"){
if(trackChr=="track" && fontSize!="custom"){
plotcircos(data.C, height=heightChr, color=colorChr, plotTypes=plotTypes, units=unitChr, rotation=rotation, gap.width=gap.width, labeltextchr=labeltextchr, poslabelschr=poslabelschr, heightlabelschr=heightlabelschr, marginlabelschr=marginlabelschr, data.CN=data.CN)
}else if(trackChr=="track" && fontSize=="custom"){
plotcircos.font(data.C, height=heightChr, color=colorChr, plotTypes=plotTypes, units=unitChr, rotation=rotation, gap.width=gap.width, cexLabel=cexlabel-0.1, labeltextchr=labeltextchr, poslabelschr=poslabelschr, heightlabelschr=heightlabelschr, marginlabelschr=marginlabelschr, data.CN=data.CN)
}else if(trackChr!="track" && fontSize!="custom"){
plotcircos.notrack(data.C, plotTypes=plotTypes, units=unitChr, rotation=rotation, gap.width=gap.width, data.CN=data.CN, labeltextchr=labeltextchr, poslabelschr=poslabelschr, heightlabelschr=heightlabelschr, marginlabelschr=marginlabelschr)
}else if(trackChr!="track" && fontSize=="custom"){
plotcircos.notrack.font(data.C, plotTypes=plotTypes, units=unitChr, rotation=rotation, gap.width=gap.width, cexLabel=cexlabel-0.1, data.CN=data.CN, labeltextchr=labeltextchr, poslabelschr=poslabelschr, heightlabelschr=heightlabelschr, marginlabelschr=marginlabelschr)
}
}else{
if(fontSize!="custom"){
plotcircos.cyto(data.C, height=heightChr, plotTypes=plotTypes, units=unitChr, rotation=rotation, gap.width=gap.width, labeltextchr=labeltextchr, poslabelschr=poslabelschr, heightlabelschr=heightlabelschr, marginlabelschr=marginlabelschr, data.CN=data.CN)
}else if(fontSize=="custom"){
plotcircos.cyto.font(data.C, height=heightChr, plotTypes=plotTypes, units=unitChr, rotation=rotation, gap.width=gap.width, cexLabel=cexlabel-0.1, labeltextchr=labeltextchr, poslabelschr=poslabelschr, heightlabelschr=heightlabelschr, marginlabelschr=marginlabelschr, data.CN=data.CN)
}
}
if(!is.null(data.T)){
takindx <- 1
if(!is.null(data.CN) && ncol(data.CN)==4 && labeltextchr==1){
takindx <- takindx+2
}
tkcolor.export <<- list()
data.TTC.export <<- list()
for(i in 1:length(data.T)){
data.TT <- data.T[[i]]
tktype <- typeTrack[i]
data.TT[,2] <- as.numeric(data.TT[,2])
data.TT[,3] <- as.numeric(data.TT[,3])
data.NN <- data.N[[i]]
## *** The fill color for track ***
data.TT$num <- 1:nrow(data.TT)
data.TTC.export[[i]] <<- ""
if(tktype!="rect" && tktype!="heatmap" && tktype!="ideogram"){
data.TTC <- NULL
coltypeTrack <- coltypeTk[i]
if(coltypeTrack==2){
tkcolor <- colorTrack[i]
tkcolor <- gsub("\\s","",strsplit(tkcolor,",")[[1]])
tkcolor <- gsub('\\"',"",tkcolor)
tkcolor <- gsub("0x","#", tkcolor)
}else if((coltypeTrack==3 && ("color" %in% colnames(data.TT))) | (coltypeTrack==3 && ncol(data.T[[i]])==4 && colnames(data.TT)[4]=="stack")){
tkcolor <- colorcusTrack[i]
tkcolor <- unlist(strsplit(tkcolor,";"))
tkcolor <- data.frame(id=tkcolor,stringsAsFactors=F)
