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plot.R
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plot.R
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source("server.R")
convert_unit_in_canvas_coordinate = function(x, unit = c("mm", "cm", "inches")) {
pin = par("pin")
usr = par("usr")
unit = match.arg(unit)
pt_per_inche1 = (usr[2] - usr[1])/pin[1]
pt_per_inche2 = (usr[4] - usr[3])/pin[2]
if(abs(pt_per_inche1 - pt_per_inche2) > 1e-3) {
warning_wrap("`convert_unit_in_data_coordinate()` only works when aspect of the coordinate is 1.")
}
inche_per_mm = 0.0393700787401575
# length in the data coordinate
if(unit == "inches") {
len = x * pt_per_inche1
} else if(unit == "mm") {
len = x * pt_per_inche1 * inche_per_mm
} else if(unit == "cm") {
len = x * pt_per_inche1 * inche_per_mm * 10
}
return(len)
}
circos.genomicInitialize.new = function(
data,
sector.names = NULL,
major.by = NULL,
plotType = c("axis", "labels"),
tickLabelsStartFromZero = TRUE,
axis.labels.cex = 0.4*par("cex"),
labels.cex = 0.8*par("cex"),
track.height = NULL,
labels_inf_chr =NULL,
data.CN = NULL,
outergap = 1,
plotother = 0,
...) {
outergap <- outergap*0.01
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_wrap("length of `sector.names` and length of sectors differ.")
}
} else {
sector.names = fa
}
names(sector.names) = fa
# calculate xlim
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(circos.par$ring) {
op = c(op[1], 0, op[3], 0)
ow = FALSE
}
if(is.null(track.height)) {
if(all(c("axis", "labels") %in% plotType)) {
track.height = convert_unit_in_canvas_coordinate(1.5, "mm") + strheight("0", cex = axis.labels.cex) +
convert_unit_in_canvas_coordinate(0.5, "mm") + strheight("chr", cex = labels.cex) + strheight("chr", cex = 1)*outergap
} else if("labels" %in% plotType) {
track.height = strheight("chr", cex = 1)*outergap + strheight("chr", cex = labels.cex)
} else if("axis" %in% plotType) {
track.height = convert_unit_in_canvas_coordinate(1.5, "mm") + strheight("0", cex = axis.labels.cex)
} else {
track.height = convert_height(3, "mm")
}
}
#label
if(!is.null(labels_inf_chr)){
if(labels_inf_chr[[2]]=="outside"){
if(ncol(data.CN) == 4){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = labels_inf_chr[[3]]/4, labels_height = (labels_inf_chr[[3]]/4)*3 , cex = (((((as.numeric(labels_inf_chr[[3]]))*4)/5)/max(strwidth(data.CN[,4])))-0.15)*labels_inf_chr[[7]] , line_col = "#000000" , col = labels_inf_chr[[4]] , padding = 0 , track.margin = c(0,0), side = "outside")
}else{
circos.genomicLabels(data.CN, labels.column = 4, connection_height = labels_inf_chr[[3]]/4, labels_height = (labels_inf_chr[[3]]/4)*3 , cex = (((((as.numeric(labels_inf_chr[[3]]))*4)/5)/max(strwidth(data.CN[,4])))-0.15)*labels_inf_chr[[7]] , line_col = "#000000" , col = data.CN[,5] , padding = 0 , track.margin = c(0,0), side = "outside")
}
}
}
# axis and chromosome names
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(all(c("axis", "labels") %in% plotType)) {
circos.genomicAxis(h = "bottom", major.by = major.by, tickLabelsStartFromZero = tickLabelsStartFromZero, labels.cex = axis.labels.cex)
circos.text(mean(xlim), convert_y(1.5, "mm") + convert_y(strheight("chr", cex = 1), "canvas")*outergap + convert_y(strheight("chr", cex = axis.labels.cex), "canvas") + convert_y(0.5, "mm"),
labels = sector.names[sector.index], cex = labels.cex, adj = c(0.5, 0), niceFacing = TRUE)
} else if("labels" %in% plotType) {
circos.text(mean(xlim), convert_y(strheight("chr", cex = 1), "canvas")*outergap , labels = sector.names[sector.index], cex = labels.cex, adj = c(0.5, 0), niceFacing = TRUE)
} else if("axis" %in% plotType) {
circos.genomicAxis(h = "bottom", major.by = major.by, tickLabelsStartFromZero = tickLabelsStartFromZero,labels.cex = axis.labels.cex)
}
}
)
if(plotother != 0){
circos.updatePlotRegion(
sector.index = data[,1][nrow(data)],
track.index = get.current.track.index(),
bg.border = NA,
bg.col = NA
)
}
}
circos.par("cell.padding" = op, "points.overflow.warning" = ow)
return(invisible(NULL))
}
legendplot <- function(tktype,data.TT,data.TT_old,i,legendpos,tkcolor,addlegend){
if(addlegend =="Yes"){
if(tktype == "heatmap-gradual"){
break1 <- min(as.numeric(as.matrix(data.TT[,-c(1:3)])))
break2 <- max(as.numeric(as.matrix(data.TT[,-c(1:3)])))
midpoint <- (break1+break2)/2
hmapcols <- gsub('\\"',"",hmapcols)
hmapcols <- unlist(strsplit(hmapcols,"\\."))
