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writeCmd-1_function.R
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writeCmd-1_function.R
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# color for ideogram plot
cytoband.col <- function(x) {
x <- as.vector(x)
col.panel <- c("gpos100" = rgb(0, 0, 0, maxColorValue = 255),
"gpos" = rgb(0, 0, 0, maxColorValue = 255),
"gpos75" = rgb(130, 130, 130, maxColorValue = 255),
"gpos66" = rgb(160, 160, 160, maxColorValue = 255),
"gpos50" = rgb(200, 200, 200, maxColorValue = 255),
"gpos33" = rgb(210, 210, 210, maxColorValue = 255),
"gpos25" = rgb(200, 200, 200, maxColorValue = 255),
"gvar" = rgb(220, 220, 220, maxColorValue = 255),
"gneg" = rgb(255, 255, 255, maxColorValue = 255),
"acen" = rgb(217, 47, 39, maxColorValue = 255),
"stalk" = rgb(100, 127, 164, maxColorValue = 255) )
col <- col.panel[x]
col[is.na(col)] <- "#FFFFFF"
names(col) <- NULL
return(col)
}
g_legend <- function(a.gplot) {
tmp <- ggplot_gtable(ggplot_build(a.gplot))
leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
legend <- tmp$grobs[[leg]]
return(legend)
}
areColors <- function(x) {
sapply(x, function(y) {
tryCatch(is.matrix(col2rgb(y)), error = function(e) FALSE)
})
}
dat_cus_cols <- function(i, cus_cols, dat) {
laycolor <- cus_cols[i]
laycolor <- unlist(strsplit(laycolor, ";"))
laycolor <- data.frame(id = laycolor, stringsAsFactors = F)
laycolor$group <- gsub("\\:.*", "", laycolor$id)
laycolor$cols <- gsub(".*\\:", "", laycolor$id)
laycolor$group <- gsub(" ", "", laycolor$group)
laycolor$cols <- gsub(" ", "", laycolor$cols)
colname <- colnames(dat)
dat <- merge(dat, laycolor, by.x = "color", by.y = "group", all.x = T)
dat <- dat[c(colname, "cols")]
return(dat)
}
# color for gradual rectangles
rect_grad_cols <- function(i, rect_grad_col, col_rect, rect_grad_cus_cols) {
rect_grad_col <- rect_grad_col[i]
if (rect_grad_col == 1) {
rectcolor <- col_rect[i]
all_rect_cols <- list(
c("#EDEDFD", "#6969F5", "#00008B"), c("#FDEDED", "#F56969", "#8B0000"),
c("#EDFBED", "#69E169", "#008B00"), c("#EDFBFB", "#69E1E1", "#008B8B"),
c("#F6F0FB", "#B27FE1", "#551A8B"), c("#FBEEF5", "#E172AE", "#8B1076"),
c("#FDF5ED", "#F5AE69", "#8B4500"), c("#FDFDED", "#EFEF1A", "#8B8B00"),
c("#EDEDF6", "#7272B8", "#000080"), c("#F2FBF6", "#4EEE94", "#2E8B57"),
c("#FFF4FB", "#FF69C7", "#8B1C62"), c("#FBFFF4", "#C6FF52", "#698B22"),
c("#FFFCF1", "#FFDD28", "#8B7500"), c("#EFF5F7", "#AFCDD7", "#68838B"),
c("#000080", "#7B7B41", "#FFFF00"), c("#551A8B", "#548994", "#54FF9F"),
c("#000080", "#7B5041", "#FFA500"), c("#000080", "#007BBD", "#00FFFF"),
c("#0000FF", "#730083", "#EE0000"), c("#00EE00", "#757800", "#EE0000")
)
names(all_rect_cols) <- c("blue", "red", "green", "cyan", "purple", "pink", "orange", "yellow", "navy",
"seagreen", "maroon", "olivedrab", "gold", "lightblue", "navy.yellow",
"purple.seagreen", "navy.orange", "navy.cyan", "blue.red", "green.red")
rect_cols <<- all_rect_cols[[rectcolor]]
} else{
rectgrad_cuscol <- rect_grad_cus_cols[i]
rect_cols <<- unlist(strsplit(rectgrad_cuscol, "\\."))