tkcolor$group <- gsub("\\:.*","",tkcolor$id)
tkcolor$cols <- gsub(".*\\:","",tkcolor$id)
tkcolor$group <- gsub(" ","",tkcolor$group)
tkcolor$cols <- gsub(" ","",tkcolor$cols)
colname <- colnames(data.TT)
if("color" %in% colnames(data.TT)){
data.TTC <- merge(data.TT,tkcolor,by.x="color",by.y="group",all.x=T)
}else if(colnames(data.TT)[4]=="stack"){
data.TTC <- merge(data.TT,tkcolor,by.x="stack",by.y="group",all.x=T)
}
data.TTC <- data.TTC[c(colname,"cols")]
data.TTC$cols[is.na(data.TTC$cols)] <- "grey"
tkcolor <- unique(data.TTC$cols)
data.TT <- data.TT[,1:4]
}else if(coltypeTrack==1 && ("color" %in% colnames(data.TT))){
selcols <- c("blue", "red", "green", "cyan", "purple", "pink", "orange", "yellow", "navy", "seagreen", "maroon", "burlywood3", "magenta2")
tkcolor <- sample(selcols,length(unique(data.TT$color)))
tkcolor.export[[i]] <<- tkcolor
tkcolor <- data.frame(group=unique(data.TT$color),cols=tkcolor,stringsAsFactors=F)
colname <- colnames(data.TT)
data.TTC <- merge(data.TT,tkcolor,by.x="color",by.y="group",all.x=T)
data.TTC <- data.TTC[c(colname,"cols")]
data.TTC$cols[is.na(data.TTC$cols)] <- "grey"
tkcolor <- unique(data.TTC$cols)
data.TT <- data.TT[,1:4]
}else if(coltypeTrack==1 && ncol(data.T[[i]])==4 && colnames(data.TT)[4]=="stack"){
selcols <- c("blue", "red", "green", "cyan", "purple", "pink", "orange", "yellow", "navy", "seagreen", "maroon", "burlywood3", "magenta2")
tkcolor <- sample(selcols,length(unique(data.TT$stack)))
tkcolor.export[[i]] <<- tkcolor
tkcolor <- data.frame(group=unique(data.TT$stack),cols=tkcolor,stringsAsFactors=F)
colname <- colnames(data.TT)
data.TTC <- merge(data.TT,tkcolor,by.x="stack",by.y="group",all.x=T)
data.TTC <- data.TTC[c(colname,"cols")]
data.TTC$cols[is.na(data.TTC$cols)] <- "grey"
tkcolor <- unique(data.TTC$cols)
data.TT <- data.TT[,1:4]
}else{
selcols <- c("blue", "red", "green", "cyan", "purple", "pink", "orange", "yellow", "navy", "seagreen", "maroon", "burlywood3", "magenta2")
tkcolor <- sample(selcols,ncol(data.T[[i]])-3)
tkcolor.export[[i]] <<- tkcolor
}
if(!is.null(data.TTC)){
data.TTC <- data.TTC[order(data.TTC$num),]
rownames(data.TTC) <- NULL
data.TTC$num <- NULL
}
data.TT$num <- NULL
if(c(ncol(data.TT)==5 | ncol(data.TT)==6 | ncol(data.TT)==7) && ("color" %in% colnames(data.TT))){
data.TT <- data.TT[,1:4]
}else if(c(ncol(data.TT)==5 | ncol(data.TT)==6 | ncol(data.TT)==7) && ("pch" %in% colnames(data.TT)) && !("color" %in% colnames(data.TT))){
data.TT <- data.TT[,1:4]
tkcolor <- tkcolor[1]
}
if(is.null(data.TTC)){
data.TTC.export[[i]] <<- ""
}else{
data.TTC.export[[i]] <<- data.TTC
}
}
## *** The backgroud color for track ***
tkbgcol <- bgcolTrack[i]
tkbgcol <- gsub("\\s","",strsplit(tkbgcol,",")[[1]])
tkbgcol <- gsub('\\"',"",tkbgcol)
tkbgcol <- gsub("0x","#", tkbgcol)
repnumcol <- round(length(unique(data.C[,1]))/length(tkbgcol))+1