f <- colorRamp2(breaks = c(break1, midpoint, break2), colors = hmapcols)
if(legendpos == "Right"){
return(
Legend(
col_fun = f,
title = paste0("track",i)
)
)
}else{
return(
Legend(
col_fun = f,
title = paste0("track",i),
direction = "horizontal"
)
)
}
}else if(tktype == "rect-gradual"){
f <- colorRamp2(breaks = c(min(data.TT[,4]), mean(data.TT[,4]), max(data.TT[,4])), colors = rectcols)
if(legendpos == "Right"){
return(
Legend(
col_fun = f,
title = paste0("track",i)
)
)
}else{
return(
Legend(
col_fun = f,
title = paste0("track",i),
direction = "horizontal"
)
)
}
}else if(tktype == "rect-discrete"){
lgdcol <- cbind(unique(data.TT_old[,4]),unique(data.TT[,4]))
lgdcol <- lgdcol[order(lgdcol[,1]),]
if(legendpos == "Right"){
return(
Legend(
at = lgdcol[,1],
legend_gp = gpar(fill = lgdcol[,2]),
nrow = 6,
title = paste0("track",i)
)
)
}else{
return(
Legend(
at = lgdcol[,1],
legend_gp = gpar(fill = lgdcol[,2]),
ncol = 4,
by_row = TRUE,
title = paste0("track",i),
direction = "horizontal"
)
)
}
}else if(tktype == "heatmap-discrete"){
lgdcol <- cbind(unique(c(t(data.TT_old[,4:length(data.TT_old)]))),unique(c(t(data.TT))))
lgdcol <- lgdcol[order(lgdcol[,1]),]
if(legendpos == "Right"){
return(
Legend(
at = lgdcol[,1],
legend_gp = gpar(fill = lgdcol[,2]),
nrow = 6,
title = paste0("track",i)
)
)
}else{
return(
Legend(
at = lgdcol[,1],
legend_gp = gpar(fill = lgdcol[,2]),
ncol = 4,
by_row = TRUE,
title = paste0("track",i),
direction = "horizontal"
)
)
}
#}else if("stack" %in% colnames(data.TT_old)){
}else if(tktype == "stack-point" | tktype == "stack-line"){
lgdcol <- cbind(unique(data.TT_old[,4],fromLast = TRUE),tkcolor)
lgdcol <- lgdcol[order(lgdcol[,1]),]
if(legendpos == "Right"){
return(
Legend(
at = lgdcol[,1],
legend_gp = gpar(fill = lgdcol[,2]),
nrow = 6,
title = paste0("track",i)
)
)
}else{
Legend(
at = lgdcol[,1],
legend_gp = gpar(fill = lgdcol[,2]),
ncol = 4,
by_row = TRUE,
title = paste0("track",i),
direction = "horizontal"
)
}
}else{NULL}
}else{NULL}
}
plotcircos <- function(x , colorChr , plotTypes , chr_height , dis_Chr , data.CN , labels_inf_chr , rotation , gap.width , labelChr_size , outAxis_size , plotother , outergap){
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 , axis.labels.cex = outAxis_size , labels.cex = labelChr_size,data.CN = data.CN,labels_inf_chr = labels_inf_chr , outergap = outergap , plotother = plotother)
if("labels" %in% plotTypes && !("axis" %in% plotTypes)){
gapgap <- 0.02
}else{
gapgap <- 0
}
circos.genomicTrackPlotRegion(ylim = c(0, 1) , bg.col = colorChr, bg.border = NA , track.height = chr_height , track.margin = c(dis_Chr,gapgap))
if(plotother != 0){
circos.updatePlotRegion(
sector.index = x[,1][nrow(x)],
track.index = get.current.track.index(),
bg.border = NA,
bg.col = NA
)
if(plotother == 2.2){
traxlim <- get.cell.meta.data("xlim", sector.index = get.current.sector.index(), track.index = get.current.track.index())
circos.text(
sector.index = get.current.sector.index(),
track.index = get.current.track.index(),
x = round((traxlim[2]-traxlim[1])/3),
y = get.cell.meta.data("ycenter", sector.index = get.current.sector.index(), track.index = get.current.track.index()),
labels = 0,
facing = "downward"
)
}else if(plotother == 1.2){
circos.text(
sector.index = get.current.sector.index(),
track.index = get.current.track.index(),
x = get.cell.meta.data("xcenter", sector.index = get.current.sector.index(), track.index = get.current.track.index()),
y = get.cell.meta.data("ycenter", sector.index = get.current.sector.index(), track.index = get.current.track.index()),