}
return(rect_cols)
}
dat_dis_col <- function(i, dis_cols, dat) {
dis_col <- dis_cols[i]
dis_col <- gsub("\\s", "", strsplit(dis_col, ",")[[1]])
dis_col <- gsub('\\"', "", dis_col)
dis_col <- gsub("0x", "#", dis_col)
if (length(dis_col) == 0) {
dis_col <- NA
}
dat$color <- dis_col
return(dat)
}
lgd_mdy_label <- function(i, lgd_labels) {
lgd_label <- gsub("\\s", "", strsplit(lgd_labels[i], ",")[[1]])
lgd_label <- gsub('\\"', "", lgd_label)
if (length(lgd_label) == 0) {
lgd_label <- "NA"
}
return(lgd_label)
}
chr_cumsum <- function(dat, i) {
chr.len <- dat$size
names(chr.len) <- dat$chr
if (i == 2) {
chr.cum.len.tmp <<- c(0, cumsum(chr.len))
}
chr.cum.len <- c(0, cumsum(chr.len)[-length(chr.len)])
names(chr.cum.len) <- names(chr.len)
return(chr.cum.len)
}
cols_adjust <- function(i, dat, col_transpt, plot_type, type) {
if ((type == 1 && (plot_type[i] %in% c("rect_discrete", "heatmap_discrete"))) |
(type == 2 && (!plot_type[i] %in% c("point_gradual", "rect_gradual")))) {
dat$color[!areColors(dat$color)] <- NA
dat$color <- adjustcolor(dat$color, alpha.f = col_transpt[i])
if (!all(is.na(dat$color))) {
dat_val <- unique(dat$raw_color[!is.na(dat$raw_color)])
dat_col <- dat$color[match(dat_val, dat$raw_color)]
} else{
dat_val <- unique(dat$raw_color[!is.na(dat$raw_color)])[1]
dat_col <- "#FFFFFF00"
}
} else if (!plot_type[i] %in% c("heatmap_gradual", "heatmap_discrete", "text",
"rect_gradual", "rect_discrete", "ideogram")){
if (!"raw_color" %in% names(dat)) {
dat$raw_color <- dat$color
}
if (!plot_type[i] %in% "segment") {
dat_val <- unique(dat$raw_color[!is.na(dat$value)])
} else{
dat_val <- unique(dat$raw_color)
}
if (plot_type[i] %in% "vertical_line") {
dat_val <- unique(dat$raw_color)
}
dat$color[!areColors(dat$color)] <- NA
dat$color <- adjustcolor(dat$color, alpha.f = col_transpt[i])
dat_col <- dat$color[match(dat_val, dat$raw_color)]
}
dat_val <- dat_val[!duplicated(dat_col)]
dat_col <- dat_col[!duplicated(dat_col)]
dat$raw_color <- factor(dat$raw_color, levels = dat_val, ordered = T)
dat$color <- factor(dat$color, levels = dat_col, ordered = T)
dat_val <<- dat_val[which(!dat_col %in% "#FFFFFF00")]
dat_col <<- dat_col[!dat_col %in% "#FFFFFF00"]
return(dat)
}
# color for discrete rectangles or discrete heatmap
dis_type_cols_v1 <- function(i, dat, col_dis, plot_type, col_dis_rand, indx, discol.export, col_dis_cus, rect_col_dis) {
if (plot_type[i] == "rect_discrete") {
colnames(dat)[4] <- "color"
}
if (col_dis[i] == 1) {
if (plot_type[i] == "heatmap_discrete") {
dat$raw_color <- dat$color
}
if (plot_type[i] == "rect_discrete") {
dat$value <- dat$color
}
if (length(unique(dat$color)) <= length(col_dis_rand)) {
selcol <- discol.export[which(indx==i)]
selcol <- unlist(strsplit(selcol,"\\."))
names(selcol) <- unique(dat$color)
dat$color <- selcol[dat$color]
} else{
dat$color <- NA
}
if(plot_type[i] == "rect_discrete"){
dat <- dat[, c(1:3, 5, 4)]
}
} else if ((plot_type[i] == "rect_discrete" & col_dis[i] == 3) |
(plot_type[i] == "heatmap_discrete" & col_dis[i] == 2)) {
dat <- dat_cus_cols(i, col_dis_cus, dat)
if (plot_type[i] == "heatmap_discrete") {
colnames(dat)[which(colnames(dat) == "color")] <- "raw_color"
} else{
colnames(dat)[4] <- "value"
}
names(dat)[ncol(dat)] <- "color"
} else if (plot_type[i] == "rect_discrete" && col_dis[i] == 2) {
dat <- dat_dis_col(i, rect_col_dis, dat)
dat$value <- dat$color
dat <- dat[, c(1:3, 5, 4)]
}
return(dat)
}
dat_val_range <- function(m, dat, plot_type, layer_index) {
val_range <- list()
for (n in unique(dat$chr)) {
dat.tmp1 <- dat[dat$chr == n, ]
if (plot_type[m] == "segment") {
num <- c(dat.tmp1$ypos1, dat.tmp1$ypos2)
} else{
num <- dat.tmp1$value
}
val_range <- c(val_range, list(c(layer_index[m], n, min(num, na.rm = T), max(num, na.rm = T))))
}
return(val_range)
}
# the main function to make a single genome plot
single_genome_plot <- function(data.chr, data.track, plot_type, layer_index, col_type, color_cus, color_mulgp, col_transpt, add_border, border_col,
rect_col, rect_col_dis, rect_col_dis_cus, col_rect, rect_grad_col, sel_heatmap_col, hmap_col, heatmap_col_cus_2cols,
heatmap_col_cus_3cols, rect_grad_cus_2cols, rect_grad_cus_3cols, hmap_col_dis, hmap_col_dis_cus, symbol_point,
sel_symbol_point, point_size, sel_point_size, line_color, line_size, fill_area, sel_area_type, border_area, linetype,
add_arrow, arrow_pos, arrow_size, text_col, text_size, font_face, text_angle, col_lgd, col_lgd_name, size_lgd,
size_lgd_name, shape_lgd, shape_lgd_name, line_type_lgd, line_type_lgd_name, col_lgd_mdy_label, col_lgd_label,
size_lgd_mdy_label, size_lgd_label, shape_lgd_mdy_label, shape_lgd_label, line_type_lgd_mdy_label, line_type_lgd_label,
ylabel, height_layer, margin_layer, laycolor.export, rect_discol.export, heatmap_discol.export){
names(data.chr) <- c("chr", "size")
chr_order <- unique(data.chr$chr)
data.chr$size <- as.numeric(data.chr$size)
layernum <- length(unique(layer_index))
