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writeCmd.R
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writeCmd.R
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writecmd <- function(data.C , data.T , dis_Chr , data.L , data.N , colorChr , tra_Margin , labels_inf = NULL , 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 , gracolinks , transparencyLinks , legendpos , addlegend , hlt_data , midplot , trapos , trac_index ,
chrfil = "", trafil = "" , labfil = "" , linfil = ""
){
dir.create("./script")
setwd("./script")
dir.create("./chromosome")
dir.create("./track")
dir.create("./label")
dir.create("./links")
cat('## Thank you for using shinyCircos- v2.0 (https://venyao.xyz/shinyCircos/)',file="code.R",append=TRUE,sep="\n")
cat('## This file is automatically generated by shinyCircos-V2.0. It is not recommended that you change it without understanding it',file="code.R",append=TRUE,sep="\n")
cat("",file="code.R",append=TRUE,sep="\n")
cat("",file="code.R",append=TRUE,sep="\n")
cat('## Please put your chromsome data at "./chromosome/", unless they are empty',file="code.R",append=TRUE,sep="\n")
cat('## Please put your chromsome data at "./chromosome/", unless they are empty',file="code.R",append=TRUE,sep="\n")
cat('## Please put your track data at "./track/", unless they are empty',file="code.R",append=TRUE,sep="\n")
cat('## Please put your label data at "./label/", unless they are empty',file="code.R",append=TRUE,sep="\n")
cat('## Please put your links data at "./links/", unless they are empty',file="code.R",append=TRUE,sep="\n")
cat('## Please make sure that the folder you specified contains the following four folders, unless they are empty',file="code.R",append=TRUE,sep="\n")
cat('## Please don’t add or subtract the number of files at will, otherwise there may be problems',file="code.R",append=TRUE,sep="\n")
cat("",file="code.R",append=TRUE,sep="\n")
cat("",file="code.R",append=TRUE,sep="\n")
cat("",file="code.R",append=TRUE,sep="\n")
cat("",file="code.R",append=TRUE,sep="\n")
cat('setwd("D:/script/") #Please specify the folder!!!',file="code.R",append=TRUE,sep="\n")
cat("
options(warn=-1)
library(circlize)
library(RColorBrewer)
library(data.table)
library(gridBase)
library(ComplexHeatmap)
library(randomcoloR)",file="code.R",append=TRUE,sep="\n")
cat("",file="code.R",append=TRUE,sep="\n")
cat("",file="code.R",append=TRUE,sep="\n")
if(!is.null(data.C)){
if("add" %in% data.C[,1]){
data.C <<- data.C[-which(data.C[,1] == "add"),]
}
fwrite(data.C,"./chromosome/data.C.csv")
}
if(!is.null(data.T)){
tratype <- unlist(tratype)
ordertrapos <- order(trapos)
for (i in 1:length(data.T)) {
data.TT <- data.T[[ordertrapos[i]]]
fwrite(data.TT,paste0("./track/data.T",i,".csv"))
}
}else{
cat("
data.T <- NULL",file="code.R",append=TRUE,sep="\n")
}
if(!is.null(data.N)){
labpos <- labels_inf[,1]
orderlabpos <- order(labpos)
for (i in 1:length(data.N)) {
data.NN <- data.N[[orderlabpos[i]]]
fwrite(data.NN,paste0("./label/data.N",i,".csv"))
}
}else{
cat("
data.N <- NULL",file="code.R",append=TRUE,sep="\n")
}
if(!is.null(data.L)){
fwrite(data.L,"./links/data.L.csv")
}else{
cat("
data.L <- NULL",file="code.R",append=TRUE,sep="\n")
}
cat(
paste0(
'
data.C <- as.data.frame(fread("./chromosome/data.C.csv", stringsAsFactors = F,data.table = FALSE))
filenameT <- list.files("./track/")
if(length(filenameT) != 0){
data.T <- lapply(1:length(filenameT), function(x) {
as.data.frame(fread(paste0("./track/",filenameT[x])), stringsAsFactors = F)
})
}
filenameL <- list.files("./links/")
if(length(filenameL) != 0){
data.L <- as.data.frame(fread("./links/data.L.csv", stringsAsFactors = F))
}
filenameN <- list.files("./label/")
if(length(filenameN) != 0){
data.N <- lapply(1:length(filenameN), function(x) {
as.data.frame(fread(paste0("./label/",filenameN[x])), stringsAsFactors = F)
})
}
dis_Chr <- ',dis_Chr,'
colorChr <- ',paste0("c('",paste0(colorChr,collapse = "','"),"')"),'
tra_Margin <- ',paste0("c(",paste0(unlist(tra_Margin),collapse = ","),")"),'
'