labels = 0,
facing = "downward"
)
}
}
if(!is.null(labels_inf_chr)){
if(labels_inf_chr[[2]]=="inside"){
if(ncol(data.CN) == 4){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = labels_inf_chr[[3]]/4, labels_height = (labels_inf_chr[[3]]/4)*3 , cex = (((((as.numeric(labels_inf_chr[[3]]))*4)/5)/max(strwidth(data.CN[,4])))-0.15)*labels_inf_chr[[7]] , line_col = "#000000" , col = labels_inf_chr[[4]] , padding = 0 , track.margin = c(0,0), side = "inside")
}else{
circos.genomicLabels(data.CN, labels.column = 4, connection_height = labels_inf_chr[[3]]/4, labels_height = (labels_inf_chr[[3]]/4)*3 , cex = (((((as.numeric(labels_inf_chr[[3]]))*4)/5)/max(strwidth(data.CN[,4])))-0.15)*labels_inf_chr[[7]] , line_col = "#000000" , col = data.CN[,5] , padding = 0 , track.margin = c(0,0), side = "inside")
}
}
}
}
plotcircos.notrack <- function(x , plotTypes , units , data.CN , labels_inf_chr , rotation , gap.width , labelChr_size , outAxis_size , plotother , outergap){
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 , axis.labels.cex = outAxis_size , labels.cex = labelChr_size,data.CN = data.CN,labels_inf_chr = labels_inf_chr , outergap = outergap , plotother = plotother)
if(!is.null(labels_inf_chr)){
if(labels_inf_chr[[2]]=="inside"){
if(ncol(data.CN) == 4){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = labels_inf_chr[[3]]/4, labels_height = (labels_inf_chr[[3]]/4)*3 , cex =(((((as.numeric(labels_inf_chr[[3]]))*4)/5)/max(strwidth(data.CN[,4])))-0.15)*labels_inf_chr[[7]] , line_col = "#000000" , col = labels_inf_chr[[4]] , padding = 0 , track.margin = c(0,0), side = "inside")
}else{
circos.genomicLabels(data.CN, labels.column = 4, connection_height = labels_inf_chr[[3]]/4, labels_height = (labels_inf_chr[[3]]/4)*3 , cex =(((((as.numeric(labels_inf_chr[[3]]))*4)/5)/max(strwidth(data.CN[,4])))-0.15)*labels_inf_chr[[7]] , line_col = "#000000" , col = data.CN[,5] , padding = 0 , track.margin = c(0,0), side = "inside")
}
}
}
}
plotcircos.cyto <- function(x , plotTypes , chr_height , dis_Chr , units , data.CN , labels_inf_chr , rotation , gap.width , labelChr_size , outAxis_size , plotother , outergap){
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 , axis.labels.cex = outAxis_size , labels.cex = labelChr_size,data.CN = data.CN,labels_inf_chr = labels_inf_chr , outergap = outergap , plotother = plotother)
if("labels" %in% plotTypes && !("axis" %in% plotTypes)){
gapgap <- 0.02
}else{
gapgap <- 0
}
circos.genomicTrackPlotRegion(x, ylim = c(0, 1), bg.border = NA, track.height = chr_height, track.margin = c(dis_Chr,gapgap) , 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 = "#000000")
}, cell.padding = c(0, 0, 0, 0))
if(plotother != 0){
circos.updatePlotRegion(
sector.index = x[,1][nrow(x)],
track.index = get.current.track.index(),
bg.border = NA,
bg.col = NA
)
if(plotother == 2.2){
traxlim <- get.cell.meta.data("xlim", sector.index = get.current.sector.index(), track.index = get.current.track.index())
circos.text(
sector.index = get.current.sector.index(),
track.index = get.current.track.index(),
x = round((traxlim[2]-traxlim[1])/3),
y = get.cell.meta.data("ycenter", sector.index = get.current.sector.index(), track.index = get.current.track.index()),
labels = 0,
facing = "downward"
)
}else if(plotother == 1.2){
circos.text(
sector.index = get.current.sector.index(),
track.index = get.current.track.index(),
x = get.cell.meta.data("xcenter", sector.index = get.current.sector.index(), track.index = get.current.track.index()),