layer_index <- as.numeric(gsub("track", "", layer_index))
val_range <- list()
data.chr$start <- 0
names(data.chr) <- c("chr", "size", "start")
data.chr <- data.chr[, c(1, 3, 2)]
val_range_chr <- melt(data = data.chr, id.vars = "chr")
val_range_chr$variable <- NULL
chr.cum.len <- chr_cumsum(data.chr, 1)
## *** Set colnames for track data ***
for (m in 1:length(data.track)) {
data.track.single <- data.track[[m]]
if (plot_type[m] %in% c("point", "line")) {
names(data.track.single)[1:3] <- c("chr", "pos", "value")
} else if (plot_type[m] == "bar") {
names(data.track.single)[1:4] <- c("chr", "xmin", "xmax", "value")
} else if (plot_type[m] == "horizontal_line") {
names(data.track.single) <- "value"
rep_num <- nrow(data.track.single)
data.track.single <- data.track.single[rep(rownames(data.track.single), length(unique(data.chr$chr))), , drop = F]
data.track.single$chr <- rep(unique(data.chr$chr), each = rep_num)
} else if (plot_type[m] == "segment") {
names(data.track.single)[1:5] <- c("chr", "xpos1", "ypos1", "xpos2", "ypos2")
} else if (plot_type[m] == "text") {
names(data.track.single) <- c("chr", "pos", "value", "symbol")
}
## *** Extract ymin and ymax of each track ***
if (plot_type[m] == "segment") {
val_range <- c(val_range, dat_val_range(m, data.track.single, plot_type, layer_index))
} else if (!plot_type[m] %in% c("rect_gradual", "rect_discrete", "heatmap_gradual", "heatmap_discrete", "vertical_line", "ideogram")) {
val_range <- c(val_range, dat_val_range(m, data.track.single, plot_type, layer_index))
}
}
if (length(val_range) > 0) {
val_range <- as.data.frame(do.call(rbind, val_range), stringsAsFactors = F)
names(val_range) <- c("layer", "chr", "min_val", "max_val")
val_range[c("layer", "min_val", "max_val")] <- sapply(val_range[c("layer", "min_val", "max_val")], as.numeric)
val_range <- val_range[, c(1, 3, 4)]
val_range <- ddply(val_range, .(layer), function(x) {
x$min_val <- min(x$min_val, na.rm = T)
x$max_val <- max(x$max_val, na.rm = T)
return(x)
})
val_range <- unique(val_range)
}
## *** Adjust the height of each track and the gap between adjacent tracks ***
track_layout <- data.frame(num = sort(layer_index), height = height_layer, gap = margin_layer, stringsAsFactors = F)
track_layout <- unique(track_layout)
height_layer <- track_layout$height
names(height_layer) <- track_layout$num
track_layout$height <- cumsum(track_layout$height)
track_layout$gap <- cumsum(track_layout$gap)
track_layout$ystart <- c(0, track_layout$height)[-(length(track_layout$height) + 1)] + c(0, track_layout$gap)[-(length(track_layout$gap) + 1)]
track_layout$yend <- track_layout$height + c(0, track_layout$gap)[-length(track_layout$gap)]
track_layout_chrs <- rep(data.chr$chr, length(unique(layer_index)))
track_layout_tmp <- track_layout[c("ystart", "yend")][rep(rownames(track_layout), each = length(track_layout_chrs) / length(unique(layer_index))), ]
track_layout$yend[track_layout$num == max(layer_index)] <- track_layout$yend[track_layout$num == max(layer_index)] - diff(c(0, track_layout$gap))[length(diff(c(0, track_layout$gap)))]
track_layout_tmp$chr <- track_layout_chrs
names(val_range_chr) <- c("chr", "pos")
val_range_chr <- merge(val_range_chr, track_layout_tmp, by = "chr", all.x = T)
if (chr_plotype == 1) {
val_range_chr$chr <- factor(val_range_chr$chr, levels = names(chr.cum.len), ordered = T)
val_range_chr$pos <- val_range_chr$pos + chr.cum.len[val_range_chr$chr]
val_range_chr$chr <- as.character(val_range_chr$chr)
val_range_chr <- val_range_chr[c(which(val_range_chr$pos == min(val_range_chr$pos)),
which(val_range_chr$pos == max(val_range_chr$pos))), ]
}
val_range_chr <- melt(data = val_range_chr, id.vars = c("chr", "pos"))
val_range_chr$variable <- NULL
col_dis_rand <- 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")
## *** Set ploting panel ***
p1 <- ggplot() + geom_point(data = val_range_chr, aes(pos, value), color = NA)
yaxis_breaks <- list()
yaxis_labels <- list()
## *** Set priority level of each dataset ***
indx <- lapply(c("heatmap_gradual", "heatmap_discrete", "rect_gradual", "rect_discrete", "ideogram", "bar",
"line", "segment", "point", "vertical_line", "horizontal_line", "text"), function(x) {
indx <- which(plot_type %in% x)
return(indx)
})
indx <- unlist(indx)
## *** Cyclic ploting for all tracks ***
for (i in indx) {
data.track.single <- data.track[[i]]
data.chr.sub <- data.chr
if (plot_type[i] %in% c("point", "line")) {
names(data.track.single)[1:3] <- c("chr", "pos", "value")
data.track.single$pos <- as.numeric(data.track.single$pos)
data.track.single$value <- as.numeric(data.track.single$value)
} else if (plot_type[i] %in% c("bar", "rect_gradual", "rect_discrete")) {
names(data.track.single)[1:4] <- c("chr", "xmin", "xmax", "value")
if(plot_type[i] %in% c("bar", "rect_gradual")){
data.track.single$value <- as.numeric(data.track.single$value)
}
} else if (plot_type[i] %in% c("heatmap_gradual", "heatmap_discrete")) {