),file="code.R",append=TRUE,sep="\n"
)
if(!is.null(labels_inf)){
cat(
paste0(
'
labels_inf <- ',paste0("data.frame(col1=c(",paste0(labels_inf[,1],collapse = ","),"),col2 =c('",paste0(labels_inf[,2],collapse = "','"),"'),col3 =c(",paste0(labels_inf[,3],collapse = ","),"),col4 =c('",paste0(labels_inf[,4],collapse = "','"),"'),col5 =c(",paste0(labels_inf[,5],collapse = ","),"),col6 =c(",paste0(labels_inf[,6],collapse = ","),"),col7 =c(",paste0(labels_inf[,7],collapse = ","),"))"),'
labels_inf[,c(1,3,5,6,7)] <- apply(labels_inf[,c(1,3,5,6,7)],c(1,2),as.numeric)
'
),file="code.R",append=TRUE,sep="\n"
)
}
cat(
paste0(
'
labelChr <- ',labelChr,'
tra_hmap_typcolhmap <- ',paste0("c('",paste0(unlist(tra_hmap_typcolhmap),collapse = "','"),"')"),'
tra_border <- ',paste0("c('",paste0(unlist(tra_border),collapse = "','"),"')"),'
tra_heatcol_dis <- ',paste0("c('",paste0(unlist(tra_heatcol_dis),collapse = "','"),"')"),'
tra_heat_heatcoldiscus <- ',paste0("c('",paste0(unlist(tra_heat_heatcoldiscus),collapse = "','"),"')"),'
trackChr <- ',paste0('"',trackChr,'"'),'
tratype <- ',paste0("c('",paste0(unlist(tratype),collapse = "','"),"')"),'
chr_height <- ',chr_height,'
datatypeChr <- ',datatypeChr,'
heightTra <- ',paste0("c(",paste0(unlist(heightTra),collapse = ","),")"),'
source_data <- "',paste0(source_data,'"'),'
tra_poi_poisiz <- ',paste0("c(",paste0(tra_poi_poisiz,collapse = ","),")"),'
heatmapcols <- ',paste0("c('",paste0(unlist(heatmapcols),collapse = "','"),"')"),'
tra_bgcol <- ',paste0("c('",paste0(unlist(tra_bgcol),collapse = "','"),"')"),'
gap.width <- ',paste0("c(",paste0(gap.width,collapse = ","),")"),'
tra_yaxis <- ',paste0("c(",paste0(tra_yaxis,collapse = ","),")"),'
tra_hmap_poslines <- ',paste0("c('",paste0(unlist(tra_hmap_poslines),collapse = "','"),"')"),'
tra_hmap_poslinhei <- ',paste0("c(",paste0(unlist(tra_hmap_poslinhei),collapse = ","),")"),'
tra_hmap_cellbord <- ',paste0("c('",paste0(unlist(tra_hmap_cellbord),collapse = "','"),"')"),'
tra_hmap_cellbord_col <- ',paste0("c('",paste0(unlist(tra_hmap_cellbord_col),collapse = "','"),"')"),'
tra_hmap_heatmapcol <- ',paste0("c(",paste0(unlist(tra_hmap_heatmapcol),collapse = ","),")"),'
plotsize <- ',paste0("c(",paste0(plotsize,collapse = ","),")"),'
outergap <- ',outergap,'
rect_gra_3Col <- ',paste0("c('",paste0(unlist(rect_gra_3Col),collapse = "','"),"')"),'#####
tra_rect_rectcol <- ',paste0("c(",paste0(unlist(tra_rect_rectcol),collapse = ","),")"),'
tra_trct_colrect <- ',paste0("c('",paste0(unlist(tra_trct_colrect),collapse = "','"),"')"),'
tra_rect_rectcoldis <- ',paste0("c('",paste0(unlist(tra_rect_rectcoldis),collapse = "','"),"')"),'
tra_rect_rectcoldiscus <- ',paste0("c('",paste0(unlist(tra_rect_rectcoldiscus),collapse = "','"),"')"),'
tra_transparency <- ',paste0("c(",paste0(unlist(tra_transparency),collapse = ","),")"),'
tra_coltype <- ',paste0("c('",paste0(unlist(tra_coltype),collapse = "','"),"')"),'
tra_colcol <- ',paste0("c('",paste0(unlist(tra_colcol),collapse = "','"),"')"),'
tra_colorcus <- ',paste0("c('",paste0(unlist(tra_colorcus),collapse = "','"),"')"),'
tra_line_fillarea <- ',paste0("c('",paste0(unlist(tra_line_fillarea),collapse = "','"),"')"),'
tra_poipch <- ',paste0("c('",paste0(unlist(tra_poipch),collapse = "','"),"')"),'
tra_colorline <- ',paste0("c('",paste0(unlist(tra_colorline),collapse = "','"),"')"),'
tra_baseline <- ',paste0("c('",paste0(unlist(tra_baseline),collapse = "','"),"')"),'
outAxis <- ',outAxis,'
outAxis_size <- ',outAxis_size,'
labelChr_size <- ',labelChr_size,'
tra_bar_direction <- ',paste0("c(",paste0(unlist(tra_bar_direction),collapse = ","),")"),'
tra_bar_Boundary <- ',paste0("c('",paste0(unlist(tra_bar_Boundary),collapse = "','"),"')"),'
tra_bar_coldir1 <- ',paste0("c('",paste0(unlist(tra_bar_coldir1),collapse = "','"),"')"),'
tra_bar_coldir2 <- ',paste0("c('",paste0(unlist(tra_bar_coldir2),collapse = "','"),"')"),'
tra_line_selrea <- ',paste0("c(",paste0(unlist(tra_line_selrea),collapse = ","),")"),'
tra_bar_borderarea <- ',paste0("c('",paste0(unlist(tra_bar_borderarea),collapse = "','"),"')"),'