y = get.cell.meta.data("ycenter", sector.index = get.current.sector.index(), track.index = get.current.track.index()),
labels = 0,
facing = "downward"
)
}
}
if(!is.null(labels_inf_chr)){
if(labels_inf_chr[[2]]=="inside"){
if(ncol(data.CN) == 4){
circos.genomicLabels(data.CN, labels.column = 4, connection_height = labels_inf_chr[[3]]/4, labels_height = (labels_inf_chr[[3]]/4)*3 , cex =(((((as.numeric(labels_inf_chr[[3]]))*4)/5)/max(strwidth(data.CN[,4])))-0.15)*labels_inf_chr[[7]] , line_col = "#000000" , col = labels_inf_chr[[4]] , padding = 0 , track.margin = c(0,0), side = "inside")
}else{
circos.genomicLabels(data.CN, labels.column = 4, connection_height = labels_inf_chr[[3]]/4, labels_height = (labels_inf_chr[[3]]/4)*3 , cex =(((((as.numeric(labels_inf_chr[[3]]))*4)/5)/max(strwidth(data.CN[,4])))-0.15)*labels_inf_chr[[7]] , line_col = "#000000" , col = data.CN[,5] , padding = 0 , track.margin = c(0,0), side = "inside")
}
}
}
}
plotfig <- function(input , output , session , data.C , data.T , dis_Chr , data.L , data.N , colorChr , tra_Margin , labels_inf , labelChr , tra_hmap_typcolhmap , tra_border , tra_heatcol_dis , tra_heat_heatcoldiscus ,
trackChr , tratype , chr_height , datatypeChr , heightTra , source_data , tra_poi_poisiz , heatmapcols , tra_bgcol , gap.width , tra_yaxis,
tra_hmap_poslines , tra_hmap_poslinhei , tra_hmap_cellbord , tra_hmap_cellbord_col , tra_hmap_heatmapcol , plotsize , outergap , rect_gra_3Col = c("red","blue","green") ,
tra_rect_rectcol , tra_trct_colrect , tra_rect_rectcoldis , tra_rect_rectcoldiscus , tra_transparency , tra_coltype , tra_colcol ,
tra_colorcus , tra_line_fillarea , tra_poipch , tra_colorline , tra_baseline , outAxis , outAxis_size , labelChr_size , tra_bar_direction ,
tra_bar_Boundary , tra_bar_coldir1 , tra_bar_coldir2 , tra_line_selrea , tra_bar_borderarea , colformatLinks , colorLinks ,
selcolorLinks , transparencyhltLinks , gracolinks , transparencyLinks , legendpos , addlegend , hlt_data , midplot , trapos , trac_index){
heilab <- 0
if(!is.null(data.N)){
heilab <- sum(as.numeric(labels_inf[,3]))
}
heihat <- 0
tramar <- 0
if(!is.null(data.T)){
for (k in 1:length(data.T)) {
if(tra_hmap_poslines[[k]] == "1"){
if(tratype[[k]] == "heatmap-gradual"|tratype[[k]] =="heatmap-discrete"){
heihat <- heihat + tra_hmap_poslinhei[[k]]
}
}
tramar <- tramar + tra_Margin[[k]]
}
}else{
heightTra <- list()
}
if(outAxis == 1 && labelChr == 1){
plotTypes <- c("labels","axis")
}else if(outAxis == 1 && labelChr == 2){
plotTypes <- "axis"
}else if(outAxis == 2 && labelChr == 1){
plotTypes <- "labels"
}else{
plotTypes <- NULL
}
allheight <- sum(heihat , tramar , dis_Chr , heilab , as.numeric(chr_height) , sum(as.numeric(unlist(heightTra))))
if(!is.null(data.L)){
if(allheight > 0.7){
if(!is.null(data.T)) {
for (k in 1:length(data.T)) {
if(tratype[[k]] == "heatmap-gradual"|tratype[[k]] =="heatmap-discrete"){
tra_hmap_poslinhei[[k]] <- 0.7*tra_hmap_poslinhei[[k]]/allheight
}
heightTra[[k]] <- 0.7*heightTra[[k]]/allheight
tra_Margin[[k]] <- 0.7*tra_Margin[[k]]/allheight
}
}
dis_Chr <- 0.7*dis_Chr/allheight
if(!is.null(data.N)){
for (k in 1:length(data.N)){
labels_inf[k,3] <- 0.7* as.numeric(labels_inf[k,3])/allheight
}
}
chr_height <- 0.7*chr_height/allheight
}
}else{
if(allheight > 0.8){
if(!is.null(data.T)){
for (k in 1:length(data.T)) {
if(tratype[[k]] == "heatmap-gradual"|tratype[[k]] =="heatmap-discrete"){
tra_hmap_poslinhei[[k]] <- 0.8*tra_hmap_poslinhei[[k]]/allheight
}
heightTra[[k]] <- 0.8*heightTra[[k]]/allheight