raw_names <- colnames(data.track.single)[-c(1:3)]
names(raw_names) <- paste("v", 1:(ncol(data.track.single) - 3), sep = "")
colnames(data.track.single) <- c(c("chr", "xmin", "xmax"), paste("v", 1:(ncol(data.track.single) - 3), sep = ""))
data.track.single <- melt(data.track.single, id = c("chr", "xmin", "xmax"))
data.track.single$variable <- as.character(data.track.single$variable)
data.track.single$raw_names <- raw_names[data.track.single$variable]
data.track.single$variable <- as.numeric(gsub("v", "", data.track.single$variable))
colnames(data.track.single) <- c("chr", "xmin", "xmax", "value", "color", "raw_names")
if(plot_type[i] %in% "heatmap_gradual"){
data.track.single$value <- as.numeric(data.track.single$value)
data.track.single$color <- as.numeric(data.track.single$color)
}
} else if (plot_type[i] == "vertical_line") {
names(data.track.single) <- c("chr", "pos")
data.track.single$ymin <- 1
data.track.single$ymax <- 10
data.track.single$pos <- as.numeric(data.track.single$pos)
} else if (plot_type[i] == "horizontal_line") {
names(data.track.single) <- "value"
data.track.single$xmin <- 0
rep_num <- nrow(data.track.single)
names(data.chr.sub) <- c("chr", "xmin", "xmax")
data.chr.sub <- data.chr.sub[, c(1, 3)]
data.track.single <- data.track.single[rep(rownames(data.track.single), length(unique(data.chr.sub$chr))), ]
data.track.single$chr <- rep(unique(data.chr.sub$chr), each = rep_num)
data.track.single <- merge(data.track.single, data.chr.sub, by.x = "chr", all.x = T)
} else if (plot_type[i] == "text") {
names(data.track.single) <- c("chr", "pos", "value", "symbol")
data.track.single[c("pos", "value")] <- sapply(data.track.single[c("pos", "value")],as.numeric)
data.track.single$symbol <- gsub('\\"', "", data.track.single$symbol)
} else if (plot_type[i] == "segment") {
names(data.track.single)[1:5] <- c("chr", "xpos1", "ypos1", "xpos2", "ypos2")
data.track.single[c("xpos1", "ypos1", "xpos2","ypos2")] <- sapply(data.track.single[c("xpos1", "ypos1", "xpos2","ypos2")],as.numeric)
} else if (plot_type[i] == "ideogram") {
names(data.track.single)[1:5] <- c("chr", "xmin", "xmax", "value1", "value2")
}
if(plot_type[i] %in% c("bar", "rect_gradual", "rect_discrete", "heatmap_gradual", "heatmap_discrete", "horizontal_line", "ideogram")) {
data.track.single[c("xmin", "xmax")] <- sapply(data.track.single[c("xmin", "xmax")], as.numeric)
}
## *** Raw value ***
if (plot_type[i] %in% c("point", "line", "bar")) {
data.track.single$raw_value <- data.track.single$value
}
## *** Color ***
if (plot_type[i] %in% c("point", "line", "bar", "segment")) {
col_typep <- col_type[i]
if (col_typep == 2) {
data.track.single <- dat_dis_col(i, color_cus, data.track.single)
} else if (col_typep == 3 & ("color" %in% colnames(data.track.single))) {
data.track.single <- dat_cus_cols(i, color_mulgp, data.track.single)
laycolor <- unique(data.track.single$cols)
data.track.single$raw_color <- data.track.single$color
data.track.single$color <- data.track.single$cols
data.track.single$cols <- NULL
} else if (col_typep == 1 & ("color" %in% colnames(data.track.single))) {
laycolor <- laycolor.export[which(indx == i)]
laycolor <- unlist(strsplit(laycolor, "\\."))
laycolor <- data.frame(group = unique(data.track.single$color), cols = laycolor, stringsAsFactors = F)
colname <- colnames(data.track.single)
data.track.single <- merge(data.track.single, laycolor, by.x = "color", by.y = "group", all.x = T)
data.track.single <- data.track.single[c(colname, "cols")]
laycolor <- unique(data.track.single$cols)
data.track.single$raw_color <- data.track.single$color
data.track.single$color <- data.track.single$cols
data.track.single$cols <- NULL
} else{
laycolor <- laycolor.export[which(indx == i)]
laycolor <- unlist(strsplit(laycolor, "\\."))
data.track.single$color <- laycolor
}
}
## *** The color for rect_gradual plot ***
if (plot_type[i] == "rect_gradual") {
if(rect_grad_col[i] == 2){
rect_grad_cus_cols <- rect_grad_cus_2cols
}else if(rect_grad_col[i] == 3){
rect_grad_cus_cols <- rect_grad_cus_3cols
}
rect_cols <<- rect_grad_cols(i, rect_grad_col, col_rect, rect_grad_cus_cols)
}
## *** The color for rect_discrete plot ***
if (plot_type[i] == "rect_discrete") {
data.track.single <- dis_type_cols_v1(i, data.track.single, rect_col, plot_type, col_dis_rand, indx, rect_discol.export, rect_col_dis_cus, rect_col_dis)
names(data.track.single)[4] <- "raw_color"
dat_val <<- NULL
dat_col <<- NULL
data.track.single <- cols_adjust(i, data.track.single, col_transpt, plot_type, 1)
rectval_1 <- dat_val
rectcol_1 <- dat_col
}
## *** The color to fill heatmap_gradual plot ***
if (plot_type[i] == "heatmap_gradual") {
if (sel_heatmap_col[i] == 1) {
hmapcols <- gsub('\\"', "", hmap_col[i])
} else if (sel_heatmap_col[i] == 2){
hmapcols <- heatmap_col_cus_2cols[i]
} else if (sel_heatmap_col[i] == 3){
hmapcols <- heatmap_col_cus_3cols[i]
}
hmapcols <- unlist(strsplit(hmapcols, "\\."))