tkbgcol <- rep(tkbgcol, repnumcol)[1:length(unique(data.C[,1]))]
## *** The track margin ***
tkmargin <- marginTrack[i]
tkmargin <- as.numeric(tkmargin)
## *** The track height ***
tkheight <- heightTrack[i]
tkheight <- as.numeric(tkheight)
## *** The y coordinates of baselines ***
tklinecoord <- baselineTrack[i]
tklinecoord <- as.numeric(unlist(strsplit(tklinecoord,",")))
## *** The symbol type & point size***
if(ncol(data.T[[i]])==4 && colnames(data.T[[i]])[4]=="stack"){
symboltype <- symbolTrack[i]
symboltype <- as.numeric(unlist(strsplit(symboltype,",")))
symboltype <- rep(symboltype, length(unique(data.T[[i]][,4])))[1:length(unique(data.T[[i]][,4]))]
pointsize <- as.numeric(pointsizeTrack[1])
}
## *** The baselines color ***
tklinecolor <- colorlineTrack[i]
if(nchar(tklinecolor)!=0){
tklinecolor <<- gsub('\\"',"",tklinecolor)
tklinecolor <<- gsub("0x","#", tklinecolor)
tklinecolor <- unlist(strsplit(tklinecolor,","))
tklinecolor <- rep(tklinecolor, length(tklinecoord))[1:length(tklinecoord)]
}
if(ncol(data.T[[i]])==4 && colnames(data.T[[i]])[4]=="stack"){
tklinecol <<- gsub('\\"',"",tklinecolor)
tklinecol <<- gsub("0x","#", tklinecol)
tklinecol <- unlist(strsplit(tklinecol,","))
tklinecol <- rep(tklinecol, length(unique(data.T[[i]][,4])))[1:length(unique(data.T[[i]][,4]))]
}
## *** The fill color for track ***
if(heatmapcol[i]==1){
hmapcols <- gsub('\\"',"",colhmapTrack[i])
}else{
hmapcols <- heatmapcols[i]
}
hmapcols <- unlist(strsplit(hmapcols,"\\."))
## *** Add connection ***
lineshmap <- lineshmapTrack[i]
if(lineshmap==1){
heightlines <<- heightlinesTrack[i]
marginlines <<- marginlinesTrack[i]
}
## *** Add border ***
tkborder <- borderTrack[i]
innergap <- 0.5 - innergapTrack[i]
gridsborder <- gridsborderTrack[i]
if(gridsborder=="add"){
tkbordercol <<- colgridsborderTrack[i]
if(nchar(tkbordercol)==0){
tkbordercol <<- NA
}
}else{
tkbordercol <<- NA
}
## *** The bar direction ***
tkbardir <- directionTrack[i]
if(tkbardir==2){
tkbarvalue <- barBoundary[i]
tkbarcol1 <- coldir1Track[i]
tkbarcol2 <- coldir2Track[i]
tktransparency <- transparencyTrack[i]
tkbarcol1 <- adjustcolor(tkbarcol1, alpha.f = tktransparency)
tkbarcol2 <- adjustcolor(tkbarcol2, alpha.f = tktransparency)
}
## *** The data color ***
tkrectcol <- rectTrack[i]
## *** Select color ***
selrectcol <- rectcolTrack[i]
if(tkrectcol==1){
rectcol <- colrectTrack[i]
if(rectcol=="blue"){
rectcols <<- c("#EDEDFD","#6969F5","#00008B")
}else if(rectcol=="red"){
rectcols <<- c("#FDEDED","#F56969","#8B0000")
}else if(rectcol=="green"){
rectcols <<- c("#EDFBED","#69E169","#008B00")
}else if(rectcol=="cyan"){
rectcols <<- c("#EDFBFB","#69E1E1","#008B8B")
}else if(rectcol=="purple"){
rectcols <<- c("#F6F0FB","#B27FE1","#551A8B")
}else if(rectcol=="pink"){
rectcols <<- c("#FBEEF5","#E172AE","#8B1076")
}else if(rectcol=="orange"){
rectcols <<- c("#FDF5ED","#F5AE69","#8B4500")