tra_Margin[[k]] <- 0.8*tra_Margin[[k]]/allheight
}
}
dis_Chr <- 0.8*dis_Chr/allheight
if(!is.null(data.N)){
for (k in 1:length(data.N)){
labels_inf[k,3] <- 0.8*as.numeric(labels_inf[k,3])/allheight
}
}
chr_height <- 0.8*chr_height/allheight
}
}
if(!is.null(data.L)){
if(ncol(data.L)==6 | ncol(data.L)==7){
data.L1 <<- data.L[,1:3]
data.L2 <<- data.L[,4:6]
data.L1[,2] <- as.numeric(data.L1[,2])
data.L1[,3] <- as.numeric(data.L1[,3])
data.L2[,2] <- as.numeric(data.L2[,2])
data.L2[,3] <- as.numeric(data.L2[,3])
data.L1$num <<- 1:nrow(data.L1)
data.L2$num <<- 1:nrow(data.L2)
rownames(data.L1) <<- data.L1$num
rownames(data.L2) <<- data.L2$num
}
}
circlize_plot <- function(){
data.C[,2] <- as.numeric(data.C[,2])
data.C[,3] <- as.numeric(data.C[,3])
circos.clear()
if(!is.null(data.N)){
ccc <- NULL
for (k in 1:nrow(labels_inf)) {
kkkk <- labels_inf[k,]
kkkk[,c(1,3,5,6,7)] <- as.numeric(kkkk[,c(1,3,5,6,7)])
if(kkkk[6] == 1){
kkkk[7] = 1
}else{
kkkk[7] = kkkk[7]*0.01
}
ccc <- rbind(ccc,kkkk)
}
labels_inf <- ccc
if(0 %in% labels_inf[,1]){
lsb_tra_index <- labels_inf[,1] %in% 0
labels_inf_chr <- labels_inf[lsb_tra_index,]
labels_inf_tra <- labels_inf[!lsb_tra_index,]
data.CN <- data.N[[as.numeric(labels_inf_chr[[5]])]]
}else{
labels_inf_tra <- labels_inf
labels_inf_chr <- NULL
}
lab_inf <- (1:length(data.T)) %in% labels_inf_tra[,1]
}else{
labels_inf_chr <- NULL
}
## *** 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)
if(1 %in% unlist(tra_yaxis) | trac_index == "Yes"){
if(1 %in% unlist(tra_yaxis) & trac_index == "Yes"){
gap.width[(length(unique(data.C[,1]))-1):length(unique(data.C[,1]))] <- c(1,2)
rotation <- 8
}else if(1 %in% unlist(tra_yaxis) & trac_index != "Yes"){
gap.width[(length(unique(data.C[,1]))-1):length(unique(data.C[,1]))] <- c(0.5,0.5)
rotation <- 5
}else{
gap.width[(length(unique(data.C[,1]))-1):length(unique(data.C[,1]))] <- c(0.5,0.5)
rotation <- 5
}
}else{
rotation <- gap.width[length(gap.width)]/2
}
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]))]
if(1 %in% unlist(tra_yaxis) | trac_index == "Yes"){
if(1 %in% unlist(tra_yaxis) & trac_index != "Yes"){
plotother <- 2.1
}else if(!(1 %in% unlist(tra_yaxis)) & trac_index == "Yes"){
plotother <- 1.2
}else{
plotother <- 2.2
}
}else{
plotother <- 0
}
if(source_data == "a"){ # upload
if(datatypeChr == "1"){ # general
if(trackChr == "track"){ #Chromosome band show
#trackChr : "Show" = "track", "Hide" = ""
plotcircos(data.C , colorChr = colorChr , plotTypes = plotTypes , chr_height = chr_height , dis_Chr = dis_Chr , labels_inf_chr = labels_inf_chr , outergap = outergap ,
data.CN = data.CN , rotation = rotation , gap.width = gap.width , outAxis_size = outAxis_size , labelChr_size = labelChr_size , plotother = plotother)
}else if(trackChr!="track"){
plotcircos.notrack(data.C , plotTypes = plotTypes , labels_inf_chr = labels_inf_chr , data.CN = data.CN , rotation = rotation , gap.width = gap.width , outergap = outergap ,
outAxis_size = outAxis_size , labelChr_size = labelChr_size , plotother = plotother)
}
}else if(datatypeChr == "2"){# cytoband
plotcircos.cyto(data.C , plotTypes=plotTypes , chr_height = chr_height , dis_Chr = dis_Chr , labels_inf_chr = labels_inf_chr , outergap = outergap ,
data.CN = data.CN , rotation = rotation , gap.width = gap.width , outAxis_size = outAxis_size , labelChr_size = labelChr_size ,
plotother = plotother)
}
}else if(source_data == "b"){ #sample
if(datatypeChr == "1"){
