R/utils.R

In jokergoo/circlize: Circular Visualization

# == title
# Convert to polar coordinate system
#
# == param
# -x            Data points on x-axis. The value can also be a two-column matrix/data frame if you put x and y data points into one variable.
# -y            Data points on y-axis.
# -sector.index Index for the sector to convert the coordinates.
# -track.index  Index for the track to convert the coordinates.
#
# == details
# This is the core function in the package. It transform data points from data coordinate system (in a specific cell) to the polar coordinate system.
#
# == values
# A matrix with two columns (``theta`` and ``rou``). ``rou`` is measured in degree.
#
# == example
# pdf(NULL)
# sectors = c("a", "b")
# circos.initialize(sectors, xlim = c(0, 1))
# circos.track(ylim = c(0, 1))
# # x = 0.5, y = 0.5 in sector a and track 1
# circlize(0.5, 0.5, sector.index = "a", track.index = 1)
# circos.clear()
# dev.off()
circlize = function(
    x, y, 
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index()) {

    if(missing(y)) {
        if(ncol(x) >= 2) {
            y = x[, 2]
            x = x[, 1]
        }
    }
    
    sector.data = get.sector.data(sector.index)
       
    theta = sector.data["start.degree"] - (x - sector.data["min.value"]) / (sector.data["max.value"] - sector.data["min.value"]) *
            abs(sector.data["start.degree"] - sector.data["end.degree"])

    if(!circos.par("xaxis.clock.wise")) {
        theta = sector.data["start.degree"] - theta + sector.data["end.degree"]
    }
    
	if(track.index == 0) {
		rou = rep(1, length(theta))
	} else {
		cell.data = get.cell.data(sector.index, track.index)
		cell.ylim = get.cell.meta.data("cell.ylim", sector.index, track.index)  
		y.range = cell.ylim[2] - cell.ylim[1] 
		rou = cell.data$track.start - (cell.ylim[2] - y) / y.range * cell.data$track.height
    }
	
    m = cbind(theta, rou)
    colnames(m) = c("theta", "rou")
    rownames(m) = NULL
    
    return(m)
}

# == title
# Convert to data coordinate system
#
# == param
# -x   degree values. The value can also be a two-column matrix/data frame if you put x and y data points into one variable.
# -y   distance to the circle center (the radius)
# -sector.index Index for the sector where the data coordinate is used
# -track.index  Index for the track where the data coordinate is used
#
# == details
# This is the reverse function of `circlize`. It transform data points from polar coordinate system to a specified data coordinate system.
#
# == values
# A matrix with two columns (``x`` and ``y``)
# 
# == example
# pdf(NULL)
# sectors = letters[1:4]
# circos.initialize(sectors, xlim = c(0, 1))
# circos.trackPlotRegion(ylim = c(0, 1))
# reverse.circlize(c(30, 60), c(0.9, 0.8))
# reverse.circlize(c(30, 60), c(0.9, 0.8), sector.index = "d", track.index = 1)
# reverse.circlize(c(30, 60), c(0.9, 0.8), sector.index = "a", track.index = 1)
# circos.clear()
# dev.off()
reverse.circlize = function(
    x, y, 
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index()) {

    if(missing(y)) {
        if(ncol(x) >= 2) {
            y = x[, 2]
            x = x[, 1]
        }
    }

    theta = x
    rou = y

	sector.data = get.sector.data(sector.index)
    if(track.index > 0) {
        cell.data = get.cell.data(sector.index, track.index)
    	cell.ylim = get.cell.meta.data("cell.ylim", sector.index, track.index)
	}

	x = (sector.data["start.degree"] - theta) / abs(sector.data["end.degree"] - sector.data["start.degree"]) *
	    (sector.data["max.value"] - sector.data["min.value"]) + sector.data["min.value"]

    if(!circos.par("xaxis.clock.wise")) {
        x = sector.data["max.value"] - x + sector.data["min.value"]
    }

	if(track.index > 0) {
        y = (cell.data$track.height - (cell.data$track.start - rou)) / cell.data$track.height * (cell.ylim[2] - cell.ylim[1]) + cell.ylim[1]
	} else {
        y = rep(1, length(x))
    }
	m = cbind(x, y)
	colnames(m) = c("x", "y")
	rownames(m) = NULL
	return(m)
}

polar2Cartesian = function(d) {
    theta = as.radian(d[, 1])
    rou = d[, 2]
    x = rou * cos(theta)
    y = rou * sin(theta)
    return(cbind(x, y))
}