}else if(rectcol=="yellow"){
rectcols <<- c("#FDFDED","#EFEF1A","#8B8B00")
}else if(rectcol=="navy"){
rectcols <<- c("#EDEDF6","#7272B8","#000080")
}else if(rectcol=="seagreen"){
rectcols <<- c("#F2FBF6","#4EEE94","#2E8B57")
}else if(rectcol=="maroon"){
rectcols <<- c("#FFF4FB","#FF69C7","#8B1C62")
}else if(rectcol=="olivedrab"){
rectcols <<- c("#FBFFF4","#C6FF52","#698B22")
}else if(rectcol=="gold"){
rectcols <<- c("#FFFCF1","#FFDD28","#8B7500")
}else if(rectcol=="lightblue"){
rectcols <<- c("#EFF5F7","#AFCDD7","#68838B")
}else if(rectcol=="navy.yellow"){
rectcols <<- c("#000080","#7B7B41","#FFFF00")
}else if(rectcol=="purple.seagreen"){
rectcols <<- c("#551A8B","#548994","#54FF9F")
}else if(rectcol=="navy.orange"){
rectcols <<- c("#000080","#7B5041","#FFA500")
}else if(rectcol=="navy.cyan"){
rectcols <<- c("#000080","#007BBD","#00FFFF")
}else if(rectcol=="blue.red"){
rectcols <<- c("#0000FF","#730083","#EE0000")
}else if(rectcol=="green.red"){
rectcols <<- c("#00EE00","#757800","#EE0000")
}
}else if(tkrectcol==2 && selrectcol==2){
rectcols <- rectcoldisTrack[i]
data.TT[,4] <- rectcols
}else if(tkrectcol==2 && selrectcol==3){
rectcols <- rectcoldiscusTrack[i]
rectcols <- unlist(strsplit(rectcols,";"))
rectcols <- data.frame(id=rectcols,stringsAsFactors=F)
rectcols$group <- gsub("\\:.*","",rectcols$id)
rectcols$cols <- gsub(".*\\:","",rectcols$id)
rectcols$group <- gsub(" ","",rectcols$group)
rectcols$cols <- gsub(" ","",rectcols$cols)
colname <- colnames(data.TT)[1:3]
data.TT <- merge(data.TT,rectcols,by.x=colnames(data.TT)[4],by.y="group",all.x=T)
data.TT <- data.TT[c(colname,"cols")]
}
## *** The transparency of color ***
tktransparency <- transparencyTrack[i]
if((tktype!="rect" && tktype!="heatmap" && tktype!="ideogram") | (tktype=="line" && fillareaTrack[i]!="add")){
tkcolor <- adjustcolor(tkcolor, alpha.f = tktransparency)
}
data.TTT <- data.T[[i]]
data.TTT$id <- paste(data.TTT[,1],data.TTT[,2],data.TTT[,3],sep="")
data.TTT$num <- 1:nrow(data.TTT)
## *** The links margin ***
if(i != length(data.T)){
lkmargin <- 0
}else{
lkmargin <- marginLinks
}
if(tkborder=="add"){
tkborder <- "grey"
}else{
tkborder <- NA
}
columns <- c(1:ncol(data.TT))[-c(1:3)]
if(!is.null(data.NN) && ncol(data.NN)==4 && labeltext[i]==1){
takindx <- takindx+2
}
if(poslabels[i]=="inner"){
takindx <- takindx-2
}
output$errorinfo4 <- renderPrint({
for(y in 1:length(data.T)){
if(input[[paste("uploadtrack",trackindx[y],sep="")]]==2 & input[[paste("coltypeTrack",trackindx[y],sep="")]]==3){
if(tkbardir==1 & !("color" %in% colnames(data.T[[y]])) & ncol(data.T[[y]])>=4 & colnames(data.T[[y]])[4]!="stack"){
validate(
need(input[[paste("coltypeTrack",trackindx[y],sep="")]]!=3, paste("Error: Data color error for Track",trackindx[y],". The type of data color should be 'Random' or 'Custom for data with multi-column' based on the uploaded data without column as 'color' or 'stack'.",sep=""))