plotcircos(data.C , colorChr = colorChr , plotTypes = plotTypes , chr_height = chr_height , dis_Chr = dis_Chr , labels_inf_chr = labels_inf_chr , data.CN = data.CN , rotation = rotation , outergap = outergap ,
gap.width = gap.width , outAxis_size = outAxis_size , labelChr_size = labelChr_size , plotother = plotother)
}else{
plotcircos.cyto(data.C , plotTypes = plotTypes , chr_height = chr_height , dis_Chr = dis_Chr , labels_inf_chr = labels_inf_chr , data.CN = data.CN , rotation = rotation , gap.width = gap.width ,
outAxis_size = outAxis_size , labelChr_size = labelChr_size , plotother = plotother , outergap = outergap)
}
}
if(!is.null(unlist(data.T))){
for(i in 1:length(data.T)){
if(!is.null(data.N)){
if(lab_inf[i]){
labels_inf <- labels_inf_tra[labels_inf_tra[,1] %in% i,]
data.NN <- data.N[[as.numeric(labels_inf[[5]])]]
labelsize <- (((((as.numeric(labels_inf[[3]]))*4)/5)/max(strwidth(data.NN[,4])))-0.15)*labels_inf[[7]]
lab_height <- as.numeric(labels_inf[[3]])
}
}else{
lab_inf <- rep(0, times=length(data.T))
}
ordertrapos <- order(trapos)
data.TT <- data.T[[ordertrapos[i]]]
data.TT_old <- data.T[[ordertrapos[i]]]
tktype <- tratype[[i]]
data.TT[,2] <- as.numeric(data.TT[,2])
data.TT[,3] <- as.numeric(data.TT[,3])
## *** The fill color for track ***
if(tktype!="rect-discrete" && tktype!="rect-gradual" && tktype!="heatmap-gradual" && tktype!="heatmap-discrete" && tktype!="ideogram"){
data.TT$num <- 1:nrow(data.TT)
data.TTC <- NULL
coltypeTrack <- as.numeric(tra_coltype[[i]])
if(tktype == "stack-point" | tktype == "stack-line"){
names(data.TT)[4] <- "stack"
names(data.TT_old) <- c("chr","start","end","stack")
if(coltypeTrack==1){ # color type(1,2,3)
selcols <- distinctColorPalette(999)
#selcols <- c("blue", "red", "green", "cyan", "purple", "pink", "orange", "yellow", "navy", "seagreen", "maroon", "burlywood3", "magenta2")
tkcolor <- sample(selcols,length(unique(data.TT$stack)))
tkcolor <- data.frame(group=unique(data.TT$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$cols)
data.TT <- data.TT[,1:4]
}else if(coltypeTrack == 2){
tkcolor <- tra_colcol[[i]]
}else if(coltypeTrack==3){
tkcolor <- tra_colorcus[[i]]
tkcolor <- unlist(strsplit(tkcolor,";"))
tkcolor <- data.frame(id=tkcolor,stringsAsFactors=F)
tkcolor$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,fromLast = TRUE)
data.TT <- data.TT[,1:4]
}
}else{
if(coltypeTrack == 2){
tkcolor <- tra_colcol[[i]]
tkcolor <- gsub("\\s","",strsplit(tkcolor,",")[[1]])
tkcolor <- gsub('\\"',"",tkcolor)
tkcolor <- gsub("0x","#", tkcolor)
}else if((coltypeTrack==3 && ("color" %in% colnames(data.TT)))){
tkcolor <- tra_colorcus[[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$cols,fromLast = TRUE)
data.TT <- data.TT[,1:4]
}else if(coltypeTrack==1 && ("color" %in% colnames(data.TT))){
selcols <- distinctColorPalette(999)
tkcolor <- sample(selcols,length(unique(data.TT$color)))
#tkcolor <- distinctColorPalette(length(unique(data.TT$color)))
tkcolor <- data.frame(group=unique(data.TT$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$cols)
data.TT <- data.TT[,1:4]
}else{
selcols <- distinctColorPalette(999)
tkcolor <- sample(selcols,ncol(data.TT_old)-3)
}
}
if(!is.null(data.TTC)){
data.TTC <- data.TTC[order(data.TTC$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]
}
}
## *** The backgroud color for track ***
tkbgcol <- tra_bgcol[[i]]
if(!is.null(tkbgcol)){
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 <- tra_Margin[[i]]
tkmargin <- as.numeric(tkmargin)
## *** The track height ***
tkheight <- heightTra[[i]]
if(!is.null(tkheight)){
tkheight <- as.numeric(tkheight)