# expand breakpoints in two points to draw an arc
# x and y are transformed and re-mapped points
lines.expand = function(x, y, sector.index = get.current.sector.index(), track.index = get.current.track.index()) {
    sector.data = get.sector.data(sector.index)
	cell.data = get.cell.data(sector.index, track.index)
    nx = x[1]
    ny = y[1]
	
    for(i in seq_along(x)) {
        if(i == 1) {
            next   
        }
        if(is.na(x[i]) || is.na(y[i])) {
        	nx = c(nx, NA)
        	ny = c(ny, NA)
        	next
        }
        if(is.na(x[i-1]) || is.na(y[i-1])) {
        	next
        }
	
		td = cbind(c(x[i-1], x[i]), c(y[i-1], y[i]))
        td = td[order(td[, 1]), ]
		td2 = circlize(td[, 1], td[, 2], sector.index = sector.index, track.index = track.index)
		
		a = as.radian(abs(td2[1, 1] - td2[2, 1]))
		b = abs(td2[1, 2] - td2[2, 2])
		l = sqrt(a^2 + b^2)
		
		ncut = l/ (2*pi/circos.par("unit.circle.segments"))
        ncut = floor(ncut)

		if(ncut) {
			j = seq_len(ncut) / (ncut + 1)
				
			nx = c(nx, x[i-1] + (x[i] - x[i-1])*j, x[i])
			ny = c(ny, y[i-1] + (y[i] - y[i-1])*j, y[i])
		} else {
            nx = c(nx, x[i])
            ny = c(ny, y[i])
        }
    }
   
    d = cbind(nx, ny)
    return(d)
}

# if x has same length as levels of factors
# the order of x is same as the order of levels
recycle.with.factors = function(x, factors) {
    le = levels(factors)
    if(length(x) == 1) {
        x = rep(x, length(factors))
    } else if(length(x) == length(le)) {
        b = factors
        levels(b) = x
        x = as.vector(b)
    }
    return(x)
}

recycle.with.levels = function(x, levels) {
    
    if(length(x) == 1) {
        x = rep(x, length(levels))
    } 
    return(x)
}

check.track.position = function(track.index, track.start, track.height) {

    track.margin = circos.par("track.margin")
    if(track.start - track.height - track.margin[2] < 0 ||
       track.start - track.height < 0 ||
       track.start < 0) {
        stop_wrap(paste("not enough space for cells at track index '", track.index, "'.\n", sep = ""))
    }
    if(track.start - track.margin[1] - track.height - track.margin[2] < 0) {
        stop_wrap(paste("not enough space for bottom margin of cells at track index '", track.index, "'.\n", sep = ""))
    }
    
    if(track.index > 1) {
        
        if(track.start > get.cell.meta.data("cell.bottom.radius", track.index = track.index - 1)) {
            stop_wrap("Track overlaps with previous track.\n")
        }
    }
}

check.points.position = function(x, y, sector.index = get.cell.meta.data("sector.index"),
	track.index = get.cell.meta.data("track.index")) {
        
    cell.xlim = get.cell.meta.data("cell.xlim", sector.index, track.index)
    cell.ylim = get.cell.meta.data("cell.ylim", sector.index, track.index)
    
    l = is.na(x) | is.na(y)
    x = x[!l]
    y = y[!l]

    xrange = cell.xlim[2] - cell.xlim[1]
    yrange = cell.ylim[2] - cell.ylim[1]
    l1 = x < cell.xlim[1] | x > cell.xlim[2]
    l2 = y < cell.ylim[1] | y > cell.ylim[2]
    l = l1 | l2
    if(sum(l) && circos.par("points.overflow.warning")) {
        message_wrap(paste("Note: ", sum(l), " point", ifelse(sum(l) == 1, " is", "s are"), " out of plotting region in sector '", sector.index, "', track '", track.index, "'.\n", sep = ""))
    }