)
}
}
}
})
outputOptions(output, "errorinfo4", suspendWhenHidden = FALSE)
output$errorinfo5 <- renderPrint({
for(e in 1:length(data.T)){
if(input[[paste("uploadtrack",trackindx[e],sep="")]]==2 && input[[paste("highlightTrack",trackindx[e],sep="")]]==1){
validate(
need(nchar(hltdata.List[[e]])>0, paste("Warning: Highlight regions are empty for Track",trackindx[e],". Please input applicable genomic regions.",sep=""))
)
}
}
})
outputOptions(output, "errorinfo5", suspendWhenHidden = FALSE)
if(tktype=="line"){
## *** Fill the area ***
if(fillareaTrack[i]!="add"){
area <- FALSE
borderset <- NA
lwdnum <- 1
}else if(fillareaTrack[i]=="add" && selreaTrack[i]==1){
area <- TRUE
lwdnum <- 0.2
}else if(fillareaTrack[i]=="add" && selreaTrack[i]==2){
area <- TRUE
borderset <- NA
if(nchar(borderareaTrack[i])!=0){
borderset <- adjustcolor(borderareaTrack[i],alpha.f = tktransparency)
}
lwdnum <- 0.2
}
if(!is.null(data.NN) && ncol(data.NN)==4 && labeltext[i]==1 && poslabels[i]=="outer"){
circos.genomicLabels(data.NN, labels.column = 4, connection_height = heightlabels[i], track.margin = c(0.01,marginlabels[i]), side = "outside")
}
if(ncol(data.T[[i]])==4 && colnames(data.T[[i]])[4]=="stack"){
bed_list <- lapply(unique(data.T[[i]][,4]),function(x){
if(coltypeTrack==2){
data.TT[data.TT[,4] %in% x,1:3]
}else{
data.TTC[data.TTC[,4] %in% x,1:3]
}
})
circos.genomicTrackPlotRegion(bed_list, stack = TRUE, track.height = tkheight, track.margin = c(lkmargin,tkmargin),
bg.col = tkbgcol, bg.border = tkborder, panel.fun = function(region, value, ...){
i = getI(...)
if(coltypeTrack==1){
circos.genomicLines(region, value, col=tkcolor[i], lty=1, ...)
}else if(coltypeTrack==2){
circos.genomicLines(region, value, col=tkcolor[1], lty=1, ...)
}else if(coltypeTrack==3){
circos.genomicLines(region, value, col=tkcolor[i], lty=1, ...)
}
})
}else{
data.TT[,ncol(data.TT)] <- as.numeric(data.TT[,ncol(data.TT)])
circos.genomicTrackPlotRegion(data.TT, track.height = tkheight, track.margin = c(lkmargin,tkmargin),
bg.col = tkbgcol, bg.border = tkborder, panel.fun = function(region,value,...){
if(nchar(tklinecolor[1])!=0){
xlim <- get.cell.meta.data("xlim")
ylim <- get.cell.meta.data("ylim")
for(k in 1:length(tklinecoord)){
y1 <- as.numeric(quantile(ylim,probs=tklinecoord[k]))
circos.lines(x=xlim,y=c(y1,y1), col=tklinecolor[k], lwd=0.1)
}
}
if((coltypeTrack==1 && !("color" %in% colnames(data.T[[i]]))) | coltypeTrack==2){
if(length(columns)==1){
tkcolor <- tkcolor[1]
}else{
tkcolor <- c(tkcolor,rep("grey",length(columns)))
tkcolor <- tkcolor[1:length(columns)]
}
if(selreaTrack[i]==1 | fillareaTrack[i]!="add"){
borderset <- adjustcolor(tkcolor,alpha.f = tktransparency)
}
circos.genomicLines(region, value, numeric.column=columns-3, col=borderset, area=area, border=tkcolor, lwd=lwdnum, lty=1, ...)