}
## *** The y coordinates of baselines ***
tklinecoord <- tra_baseline[[i]]
if(!is.null(tklinecoord)){
tklinecoord <- as.numeric(unlist(strsplit(tklinecoord,",")))
}else{
tklinecoord <- c(0.25,0.75)
}
## *** The baselines color ***
tklinecolor <- tra_colorline[[i]]
if(!is.null(tklinecolor)){
tklinecolor <<- gsub('\\"',"",tklinecolor)
tklinecolor <<- gsub("0x","#", tklinecolor)
tklinecolor <- unlist(strsplit(tklinecolor,","))
tklinecolor <- rep(tklinecolor, length(tklinecoord))[1:length(tklinecoord)]
}
if(ncol(data.TT_old)==4 && colnames(data.TT_old)[4]=="stack"){
tklinecol <<- gsub('\\"',"",tklinecolor)
tklinecol <<- gsub("0x","#", tklinecol)
tklinecol <- unlist(strsplit(tklinecol,","))
tklinecol <- rep(tklinecol, length(unique(data.TT_old[,4])))[1:length(unique(data.TT_old[,4]))]
}
## *** Add connection ***
if(!is.null(tra_hmap_poslines[[i]])){
if(tra_hmap_poslines[[i]] == "1"){
heightlines <<- tra_hmap_poslinhei[[i]]
}
}
## *** Add border ***
tkborder <- tra_border[[i]]
if(!is.null(tra_hmap_cellbord[[i]])){
if(tra_hmap_cellbord[[i]] == "add"){
tkbordercol <<- tra_hmap_cellbord_col[[i]]
}else{
tkbordercol <<- NA
}
}
if(!is.null(tra_hmap_heatmapcol[[i]])){
if(tra_hmap_heatmapcol[[i]] == 1){ #heatmap color type, 1 is "typical"
hmapcols <<- gsub('\\"',"",tra_hmap_typcolhmap[[i]])
}else{
hmapcols <<- heatmapcols[[i]]
}
hmapcols <<- unlist(strsplit(hmapcols,"\\."))
}
#
##
## *** The bar direction ***
tkbardir <- tra_bar_direction[[i]]
if(!is.null(tkbardir)){
if(tkbardir==2){
tkbarvalue <- tra_bar_Boundary[[i]]
tkbarcol1 <- tra_bar_coldir1[[i]]
tkbarcol2 <- tra_bar_coldir2[[i]]
tktransparency <- tra_transparency[[i]]
tkbarcol1 <- adjustcolor(tkbarcol1, alpha.f = tktransparency)
tkbarcol2 <- adjustcolor(tkbarcol2, alpha.f = tktransparency)
}
}
if(tktype == "heatmap-discrete"){
tra_heatcol_dis_tr <- tra_heatcol_dis[[i]]
#tra_heatcol_dis,tra_heat_heatcoldiscus
data.TT_hat_dis <- data.TT
for(li in 4:length(data.TT)){
data.TT_hat_dis[,li] <- as.numeric(as.factor(data.TT[,li]))
}
if(tra_heatcol_dis_tr == 2){
heat_dis_cols <- tra_heat_heatcoldiscus[[i]]
heat_dis_cols <- unlist(strsplit(heat_dis_cols,";"))
heat_dis_cols <- data.frame(id=heat_dis_cols,stringsAsFactors=F)
heat_dis_cols$group <- gsub("\\:.*","",heat_dis_cols$id)
heat_dis_cols$cols <- gsub(".*\\:","",heat_dis_cols$id)
heat_dis_cols$group <- gsub(" ","",heat_dis_cols$group)
heat_dis_cols$cols <- gsub(" ","",heat_dis_cols$cols)
heat_dis_cols[,2] <- as.numeric(as.factor(heat_dis_cols[,2]))
data_TT_col <- apply(data.TT_hat_dis[,4:length(data.TT_hat_dis)], MARGIN = c(1,2), function(x){
if(length(which(heat_dis_cols[,2] == x)) != 0){
heat_dis_cols[which(heat_dis_cols[,2] == x),3]
}else{
"#FFFFFF"
}
})
}else{
cols <- c(brewer.pal(11,'Set3'),brewer.pal(9,'Set1')[c(-1,-3,-6)],brewer.pal(8,'Dark2'),"chartreuse","aquamarine","cornflowerblue","blue","cyan","bisque1","darkorchid2","firebrick1","gold1","magenta1","olivedrab1","navy","maroon1","tan","yellow3","black","bisque4","seagreen3","plum2","yellow1","springgreen","slateblue1","lightsteelblue1","lightseagreen","limegreen")
selcol <- sample(cols,length(unique(unlist(data.TT_hat_dis[,4:length(data.TT_hat_dis)]))),replace = TRUE)
data_ht_col <- data.TT_hat_dis
for(ki in 4:length(data.TT_hat_dis)){
data_ht_col[,ki] <- selcol[data.TT_hat_dis[,ki]]
}
data_TT_col <- data_ht_col[,4:length(data_ht_col)]
}
data_TT_col <- as.matrix(data_TT_col)
}
## *** Two kinds of rect plot type color ***
selrectcol <- tra_rect_rectcol[[i]]
if(tktype == "rect-gradual"){
if(selrectcol==1){