    return(invisible(NULL))
}

as.radian = function(degree) {
	return(degree/180*pi)
}

as.degree = function(radian) {
	return(radian/pi*180)
}


# == title
# Color interpolation
#
# == param
# -breaks A vector indicating numeric breaks
# -colors A vector of colors which correspond to values in ``breaks``
# -transparency A single value in ``[0, 1]``. 0 refers to no transparency and 1 refers to full transparency
# -space color space in which colors are interpolated. Value should be one of "RGB", "LAB", "XYZ", "sRGB", "LUV", see `colorspace::color-class` for detail.
# -hcl_palette Name of the HCL palette. Value should be supported in `grDevices::hcl.pals`.
# -reverse Whether should the colors in ``hcl_palette`` be reversed.
#
# == details
# Colors are linearly interpolated according to break values and corresponding colors through CIE Lab color space (`colorspace::LAB`) by default. 
# Values exceeding breaks will be assigned with corresponding maximum or minimum colors.
#
# == values
# It returns a function which accepts a vector of numeric values and returns interpolated colors.
#
# == seealso
# `col2value` converts back to the original values by providing the color mapping function generated by `colorRamp2`.
#
# == example
# col_fun = colorRamp2(c(-1, 0, 1), c("green", "white", "red"))
# col_fun(c(-2, -1, -0.5, 0, 0.5, 1, 2))
colorRamp2 = function(breaks, colors, transparency = 0, space = "LAB", 
    hcl_palette = NULL, reverse = FALSE) {

    breaks_o = breaks
    if(!is.null(hcl_palette)) {
        breaks = sort(breaks)
        if(length(breaks) == 2) {
            breaks2 = seq(breaks[1], breaks[2], length = 1000)
            colors = hcl.colors(1000, palette = hcl_palette, rev = reverse)
        } else {
            nb = length(breaks)
            nl = ceiling(1000/nb)
            breaks2 = seq(breaks[1], breaks[2], length = nl)
            for(i in 2:(nb-1)) {
                breaks2  = c(breaks2, seq(breaks[i], breaks[i+1], length = nl)[-1])
            }
            colors = hcl.colors(length(breaks2), palette = hcl_palette, rev = reverse)
        }
        breaks_o = breaks
        breaks = breaks2
    }

    if(length(breaks) != length(colors)) {
        stop_wrap("Length of `breaks` should be equal to `colors`.\n")
    }

    od = order(breaks)
    breaks = breaks[od]

    colors = colors[od]
    
    l = duplicated(breaks)
    breaks = breaks[!l]
    colors = colors[!l]

    if(length(breaks) == 1) {
        stop_wrap("You should have at least two distinct break values.")
    } 


    if(! space %in% c("RGB", "LAB", "XYZ", "sRGB", "LUV", "HLS")) {
        stop_wrap("`space` should be in 'RGB', 'LAB', 'XYZ', 'sRGB', 'LUV'")
    }

    colors = t(col2rgb(colors)/255)

    
    if(space == "LUV") {
        i = which(apply(colors, 1, function(x) all(x == 0)))
        colors[i, ] = 1e-5
    }

    transparency = 1-ifelse(transparency > 1, 1, ifelse(transparency < 0, 0, transparency))[1]
    transparency_str = sprintf("%X", round(transparency*255))
    if(nchar(transparency_str) == 1) transparency_str = paste0("0", transparency_str)

    fun = function(x = NULL, return_rgb = FALSE, max_value = 1) {
        if(is.null(x)) {
            stop_wrap("Please specify `x`\n")
        }

        att = attributes(x)
        if(is.data.frame(x)) x = as.matrix(x)

        l_na = is.na(x)
        if(all(l_na)) {
            return(rep(NA, length(l_na)))
        }

        x2 = x[!l_na]

        x2 = ifelse(x2 < breaks[1], breaks[1],
                   ifelse(x2 > breaks[length(breaks)], breaks[length(breaks)],
                          x2
                   ))
        ibin = .bincode(x2, breaks, right = TRUE, include.lowest = TRUE)
        res_col = character(length(x2))
        for(i in unique(ibin)) {
            l = ibin == i
            res_col[l] = .get_color(x2[l], breaks[i], breaks[i+1], colors[i, ], colors[i+1, ], space = space)
        }
        res_col = paste(res_col, transparency_str[1], sep = "")

        if(return_rgb) {
            res_col = t(col2rgb(as.vector(res_col), alpha = TRUE)/255)
            return(res_col)
        } else {
            res_col2 = character(length(x))
            res_col2[l_na] = NA
            res_col2[!l_na] = res_col

            attributes(res_col2) = att
            return(res_col2)
        }
    }

    attr = list(breaks = breaks_o, colors = fun(breaks_o), transparency = 1-transparency, space = space)

    attributes(fun) = attr
    return(fun)
}

.restrict_in = function(x, lower, upper) {
    x[x > upper] = upper
    x[x < lower] = lower
    x
}