colformatLinks <- ',colformatLinks,'#########
colorLinks <- ',colorLinks,'
selcolorLinks <- ',paste0("c('",paste0(unlist(selcolorLinks),collapse = "','"),"')"),'
gracolinks <- ',paste0("c('",paste0(unlist(gracolinks),collapse = "','"),"')"),'
transparencyLinks <- ',transparencyLinks,'
legendpos <- ',paste0("c('",paste0(unlist(legendpos),collapse = "','"),"')"),'
addlegend <- ',paste0("c('",paste0(unlist(addlegend),collapse = "','"),"')"),'
'
),file="code.R",append=TRUE,sep="\n"
)
if(!is.null(hlt_data)){
cat(
paste0(
'
hlt_data <- ',paste0("data.frame(chr=c('",paste0(hlt_data[,1],collapse = "','"),"'),start =c(",paste0(hlt_data[,2],collapse = ","),"),start =c(",paste0(hlt_data[,3],collapse = ","),"),start =c('",paste0(hlt_data[,4],collapse = "','"),"'))"),' #########data.frame(chr=hlt_data[,1],start=hlt_data[,2],end=hlt_data[,3],color=hlt_data[,4])
'
),file="code.R",append=TRUE,sep="\n"
)
}
cat(
paste0(
'
midplot <- ',midplot,'
trapos <- ',paste0("c(",paste0(unlist(trapos),collapse = ","),")"),'
trac_index <- ',paste0("c('",paste0(unlist(trac_index),collapse = "','"),"')"),'
'
),file="code.R",append=TRUE,sep="\n"
)
cat(
paste0(
'
pdf("./plot.pdf", width = ',plotsize[1],'/72, height = ',plotsize[2],'/72,onefile = FALSE)
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 <- unlist(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"
)
}
}
}
}
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 <- NULL
}
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
}
}
grid.newpage()
lgdplot <- list()
if(addlegend == "Yes"){
if(legendpos == "Right"){
circle_size = unit(1, "snpc")
pushViewport(
viewport(
x = 0,
y = 0.5,
width = circle_size,
height = circle_size,
just = c("left", "center")
)
)
par(omi = gridOMI(), new = TRUE)
}else{
circle_size = unit(1, "snpc")
pushViewport(
viewport(
x = 0.5,
y = 1,
width = circle_size,
height = circle_size,
just = c("center", "top")
)
)
par(omi = gridOMI(), new = TRUE)
}
}else{
circle_size = unit(1, "snpc")
pushViewport(
viewport(
x = 0,
y = 0.5,
width = circle_size,
height = circle_size,
just = c("left", "center")
)
)
par(omi = gridOMI(), new = TRUE)
}
data.C[,2] <- as.numeric(data.C[,2])
data.C[,3] <- as.numeric(data.C[,3])
if(1 %in% unlist(tra_yaxis) | trac_index == "Yes"){
if(ncol(data.C) == 3){
print(sum(data.C[,3]))
data.C <<- rbind(data.C,c("add",1,round(0.025*sum(data.C[,3]))))
}else{
kk <- tapply(data.C[,3],data.C[,1],max)
data.C <<- rbind(data.C,c("add",1,round(0.025*sum(kk)),"1","1"))
}
}
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
}
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" = ""
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(data.C,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 = data.C[,1][nrow(data.C)],
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")
}
}
}
}else if(trackChr!="track"){
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(data.C,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")
}
}
}
}
}else if(datatypeChr == "2"){# cytoband
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(data.C,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(data.C, 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 = data.C[,1][nrow(data.C)],
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")
}
}
}
}
}else if(source_data == "b"){ #sample
if(datatypeChr == "1"){
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(data.C,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 = data.C[,1][nrow(data.C)],
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")
}
}
}
}else{
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(data.C,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(data.C, 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 = data.C[,1][nrow(data.C)],
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")
}
}
}
}
}
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){
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 <- 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 ***