rectcol <- tra_trct_colrect[[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(selrectcol==2){
rectcols <- rect_gra_3Col[i,]
}
}else if(tktype == "rect-discrete"){
if(selrectcol==2){
rectcols <- tra_rect_rectcoldis[[i]]
data.TT[,4] <- rectcols
}else if(selrectcol==3){
rectcols <- tra_rect_rectcoldiscus[[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 <- tra_transparency[[i]]
if((tktype!="rect-gradual" && tktype!="rect-discrete" && tktype!="heatmap-gradual" && tktype!="heatmap-discrete" && tktype!="ideogram") | (tktype=="line" && tra_line_fillarea[[i]]!="add")){
tkcolor <- adjustcolor(tkcolor, alpha.f = tktransparency)
}
# data.TTT <- data.TT
# data.TTT$id <- paste(data.TTT[,1],data.TTT[,2],data.TTT[,3],sep="")
# data.TTT$num <- 1:nrow(data.TTT)
## *** The track border
if(!is.null(tkborder)){
if(tkborder=="add"){
tkborder <- "grey"
}else{
tkborder <- NA
}
}
## *** The symbol type & point size***
if(tktype == "point" & !("pch" %in% colnames(data.TT))){
if(!is.null(tra_poipch[[i]])){
symboltype <- tra_poipch[[i]]
if(!is.null(symboltype)){
symboltype <- as.numeric(unlist(strsplit(symboltype,",")))
#symboltype <- symboltype[1]
symboltype <- rep(symboltype, length(unique(data.TT_old[,4])))[1:length(unique(data.TT_old[,4]))]
}
}
}
if(tktype == "point" & !("cex" %in% colnames(data.TT))){
if(!is.null(tra_poi_poisiz[[i]])){
pointsize <- as.numeric(tra_poi_poisiz[[i]])
}
}
if(tktype == "stack-point"){
if(!is.null(tra_poipch[[i]])){
symboltype <- tra_poipch[[i]]
if(!is.null(symboltype)){
symboltype <- as.numeric(unlist(strsplit(symboltype,",")))
symboltype <- rep(symboltype, length(unique(data.TT_old[,4])))[1:length(unique(data.TT_old[,4]))]
}
}
if(!is.null(tra_poi_poisiz[[i]])){
pointsize <- as.numeric(tra_poi_poisiz[[i]])
}
}
columns <- c(1:ncol(data.TT))[-c(1:3)]
if(lab_inf[i]){
if(labels_inf[[2]]=="outside"){
if(ncol(data.NN) == 4){
circos.genomicLabels(data.NN, labels.column = 4, connection_height = lab_height/4, labels_height = (lab_height/4)*3 , cex =labelsize , line_col = "#000000" , col = labels_inf[[4]] , padding = 0 , track.margin = c(0,0), side = "outside")
}else{
circos.genomicLabels(data.NN, labels.column = 4, connection_height = lab_height/4, labels_height = (lab_height/4)*3 , cex =labelsize , line_col = "#000000" , col = data.NN[,5] , padding = 0 , track.margin = c(0,0), side = "outside")
}
}
}
if(tktype == "line"){
## *** Fill the area ***
if(tra_line_fillarea[[i]]!="add"){
area <- FALSE
borderset <- NA
lwdnum <- 1
}else if(tra_line_fillarea[[i]]=="add" && tra_line_selrea[[i]]==1){
area <- TRUE
lwdnum <- 0.2
}else if(tra_line_fillarea[[i]]=="add" && tra_line_selrea[[i]]==2){
area <- TRUE
borderset <- NA
if(nchar(tra_bar_borderarea[[i]])!=0){
borderset <- adjustcolor(tra_bar_borderarea[[i]],alpha.f = tktransparency)
}
lwdnum <- 0.2
}
data.TT[,ncol(data.TT)] <- as.numeric(data.TT[,ncol(data.TT)])
circos.genomicTrackPlotRegion(data.TT, track.height = tkheight, track.margin = c(tkmargin,0) , 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.TT_old))) | coltypeTrack==2){
if(length(columns)==1){
tkcolor <- tkcolor[1]
}else{
tkcolor <- c(tkcolor,rep("grey",length(columns)))
tkcolor <- tkcolor[1:length(columns)]
}
if(tra_line_selrea[[i]]==1 | tra_line_fillarea[[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, ...)
}
})
takindx <- get.current.track.index()
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){
circos.updatePlotRegion(sector.index = x, track.index=takindx , 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)