}
## *** The color to fill heatmap_discrete plot ***
if (plot_type[i] == "heatmap_discrete") {
data.track.single <- dis_type_cols_v1(i, data.track.single, hmap_col_dis, plot_type, col_dis_rand, indx, heatmap_discol.export, hmap_col_dis_cus)
dat_val <<- NULL
dat_col <<- NULL
data.track.single <- cols_adjust(i, data.track.single, col_transpt, plot_type, 1)
hmapval_1 <- dat_val
hmapcol_1 <- dat_col
}
## *** The color for vertical_line or horizontal_line plot ***
if (plot_type[i] %in% c("vertical_line", "horizontal_line")) {
data.track.single <- dat_dis_col(i, line_color, data.track.single)
}
## *** Color transparency ***
if (!plot_type[i] %in% c("heatmap_gradual", "heatmap_discrete", "text",
"rect_gradual", "rect_discrete", "ideogram")) {
dat_val <<- NULL
dat_col <<- NULL
data.track.single <- cols_adjust(i, data.track.single, col_transpt, plot_type, 1)
labelscol <- dat_val
breakscol <- dat_col
}
## *** Text color ***
if (plot_type[i] == "text") {
labelscol <- text_col[i]
}
## *** color to fill the area under the line ***
if (plot_type[i] == "line") {
if (fill_area[i] == 1) {
if (sel_area_type[i] == 1) {
data.track.single$areacol <- data.track.single$color
} else{
areacol <- unlist(strsplit(border_area[i], ","))
if (length(areacol) == 0) {
areacol <- rep(NA, length(unique(data.track.single$color)))
} else{
areacol <- rep(areacol, length(unique(data.track.single$color)))
areacol <- areacol[1:length(unique(data.track.single$color))]
}
areacol[!areColors(areacol)] <- NA
names(areacol) <- unique(data.track.single$color)
data.track.single$areacol <- adjustcolor(areacol[data.track.single$color], alpha.f = col_transpt[i])
}
}
}
## *** Point type and size ***
if (plot_type[i] == "point") {
if (sel_symbol_point[i] == 1) {
data.track.single$shape <- as.numeric(symbol_point[i])
} else if (sel_symbol_point[i] == 2 & (!"shape" %in% names(data.track.single))) {
data.track.single$shape <- 16
}
if (sel_point_size[i] == 1) {
data.track.single$size <- as.numeric(point_size[i])
} else if (sel_point_size[i] == 2 & (!"size" %in% names(data.track.single))) {
data.track.single$size <- 0.8
}
breakspch <- unique(data.track.single$shape[!is.na(data.track.single$value)])
labelspch <- breakspch
breakscex <- unique(data.track.single$size[!is.na(data.track.single$value)])
labelscex <- breakscex
}
## *** Line type ***
if (plot_type[i] %in% c("line", "segment", "vertical_line", "horizontal_line")) {
linetypep <- linetype[i]
labels_line_type <- linetypep
}
## *** Bars direction ***
if (plot_type[i] == "bar") {
if (all(data.track.single$raw_value < 0)) {
directbarp <- 2
} else{
directbarp <- 1
}
}
## *** Borders ***
add_borderp <- add_border[i]
if (add_borderp == 1) {
border_colp <- border_col[i]
} else{
border_colp <- NA
}
## *** Legends ***
add_col_lgd <- "none"; add_size_lgd <- "none"; add_shape_lgd <- "none"; add_line_type_lgd <- "none"
if (col_lgd[i] == 1) {
add_col_lgd <- "legend"
if (col_lgd_mdy_label[i] == 1) {
col_lgd_label_1 <- lgd_mdy_label(i, col_lgd_label)
if (!plot_type[i] %in% c("heatmap_gradual", "heatmap_discrete", "text", "rect_gradual", "rect_discrete", "ideogram")) {
col_lgd_label_1 <- rep(col_lgd_label_1, length(breakscol))[1:length(breakscol)]
names(col_lgd_label_1) <- labelscol
data.track.single$raw_color <- as.character(data.track.single$raw_color)
data.track.single$raw_color <- col_lgd_label_1[data.track.single$raw_color]
labelscol <- unname(col_lgd_label_1)
data.track.single$raw_color <- factor(data.track.single$raw_color, levels = unique(labelscol), ordered = T)
} else if (plot_type[i] == "rect_discrete") {
col_lgd_label_1 <- rep(col_lgd_label_1, length(rectcol_1))[1:length(rectcol_1)]
names(col_lgd_label_1) <- rectval_1
data.track.single$raw_color <- as.character(data.track.single$raw_color)
data.track.single$raw_color <- col_lgd_label_1[data.track.single$raw_color]
rectval_1 <- unname(col_lgd_label_1)
data.track.single$raw_color <- factor(data.track.single$raw_color, levels = unique(rectval_1), ordered = T)
} else if (plot_type[i] == "heatmap_discrete") {
col_lgd_label_1 <- rep(col_lgd_label_1, length(hmapcol_1))[1:length(hmapcol_1)]
names(col_lgd_label_1) <- hmapval_1
hmapval_1 <- unname(col_lgd_label_1)
} else if (plot_type[i] == "text") {
labelscol <- col_lgd_label_1[1]
}
}
}
if (plot_type[i] == "point" && size_lgd[i] == 1) {
add_size_lgd <- "legend"
if (size_lgd_mdy_label[i] == 1) {
size_lgd_labelp <- lgd_mdy_label(i, size_lgd_label)
labelscex <- rep(size_lgd_labelp, length(breakscex))[1:length(breakscex)]
}
}
if (plot_type[i] == "point" && shape_lgd[i] == 1) {
add_shape_lgd <- "legend"
if (shape_lgd_mdy_label[i] == 1) {
shape_lgd_labelp <- lgd_mdy_label(i, shape_lgd_label)
labelspch <- rep(shape_lgd_labelp, length(breakspch))[1:length(breakspch)]
}
}
if (plot_type[i] %in% c("vertical_line", "horizontal_line") && line_type_lgd[i] == 1) {
add_line_type_lgd <- "legend"
if (line_type_lgd_mdy_label[i] == 1) {
line_type_lgd_labelp <- lgd_mdy_label(i, line_type_lgd_label)
labels_line_type <- rep(line_type_lgd_labelp, length(linetypep))[1:length(linetypep)]
}
}
## *** Legend of fill area ***
if (plot_type[i] == "line" & fill_area[i] == 1 & add_col_lgd == "legend") {
data.track.single$raw_areacol <- as.character(data.track.single$raw_color)
raw_areacol_1 <- unique(data.track.single$raw_areacol[!is.na(data.track.single$value)])
areacol_1 <- data.track.single$areacol[match(raw_areacol_1, data.track.single$raw_areacol)]
raw_areacol_1 <- raw_areacol_1[!duplicated(areacol_1)]
areacol_1 <- areacol_1[!duplicated(areacol_1)]
data.track.single$areacol <- factor(data.track.single$areacol, levels = areacol_1, ordered = T)
data.track.single$raw_areacol <- factor(data.track.single$raw_areacol, levels = raw_areacol_1, ordered = T)