# x: vector
# break1 single value
# break2 single value
# rgb1 vector with 3 elements
# rgb2 vector with 3 elements
.get_color = function(x, break1, break2, col1, col2, space) {

    col1 = coords(as(sRGB(col1[1], col1[2], col1[3]), space))
    col2 = coords(as(sRGB(col2[1], col2[2], col2[3]), space))

    res_col = matrix(ncol = 3, nrow = length(x))
    for(j in 1:3) {
    xx = (x - break2)*(col2[j] - col1[j]) / (break2 - break1) + col2[j]
    res_col[, j] = xx
    }

    res_col = get(space)(res_col)
    res_col = coords(as(res_col, "sRGB"))
    res_col[, 1] = .restrict_in(res_col[,1], 0, 1)
    res_col[, 2] = .restrict_in(res_col[,2], 0, 1)
    res_col[, 3] = .restrict_in(res_col[,3], 0, 1)
    hex(sRGB(res_col))
}

# will be considered in the future
circos.approx = function(x, y, resolution = 0.1, sector.index = get.cell.meta.data("sector.index"),
	track.index = get.cell.meta.data("track.index"),
	approxFun = function(x) sample(x, 1)) {
	
	od = order(x)
	x = x[od]
	y = y[od]
	
	xplot = get.cell.meta.data("xplot", sector.index = sector.index, track.index = track.index)
	cell.xlim = get.cell.meta.data("cell.xlim", sector.index = sector.index, track.index = track.index)
	
	window.size = resolution/(xplot[1] - xplot[2])*(cell.xlim[2] - cell.xlim[1])
	window = seq(cell.xlim[1], cell.xlim[2], by = window.size)
	
	newx = rep(NA, length(x))
	newy = rep(NA, length(y))
	
	for(i in seq_along(window)[-1]) {
		l = x >= window[i-1] & x < window[i]
		# if there are points in current window
		if(sum(l)) {
			newx[i] = (window[i-1] + window[i])/2
			newy[i] = approxFun(y[l])
		}
	}
	
	newx = newx[!is.na(newx)]
	newy = newy[!is.na(newy)]
	
	return(list(x = newx, y = newy))
}

# == title
# Add transparency to colors
#
# == param
# -col A vector of colors.
# -transparency Transparency, numeric value between 0 and 1.
#
# == value
# A vector of colors.
#
# == example
# add_transparency("red", 0.5)
# add_transparency(1, 0.5)
# add_transparency("#FF000080", 0.2)
add_transparency = function (col, transparency = 0) {
    rgb(t(col2rgb(col)/255), alpha = 1 - transparency)
}

# == title
# Get the inside radius of the most inner track
#
get_most_inside_radius = function() {
	tracks = get.all.track.index()
	if(length(tracks) == 0) {
	    1
	} else {
	    n = length(tracks)
	    get.cell.meta.data("cell.bottom.radius", track.index = tracks[n]) - get.cell.meta.data("track.margin", track.index = tracks[n])[1] - circos.par("track.margin")[2]
	}
}

# == title
# Convert adjacency list to an adjacency matrix
#
# == param
# -lt A data frame which contains adjacency list.
# -square Should the returned matrix be a square matrix?
#
# == example
# set.seed(123)
# df = data.frame(from = sample(letters, 10, replace = TRUE), 
#                 to = sample(letters, 10, replace = TRUE), 
#                 value = 1:10)
# adjacencyList2Matrix(df)
# adjacencyList2Matrix(df, square = TRUE)
adjacencyList2Matrix = function(lt, square = FALSE) {
	lt = as.data.frame(lt)
	if(ncol(lt) == 2) {
		lt = cbind(lt, rep(1, nrow(lt)))
	}
	if(ncol(lt) < 3) {
		stop_wrap("`lt` should be a data frame with three columns")
	}

	if(!is.numeric(lt[[3]])) {
		stop_wrap("Third column in `lt` should be numeric.")
	}

	lt[[1]] = as.vector(lt[[1]])
	lt[[2]] = as.vector(lt[[2]])

	rn = unique(lt[[1]])
	cn = unique(lt[[2]])

	if(square) {
		nm = union(rn, cn)
		mat = matrix(0, ncol = length(nm), nrow = length(nm))
		rownames(mat) = nm
		colnames(mat) = nm
	} else {
		mat = matrix(0, ncol = length(cn), nrow = length(rn))
		rownames(mat) = rn
		colnames(mat) = cn
	}