}
})
if(coltypeTrack==3 && ncol(data.TTC)>=6 && ("cols" %in% colnames(data.TTC))){
data.TTC$id <- paste(data.TTC[,1],data.TTC[,2],data.TTC[,3],sep="")
data.TTC$num <- 1:nrow(data.TTC)
lapply(unique(data.TTC[,1]),function(x){
if(trackChr=="track"){
circos.updatePlotRegion(sector.index = x, track.index=takindx+2, bg.col = tkbgcol[which(unique(data.C[,1])==x)], bg.border = tkborder)
}else{
circos.updatePlotRegion(sector.index = x, track.index=takindx+1, bg.col = tkbgcol[which(unique(data.C[,1])==x)], bg.border = tkborder)
}
if(nchar(tklinecolor[1])!=0){
xlim <- get.cell.meta.data("xlim")
ylim <- get.cell.meta.data("ylim")
for(k in 1:length(tklinecoord)){
y1 <- as.numeric(quantile(ylim,probs=tklinecoord[k]))
circos.lines(x=xlim,y=c(y1,y1), col=tklinecolor[k], lwd=0.1)
}
}
dat <- data.TTC[data.TTC[,1] %in% x,]
lapply(unique(dat$cols),function(m){
datt <- dat[dat$cols %in% m,]
ind <- which(data.TTC$id %in% datt$id)
datt.fil <- na.omit(unique(data.TTC[ind,]))
datt.fil <- datt.fil[datt.fil[,1] %in% x,]
rownum <- datt.fil$num
rownumdif <- diff(rownum)
indx <- which(rownumdif != 1)
indx1 <- c(0,indx)
rownumdif1 <- c(1,rownumdif)
if(length(indx)==0){
rownumdif1 <- 1
}else{
for(k in 1:length(which(rownumdif!=1))){
rownumdif1[(indx1[k]+1):indx[k]] <- k
if(k==length(which(rownumdif!=1))){
rownumdif1[(indx[k]+1):length(rownumdif1)] <- k+1
}
}
}
datt.fil$indx <- rownumdif1
lapply(unique(rownumdif1),function(h){
datt.fill <- datt.fil[datt.fil$indx == h,]
minnum <- min(datt.fill$num)
datt.fill <- rbind(datt.fill,as.character(c(dat[dat$num==(minnum-1),],h)))
datt.fill[,2] <- as.numeric(datt.fill[,2])
datt.fill[,3] <- as.numeric(datt.fill[,3])
datt.fill[,4] <- as.numeric(datt.fill[,4])
datt.fill$indx <- as.numeric(datt.fill$indx)
datt.fill <- datt.fill[!is.na(datt.fill[,2]),]
datt.fill <- datt.fill[order(datt.fill[,2],datt.fill[,3]),]
if(selreaTrack[i]==1 | fillareaTrack[i]!="add"){
borderset <- adjustcolor(m,alpha.f = tktransparency)
}
circos.lines((datt.fill[,2]+datt.fill[,3])/2,datt.fill[,4], col=borderset, area=area, border=m, lwd=lwdnum, lty=1)
})
})
})
}else if(coltypeTrack==1 && ("color" %in% colnames(data.T[[i]])) && ("cols" %in% colnames(data.TTC))){
data.TTC$id <- paste(data.TTC[,1],data.TTC[,2],data.TTC[,3],sep="")
data.TTC$num <- 1:nrow(data.TTC)
lapply(unique(data.TTC[,1]),function(x){
if(trackChr=="track"){
circos.updatePlotRegion(sector.index = x, track.index=takindx+2, bg.col = tkbgcol[which(unique(data.C[,1])==x)], bg.border = tkborder)
}else{
circos.updatePlotRegion(sector.index = x, track.index=takindx+1, bg.col = tkbgcol[which(unique(data.C[,1])==x)], bg.border = tkborder)
}
if(nchar(tklinecolor[1])!=0){
xlim <- get.cell.meta.data("xlim")
ylim <- get.cell.meta.data("ylim")
for(k in 1:length(tklinecoord)){
y1 <- as.numeric(quantile(ylim,probs=tklinecoord[k]))
circos.lines(x=xlim,y=c(y1,y1), col=tklinecolor[k], lwd=0.1)
}
}
dat <- data.TTC[data.TTC[,1] %in% x,]
lapply(unique(dat$cols),function(m){
datt <- dat[dat$cols %in% m,]
ind <- which(data.TTC$id %in% datt$id)
datt.fil <- na.omit(unique(data.TTC[ind,]))
datt.fil <- datt.fil[datt.fil[,1] %in% x,]
rownum <- datt.fil$num
rownumdif <- diff(rownum)
indx <- which(rownumdif != 1)
indx1 <- c(0,indx)