}
## *** Number of chromosomes ***
data.track.single$layer <- layer_index[i]
data.track.single <- merge(data.track.single, track_layout, by.x = "layer", by.y = "num", all.x = T)
if (!plot_type[i] %in% c("rect_gradual", "rect_discrete", "heatmap_gradual",
"heatmap_discrete", "vertical_line", "ideogram")) {
min_val <- val_range$min_val[val_range$layer == layer_index[i]]
max_val <- val_range$max_val[val_range$layer == layer_index[i]]
if (min_val > 0 & plot_type[i] == "horizontal_line" & length(which(layer_index == layer_index[i])) == 1) {
fold_1 <- abs(as.numeric(height_layer[names(height_layer) == layer_index[i]]) / (1.02 * max_val))
} else{
if (max_val != min_val) {
fold_1 <- abs(as.numeric(height_layer[names(height_layer) == layer_index[i]]) / (1.02 * (max_val - min_val)))
} else if (max_val == min_val & max_val == 0) {
fold_1 <- abs(as.numeric(height_layer[names(height_layer) == layer_index[i]]) / 1.02)
} else if (max_val == min_val & max_val != 0) {
fold_1 <- abs(as.numeric(height_layer[names(height_layer) == layer_index[i]]) / (1.02 * max_val))
}
}
if (min_val < 0) {
minnum_1 <- unique(abs(min_val) * fold_1 + data.track.single$ystart)
} else{
minnum_1 <- unique(data.track.single$ystart)
}
minnum_p <- minnum_1
if (plot_type[i] == "segment") {
if (min_val < 0) {
data.track.single$ypos1 <- data.track.single$ypos1 + abs(min_val)
data.track.single$ypos2 <- data.track.single$ypos2 + abs(min_val)
}
data.track.single$ypos1 <- data.track.single$ypos1 * fold_1 + data.track.single$ystart
data.track.single$ypos2 <- data.track.single$ypos2 * fold_1 + data.track.single$ystart
} else{
if (min_val < 0) {
data.track.single$value <- data.track.single$value + abs(min_val)
}
data.track.single$yvalue <- data.track.single$value * fold_1 + data.track.single$ystart
}
minnum_p <- minnum_1
}
if (plot_type[i] == "heatmap_gradual") {
fold_2 <- as.numeric(height_layer[names(height_layer) == layer_index[i]]) / max(data.track.single$value, na.rm = T)
data.track.single$yvalue <- fold_2 * data.track.single$value - fold_2 / 2 + data.track.single$ystart[1]
}
if (plot_type[i] == "heatmap_discrete") {
fold_2 <- as.numeric(height_layer[names(height_layer) == layer_index[i]]) / max(as.numeric(as.character(data.track.single$value)), na.rm = T)
data.track.single$yvalue1 <- fold_2 * as.numeric(as.character(data.track.single$value)) - fold_2 + data.track.single$ystart[1]
data.track.single$yvalue2 <- fold_2 * as.numeric(as.character(data.track.single$value)) + data.track.single$ystart[1]
}
if (plot_type[i] %in% c("heatmap_gradual", "heatmap_discrete")) {
data.track.single$xpos <- (data.track.single$xmin + data.track.single$xmax) / 2
data.track.single$width <- (data.track.single$xmax - data.track.single$xpos) * 2
}
data.track.single.lgd <- data.track.single
data.track.single <- data.track.single[data.track.single$chr %in% chr_order,]
## *** Fix the chromosomes order ***
data.track.single$chr.f <- factor(data.track.single$chr, levels = chr_order, ordered = T)
data.track.single.lgd$chr <- factor(data.track.single.lgd$chr, levels = names(chr.cum.len), ordered = T)
## *** The position of concatenated chromosomes ***
if (plot_type[i] %in% c("point", "line", "vertical_line", "text")) {
data.track.single.lgd$pos <- data.track.single.lgd$pos + chr.cum.len[data.track.single.lgd$chr]
} else if (plot_type[i] == "horizontal_line") {
data.track.single.lgd$xmax <- data.track.single.lgd$xmax + chr.cum.len[data.track.single.lgd$chr]
data.track.single.lgd <- data.track.single.lgd[c("chr", "xmin", "xmax", "yvalue", "color")]
data.track.single.lgd <- data.track.single.lgd[which(data.track.single.lgd$xmax == max(data.track.single.lgd$xmax, na.rm = T)), ]
} else if (plot_type[i] == "segment") {
data.track.single.lgd$xpos1 <- data.track.single.lgd$xpos1 + chr.cum.len[data.track.single.lgd$chr]
data.track.single.lgd$xpos2 <- data.track.single.lgd$xpos2 + chr.cum.len[data.track.single.lgd$chr]
} else if (plot_type[i] %in% c("rect_gradual", "rect_discrete", "ideogram")) {
data.chr.ideo <- data.chr
data.chr.ideo$start <- data.chr.ideo$start + chr.cum.len[data.chr.ideo$chr]
data.chr.ideo$size <- data.chr.ideo$size + chr.cum.len[data.chr.ideo$chr]
}
if (plot_type[i] %in% c("bar", "rect_gradual", "rect_discrete", "heatmap_gradual", "heatmap_discrete", "ideogram")) {
data.track.single.lgd$xmin <- data.track.single.lgd$xmin + chr.cum.len[data.track.single.lgd$chr]
data.track.single.lgd$xmax <- data.track.single.lgd$xmax + chr.cum.len[data.track.single.lgd$chr]
}
if (plot_type[i] %in% c("heatmap_gradual", "heatmap_discrete")) {
data.track.single.lgd$xpos <- (data.track.single.lgd$xmin + data.track.single.lgd$xmax) / 2
data.track.single.lgd$width <- (data.track.single.lgd$xmax - data.track.single.lgd$xpos) * 2
data.track.single$xpos <- (data.track.single$xmin + data.track.single$xmax) / 2
data.track.single$width <- (data.track.single$xmax - data.track.single$xpos) * 2
}
data.track.single.lgd$chr <- as.character(data.track.single.lgd$chr)
## *** Concatenated chromosomes or Separated chromosomes ***
if (chr_plotype == 1) {
data.track.single <- data.track.single.lgd
}
## *** Point ***
if (plot_type[i] == "point") {
if (any(c(add_col_lgd, add_size_lgd, add_shape_lgd) == "legend")) {
if (is.numeric(labelscex)) {
labelscex <- sprintf("%.1f", sort(labelscex))
}
if (is.numeric(labelspch)) {
labelspch <- sort(labelspch)
}
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_point(data = data.track.single.lgd, aes(pos, yvalue, color = color, shape = as.character(shape), size = size))
lg1 <- lg1 + scale_color_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + scale_size_identity(name = size_lgd_name[i], guide = add_size_lgd, breaks = sort(breakscex), labels = labelscex)