	for(i in seq_len(nrow(lt))) {
		mat[lt[i, 1], lt[i, 2]] = lt[i, 3]
	}

	return(mat)
}


# == title
# Convert adjacency matrix to an adjacency list
#
# == param
# -mat A numeric matrix.
# -keep.zero Whether to keep the interactions with value zero.
#
# == example
# set.seed(999)
# mat = matrix(sample(18, 18), 3, 6) 
# rownames(mat) = paste0("S", 1:3)
# colnames(mat) = paste0("E", 1:6)
# adjacencyMatrix2List(mat)
adjacencyMatrix2List = function(mat, keep.zero = FALSE) {
    if(is.null(rownames(mat))) rownames(mat) = as.character(seq_len(nrow(mat)))
    if(is.null(colnames(mat))) colnames(mat) = as.character(seq_len(ncol(mat)))
    df = data.frame(from = rep(rownames(mat), times = ncol(mat)),
        to = rep(colnames(mat), each = nrow(mat)),
        value = as.vector(mat),
        stringsAsFactors = FALSE)
    if(!keep.zero) df = df[df$value != 0, , drop = FALSE]
    return(df)
}


# == title
# Transform back from colors to values
#
# == param
# -r red channel in `colorspace::sRGB` color space, value should be between 0 and 1. 
#    The ``r``, ``g`` and ``b`` argumentc can be wrapped into one variable which is either a three-column matrix
#    or a vector of colors.
# -g green channel in `colorspace::sRGB` color space, value should be between 0 and 1.
# -b blue channel in `colorspace::sRGB` color space, value should be between 0 and 1.
# -col_fun the color mapping function generated by `colorRamp2`.
#
# == details
# `colorRamp2` transforms values to colors and this function does the reversed job.
# Note for some color spaces, it cannot transform back to the original value perfectly.
#
# == value
# A vector of original numeric values.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# x = seq(0, 1, length.out = 11)
# col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"))
# col = col_fun(x)
# col2value(col, col_fun = col_fun)
# col2value("red", col_fun = col_fun)
#
# col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"), space = "sRGB")
# col = col_fun(x)
# col2value(col, col_fun = col_fun)
col2value = function(r, g, b, col_fun) {
    if(missing(g) && missing(b)) {
        if(is.character(r)) {
            rgb = col2rgb(r)/255
            r = rgb[1, ]
            g = rgb[2, ]
            b = rgb[3, ]
        } else {
            if(is.list(r)) {
                g = r[[2]]
                b = r[[3]]
                r = r[[1]]
            } else if(is.data.frame(r) || is.matrix(r)) {
                g = r[, 2]
                b = r[, 3]
                r = r[, 1]
            }
        }
    }

    breaks = attr(col_fun, "breaks")
    colors = attr(col_fun, "colors")
    space = attr(col_fun, "space")

    n = length(r)

    if(inherits(colors, "character")) {
        colors = t(col2rgb(colors))/255
    }

    ## convert all colors to the specified space
    m = coords(as(sRGB(r, g, b), space))
    breaks_m = coords(as(sRGB(colors), space))
    n_breaks = length(breaks)

    # interpolation for the three channels seperatedly
    v = numeric()
    for(i in seq_len(nrow(m))) {
        l1 = (breaks_m[-n_breaks, 1] <= m[i, 1] & breaks_m[-1, 1] >= m[i, 1]) | (breaks_m[-n_breaks, 1] >= m[i, 1] & breaks_m[-1, 1] <= m[i, 1])
        l2 = (breaks_m[-n_breaks, 2] <= m[i, 2] & breaks_m[-1, 2] >= m[i, 2]) | (breaks_m[-n_breaks, 2] >= m[i, 2] & breaks_m[-1, 2] <= m[i, 2])
        l3 = (breaks_m[-n_breaks, 3] <= m[i, 3] & breaks_m[-1, 3] >= m[i, 3]) | (breaks_m[-n_breaks, 3] >= m[i, 3] & breaks_m[-1, 3] <= m[i, 3])
        k = which(l1 & l2 & l3)[1]
        v1 = (breaks[k] - breaks[k+1])/(breaks_m[k, 1] - breaks_m[k+1, 1]) * (m[i, 1] - breaks_m[k, 1]) + breaks[k]
        v2 = (breaks[k] - breaks[k+1])/(breaks_m[k, 2] - breaks_m[k+1, 2]) * (m[i, 2] - breaks_m[k, 2]) + breaks[k]
        v3 = (breaks[k] - breaks[k+1])/(breaks_m[k, 3] - breaks_m[k+1, 3]) * (m[i, 3] - breaks_m[k, 3]) + breaks[k]
        vv = c(v1, v2, v3)
        v[i] = mean(vv, na.rm = TRUE)
    }
    return(v)
}