rownumdif1 <- c(1,rownumdif)
if(length(indx)==0){
rownumdif1 <- 1
}else{
for(k in 1:length(which(rownumdif!=1))){
rownumdif1[(indx1[k]+1):indx[k]] <- k
if(k==length(which(rownumdif!=1))){
rownumdif1[(indx[k]+1):length(rownumdif1)] <- k+1
}
}
}
datt.fil$indx <- rownumdif1
lapply(unique(rownumdif1),function(h){
datt.fill <- datt.fil[datt.fil$indx == h,]
minnum <- min(datt.fill$num)
datt.fill <- rbind(datt.fill,as.character(c(dat[dat$num==(minnum-1),],h)))
datt.fill[,2] <- as.numeric(datt.fill[,2])
datt.fill[,3] <- as.numeric(datt.fill[,3])
datt.fill[,4] <- as.numeric(datt.fill[,4])
datt.fill$indx <- as.numeric(datt.fill$indx)
datt.fill <- datt.fill[!is.na(datt.fill[,2]),]
datt.fill <- datt.fill[order(datt.fill[,2],datt.fill[,3]),]
if(selreaTrack[i]==1 | fillareaTrack[i]!="add"){
borderset <- adjustcolor(m,alpha.f = tktransparency)
}
circos.lines((datt.fill[,2]+datt.fill[,3])/2,datt.fill[,4], col=borderset, area=area, border=m, lwd=lwdnum, lty=1)
})
})
})
}
assign("hltTrack",hltTrack.List[[i]])
assign("hltdata",hltdata.List[[i]])
if(hltTrack==1 && !is.null(nrow(hltregion.List[[i]])) && nrow(hltregion.List[[i]])>0 && (length(columns)==1 | colnames(data.T[[i]])[5]=="color") && ((!("color" %in% colnames(data.T[[i]])) && coltypeTrack!=3) | ("color" %in% colnames(data.T[[i]])))){
assign("hltregion",hltregion.List[[i]])
hlttransparency <- transparencyHlt[i]
hltregion$color <- adjustcolor(hltregion$color, alpha.f = hlttransparency)
hltregion$color <- gsub("0x","#", hltregion$color)
chrr <- unique(hltregion[,1])
lapply(chrr, function(x){
datt <- hltregion[hltregion[,1] %in% x,]
trackk <- data.TTT[data.TTT[,1] %in% x,]
trackk <- trackk[!trackk$id %in% datt$id,]
col <- unique(datt$color)
if(trackChr=="track"){
circos.updatePlotRegion(sector.index = x, track.index=takindx+2, bg.col = tkbgcol[which(unique(data.C[,1])==x)], bg.border = tkborder)
}else{
circos.updatePlotRegion(sector.index = x, track.index=takindx+1, bg.col = tkbgcol[which(unique(data.C[,1])==x)], bg.border = tkborder)
}
if(nchar(tklinecolor[1])!=0){
xlim <- get.cell.meta.data("xlim")
ylim <- get.cell.meta.data("ylim")
for(k in 1:length(tklinecoord)){
y1 <- as.numeric(quantile(ylim,probs=tklinecoord[k]))
circos.lines(x=xlim,y=c(y1,y1), col=tklinecolor[k], lwd=0.1)
}
}
lapply(col, function(m){
dattt <- datt[datt$color %in% m,]
ind <- which(data.TTT$id %in% dattt$id)
ind <- unique(c(ind-1,ind,ind+1))
dattt.fil <- na.omit(unique(data.TTT[ind,]))
dattt.fil <- dattt.fil[dattt.fil[,1] %in% x,]
dattt.fil <- dattt.fil[order(dattt.fil$num),]
dattt.fil$groups <- c(diff(dattt.fil$num),diff(dattt.fil$num)[1])
dattt.fill <- dattt.fil[dattt.fil$groups==1,]
borderset <- m
circos.lines((dattt.fill[,2]+dattt.fill[,3])/2,dattt.fill[,4], col=borderset, area=area, border=m, lwd=lwdnum, lty=1)
})
if("color" %in% colnames(trackk)){
data.TTC$id <- paste(data.TTC[,1],data.TTC[,2],data.TTC[,3],sep="")
data.TTC1 <- data.TTC[!data.TTC$id %in% datt$id,]
indd <- which(data.TTC1$id %in% trackk$id)
indd <- unique(c(indd-1,indd,indd+1))
trackkk <- na.omit(unique(data.TTC1[indd,]))
trackkk <- trackkk[trackkk[,1] %in% x,]
lapply(unique(trackkk$cols),function(f){
trackkkk <- trackkk[trackkk$cols %in% f,]
rownum <- as.numeric(rownames(trackkkk))