lg1 <- lg1 + scale_shape_manual(name = shape_lgd_name[i], guide = add_shape_lgd, values = sort(breakspch), labels = labelspch)
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
lg1 <- lg1 + guides(color = guide_legend(order = 1), size = guide_legend(order = 2))
} else{
lg1 <- ggplot() + geom_point(data = data.track.single.lgd, aes(pos, yvalue, color = color, shape = as.character(shape), size = size))
lg1 <- lg1 + scale_color_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + scale_size_identity(name = size_lgd_name[i], guide = add_size_lgd, breaks = sort(breakscex), labels = labelscex)
lg1 <- lg1 + scale_shape_manual(name = shape_lgd_name[i], guide = add_shape_lgd, values = sort(breakspch), labels = labelspch)
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
lg1 <- lg1 + guides(color = guide_legend(order = 1), size = guide_legend(order = 2))
}
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
for (f in unique(data.track.single$chr)) {
dat <- data.track.single[data.track.single$chr %in% f, ]
p1 <- p1 + geom_point(data = dat, aes(pos, yvalue), color = as.character(dat$color), shape = dat$shape, size = as.numeric(dat$size))
}
}
## *** Line ***
if (plot_type[i] == "line") {
if (length(unique(data.track.single.lgd$color)) > 1) {
linetypep <- "solid"
}
if (fill_area[i] == 2) {
if (add_col_lgd == "legend") {
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_line(data = data.track.single.lgd, aes(pos, yvalue, color = color), size = line_size[i], linetype = linetypep)
lg1 <- lg1 + scale_color_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
} else{
lg1 <- ggplot() + geom_line(data = data.track.single.lgd, aes(pos, yvalue, color = color), size = line_size[i], linetype = linetypep)
lg1 <- lg1 + scale_color_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
}
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
for (f in unique(data.track.single$chr)) {
for (j in unique(data.track.single$color[data.track.single$chr %in% f])) {
dat <- data.track.single[data.track.single$chr %in% f & data.track.single$color %in% j, ]
p1 <- p1 + geom_line(data = dat, aes(pos, yvalue), color = as.character(dat$color), size = line_size[i], linetype = linetypep)
}
}
} else{
if (add_col_lgd == "legend") {
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_line(data = data.track.single.lgd, aes(pos, yvalue), color = as.character(data.track.single.lgd$color),
size = line_size[i], linetype = linetypep)
lg1 <- lg1 + geom_area(data = data.track.single.lgd, aes(x = pos, y = yvalue, fill = areacol))
lg1 <- lg1 + scale_fill_identity( name = col_lgd_name[i], guide = add_col_lgd, breaks = areacol_1, labels = raw_areacol_1)
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
} else{
lg1 <- ggplot() + geom_line(data = data.track.single.lgd, aes(pos, yvalue), color = as.character(data.track.single.lgd$color),
size = line_size[i], linetype = linetypep)
lg1 <- lg1 + geom_area(data = data.track.single.lgd, aes(x = pos, y = yvalue, fill = areacol))
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = areacol_1, labels = raw_areacol_1)
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
}
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
for (f in unique(data.track.single$chr)) {
for (j in unique(data.track.single$color[data.track.single$chr %in% f])) {
dat <- data.track.single[data.track.single$chr %in% f & data.track.single$color %in% j, ]
p1 <- p1 + geom_line(data = dat, aes(pos, yvalue), color = as.character(j), size = line_size[i], linetype = linetypep)
p1 <- p1 + geom_ribbon(data = dat, aes(x = pos), ymin = pmin(dat$yvalue, minnum_p), fill = unique(as.character(dat$areacol)), ymax = minnum_p)
p1 <- p1 + geom_ribbon(data = dat, aes(x = pos), ymax = pmax(dat$yvalue, minnum_p), fill = unique(as.character(dat$areacol)), ymin = minnum_p)
}
}
}
}
## *** Bar ***
if (plot_type[i] == "bar") {
if (max(data.track[[i]][, 4], na.rm = T) <= 0 | min(data.track[[i]][, 4], na.rm = T) >= 0) {
if (directbarp == 1) {
if (length(which(layer_index == layer_index[i])) > 1) {
if (add_col_lgd == "legend") {
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymax = yvalue, fill = color),
ymin = data.track.single.lgd$ystart + minnum_1, color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
} else{
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymax = yvalue, fill = color),
ymin = data.track.single.lgd$ystart + minnum_1, color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
}
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
for (f in unique(data.track.single$chr)) {
for (j in unique(data.track.single$color[data.track.single$chr %in% f])) {
dat <- data.track.single[data.track.single$chr %in% f & data.track.single$color %in% j, ]
p1 <- p1 + geom_rect(data = dat, aes(xmin = xmin, xmax = xmax, ymax = yvalue), ymin = dat$ystart[1],
fill = as.character(dat$color), color = border_colp)
}
}
} else{
if (add_col_lgd == "legend") {
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yvalue,
fill = color), color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
} else{
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yvalue,
fill = color), color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
}
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
for (f in unique(data.track.single$chr)) {
for (j in unique(data.track.single$color[data.track.single$chr %in% f])) {
dat <- data.track.single[data.track.single$chr %in% f & data.track.single$color %in% j, ]
p1 <- p1 + geom_rect(data = dat, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yvalue),
fill = as.character(dat$color), color = border_colp)
}
}
}
} else if (directbarp == 2) {
if (add_col_lgd == "legend") {
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymax = yvalue, fill = color),
ymin = minnum_1, color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
} else{
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymax = yvalue, fill = color),
ymin = minnum_1, color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
}
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
for (f in unique(data.track.single$chr)) {
for (j in unique(data.track.single$color[data.track.single$chr %in% f])) {
dat <- data.track.single[data.track.single$chr %in% f & data.track.single$color %in% j, ]
p1 <- p1 + geom_rect(data = dat, aes(xmin = xmin, xmax = xmax, ymax = yvalue), ymin = minnum_p,
fill = as.character(dat$color), color = border_colp)
}
}
}
} else{
if (min_val < 0) {
if (add_col_lgd == "legend") {
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymax = yvalue, fill = color),
ymin = minnum_1, color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
} else{
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymax = yvalue, fill = color),
ymin = minnum_1, color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
}
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
for (f in unique(data.track.single$chr)) {
for (j in unique(data.track.single$color[data.track.single$chr %in% f])) {
dat <- data.track.single[data.track.single$chr %in% f & data.track.single$color %in% j, ]
p1 <- p1 + geom_rect(data = dat, aes(xmin = xmin, xmax = xmax, ymax = yvalue), ymin = minnum_p,
fill = as.character(dat$color), color = border_colp)
}
}
} else{
if (add_col_lgd == "legend") {
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yvalue,
fill = color), color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
} else{
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yvalue,
fill = color), color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = breakscol, labels = labelscol)
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
}
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
for (f in unique(data.track.single$chr)) {
for (j in unique(data.track.single$color[data.track.single$chr %in% f])) {
dat <- data.track.single[data.track.single$chr %in% f & data.track.single$color %in% j, ]
p1 <- p1 + geom_rect(data = dat, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yvalue),
fill = as.character(dat$color), color = border_colp)
}
}
}
}
}
## *** Rect_gradual ***
if (plot_type[i] == "rect_gradual") {
if (is.numeric(data.track.single.lgd$value)) {
midpoint <- mean(data.track.single.lgd$value, na.rm = T)
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yend,
fill = value), color = border_colp)
if(rect_grad_col[i] == 2){
lg1 <- lg1 + scale_fill_gradient(name = col_lgd_name[i], low = rect_cols[1], high = rect_cols[2], na.value = "#FFFFFF00")
} else{
lg1 <- lg1 + scale_fill_gradient2(name = col_lgd_name[i], low = rect_cols[1], midpoint = midpoint,
mid = rect_cols[2], high = rect_cols[3], na.value = "#FFFFFF00")
}
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
} else{
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yend,
fill = value), color = border_colp)
if(rect_grad_col[i] == 2){
lg1 <- lg1 + scale_fill_gradient(name = col_lgd_name[i], low = rect_cols[1], high = rect_cols[2], na.value = "#FFFFFF00")
} else{
lg1 <- lg1 + scale_fill_gradient2(name = col_lgd_name[i], low = rect_cols[1], midpoint = midpoint,
mid = rect_cols[2], high = rect_cols[3], na.value = "#FFFFFF00")
}
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
lg1 <- lg1 + guides(fill = guide_colourbar(title.vjust = 0.8, title.hjust = 0.4))
}
g1 <- ggplot_build(lg1)
data.track.single$fillcol <- g1$data[[1]][, "fill"]
if (add_col_lgd == "legend") {
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
p1 <- p1 + geom_rect(data = data.track.single, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yend),
fill = as.character(data.track.single$fillcol), color = border_colp)
} else{
assign(paste("legend", i, sep = ""), NA)
}
}
## *** Rect_discrete ***
if (plot_type[i] == "rect_discrete") {
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yend,
fill = color), color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = rectcol_1, labels = rectval_1)
lg1 <- lg1 + theme(legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
} else{
lg1 <- ggplot() + geom_rect(data = data.track.single.lgd, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yend,
fill = color), color = border_colp)
lg1 <- lg1 + scale_fill_identity(name = col_lgd_name[i], guide = add_col_lgd, breaks = rectcol_1, labels = rectval_1)
lg1 <- lg1 + theme(legend.position = "bottom", legend.title = element_text(size = lgd_title_size, face = lgd_title_font_face),
legend.text = element_text(size = lgd_text_size, face = lgd_text_font_face), legend.key = element_rect(fill = NA))
}
if (add_col_lgd == "legend") {
assign(paste("legend", i, sep = ""), g_legend(lg1))
} else{
assign(paste("legend", i, sep = ""), NA)
}
for (f in unique(data.track.single$chr)) {
dat <- data.track.single[data.track.single$chr %in% f, ]
p1 <- p1 + geom_rect(data = dat, aes(xmin = xmin, xmax = xmax, ymin = ystart, ymax = yend),
fill = as.character(dat$color), color = border_colp)
}
}
## *** Heatmap_gradual ***
if (plot_type[i] == "heatmap_gradual") {
midpoint <- mean(data.track.single.lgd$color, na.rm = T)
if (lgd_pos == 1) {
lg1 <- ggplot() + geom_tile(data = data.track.single.lgd, aes(x = xpos, y = yvalue, fill = color), width = data.track.single.lgd$width,
height = as.numeric(height_layer[names(height_layer) == layer_index[i]]), color = border_colp)
if(sel_heatmap_col[i] == 2){
lg1 <- lg1 + scale_fill_gradient(name = col_lgd_name[i], low = hmapcols[1], high = hmapcols[2], na.value = "#FFFFFF00")
}else{