rownumdif <- diff(rownum)
indx <- which(rownumdif != 1)
indx1 <- c(0,indx)
rownumdif1 <- c(1,rownumdif)
if(length(indx)==0){
rownumdif1 <- 1
}else{
for(k in 1:length(which(rownumdif!=1))){
rownumdif1[(indx1[k]+1):indx[k]] <- k
if(k==length(which(rownumdif!=1))){
rownumdif1[(indx[k]+1):length(rownumdif1)] <- k+1
}
}
}
trackkkk$indx <- rownumdif1
lapply(unique(rownumdif1),function(h){
trackkkkk <- trackkkk[trackkkk$indx == h,]
minnum <- min(as.numeric(rownames(trackkkkk)))
trackkkkk <- rbind(trackkkkk,as.character(c(trackkk[rownames(trackkk)==(minnum-1),]),h))
trackkkkk[,2] <- as.numeric(trackkkkk[,2])
trackkkkk[,3] <- as.numeric(trackkkkk[,3])
trackkkkk[,4] <- as.numeric(trackkkkk[,4])
trackkkkk$indx <- as.numeric(trackkkkk$indx)
trackkkkk <- trackkkkk[!is.na(trackkkkk[,2]),]
trackkkkk <- trackkkkk[order(trackkkkk[,2],trackkkkk[,3]),]
if(selreaTrack[i]==1 | fillareaTrack[i]!="add"){
borderset <- adjustcolor(f,alpha.f = tktransparency)
}
circos.lines((trackkkkk[,2]+trackkkkk[,3])/2,trackkkkk[,4], col=borderset, area=area, border=f, lwd=lwdnum, lty=1)
})
})
}else{
rownum <- as.numeric(rownames(trackk))
rownumdif <- diff(rownum)
indx <- which(rownumdif != 1)
indx1 <- c(0,indx)
rownumdif1 <- c(1,rownumdif)
if(length(indx)==0){
rownumdif1 <- 1
}else{
for(k in 1:length(which(rownumdif!=1))){
rownumdif1[(indx1[k]+1):indx[k]] <- k
if(k==length(which(rownumdif!=1))){
rownumdif1[(indx[k]+1):length(rownumdif1)] <- k+1
}
}
}
trackk$indx <- rownumdif1
lapply(unique(rownumdif1),function(h){
trackkkkk <- trackk[trackk$indx == h,]
if(selreaTrack[i]==1 | fillareaTrack[i]!="add"){
borderset <- adjustcolor(tkcolor,alpha.f = tktransparency)
}
circos.lines((trackkkkk[,2]+trackkkkk[,3])/2,trackkkkk[,4], col=borderset[1], area=area, border=tkcolor[1], lwd=lwdnum, lty=1)
})
}
})
}
}
if(!is.null(data.NN) && ncol(data.NN)==4 && labeltext[i]==1 && poslabels[i]=="inner"){
circos.genomicLabels(data.NN, labels.column = 4, connection_height = heightlabels[i], track.margin = c(0.01,marginlabels[i]), side = "inside")
}
}else if(tktype=="point"){
if(!is.null(data.NN) && ncol(data.NN)==4 && labeltext[i]==1 && poslabels[i]=="outer"){
circos.genomicLabels(data.NN, labels.column = 4, connection_height = heightlabels[i], track.margin = c(0.01,marginlabels[i]), side = "outside")
}
if(ncol(data.T[[i]])==4 && colnames(data.T[[i]])[4]=="stack"){
bed_list <- lapply(unique(data.T[[i]][,4]),function(x){
if(coltypeTrack==2){
data.TT[data.TT[,4] %in% x,1:3]
}else{
data.TTC[data.TTC[,4] %in% x,1:3]
}
})
circos.genomicTrackPlotRegion(bed_list, stack = TRUE, track.height = tkheight, track.margin = c(lkmargin,tkmargin),
bg.col = tkbgcol, bg.border = tkborder, panel.fun = function(region, value, ...){
i = getI(...)
if(coltypeTrack==1){
circos.lines(CELL_META$cell.xlim, c(i, i), lty = 2, col = tklinecol[i])
circos.genomicPoints(region, value, pch = symboltype[i], cex = pointsize, col = tkcolor[i],...)
}else if(coltypeTrack==2){
circos.lines(CELL_META$cell.xlim, c(i, i), lty = 2, col = tklinecol[i])
circos.genomicPoints(region, value, pch = symboltype[i], cex = pointsize, col = tkcolor[1],...)
}else if(coltypeTrack==3){
circos.lines(CELL_META$cell.xlim, c(i, i), lty = 2, col = tklinecol[i])