# == title
# Convert units
#
# == param
# -x a numeric vector
# -unit supported units, only "mm", "cm", "inches".
#
# == details
# This function coverts mm/cm/inches units to units measured in the canvas coordinate,
# e.g. how much is it in the canvas coordinate for 1 mm/cm/inches.
#
# Since in the circular plot, the aspect ratio is always 1, it does not matter this conversion
# is applied on x direction or y direction.
#
# This function is mainly used in the radical direction.
#
# == seealso
# `convert_x` and `convert_y` convert absolute units into a data coordinate in a specified cell.
#
# https://jokergoo.github.io/circlize_book/book/circular-layout.html#convert-functions
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# sectors = letters[1:10]
# circos.par(cell.padding = c(0, 0, 0, 0), track.margin = c(0, 0))
# circos.initialize(sectors, xlim = cbind(rep(0, 10), runif(10, 0.5, 1.5)))
# circos.track(ylim = c(0, 1), track.height = mm_h(5))
# circos.par(track.margin = c(0, mm_h(2)))
# circos.track(ylim = c(0, 1), track.height = cm_h(1))
# circos.par(track.margin = c(0, mm_h(5)))
# circos.track(ylim = c(0, 1), track.height = inch_h(1))
# circos.clear()
convert_length = 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_length()` 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)
}

# == title
# Convert units
#
# == param
# -... pass to `convert_length`
#
# == details
# This function is same as `convert_length`. The reason for naming this function
# is `convert_length` is mostely used for defining the height of tracks and track margins.
#
# == seealso
# For pre-defined units, users can use `cm_h`, `mm_h` and `inches_h`.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see example in `convert_length` page
# NULL
convert_height = function(...) {
    convert_length(...)
}

# == title
# Convert units
#
# == param
# -... pass to `convert_length`.
#
# == details
# Please do not use this function. Use `mm_h`/`cm_h`/inches_h` instead.
#
uh = function(...) {
    convert_length(...)
}

convert_unit_in_data_coordinate = function(x, unit = c("mm", "cm", "inches", "canvas"),
    direction = c("x", "y"),
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    h = get.cell.meta.data("ycenter", sector.index = sector.index, 
        track.index = track.index)) {

    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.")
    }

    direction = match.arg(direction)

    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
    } else if(unit == "canvas") {
        len = x
    }

    xlim = get.cell.meta.data("xlim", sector.index = sector.index, track.index = track.index)
    ylim = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)

    
    if(direction == "x") {
        if(length(h) == 1) {
            h = rep(h, length(x))
        }
        w_in_data = xlim[2] - xlim[1]
        w_in_canvas = numeric(length(x))
        for(i in seq_along(x)) {
            coor_polar = circlize(xlim, c(h[i], h[i]), sector.index = sector.index, track.index = track.index)
            w_in_canvas[i] = abs(coor_polar[1, 1] - coor_polar[2, 1])/180*pi* coor_polar[1, 2]
        }
    } else {
        coor_polar = circlize(c(xlim[1], xlim[1]), ylim, sector.index = sector.index, track.index = track.index)
        w_in_data = ylim[2] - ylim[1]
        w_in_canvas = abs(coor_polar[2, 2] - coor_polar[1, 2])
    }

    len = len * abs(w_in_data/w_in_canvas)
    return(len)
}

# == title
# Convert unit on x direction in data coordinate
#
# == param
# -x a numeric vector.
# -unit supported units, only "mm", "cm", "inches".
# -sector.index index for the sector where the conversion is applied.
# -track.index index for the track where the conversion is applied.
# -h since the width of the cell is not identical from the top to the bottom in the cell, the position on
#   y direction needs to be specified. By default it is at the middle point on y-axis.
#
# == value
# A vector of numeric values which are measured in the specified data coordinate.
#
# == seealso
# For pre-defined units, users can use `cm_x`, `mm_x` and `inches_x`.
#
# `convert_y` converts on y direction.
#
# https://jokergoo.github.io/circlize_book/book/circular-layout.html#convert-functions
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# sectors = letters[1:10]
# circos.par(cell.padding = c(0, 0, 0, 0), track.margin = c(0, 0))
# circos.initialize(sectors, xlim = cbind(rep(0, 10), runif(10, 0.5, 1.5)))
# circos.track(ylim = c(0, 1), track.height = mm_h(5),
#     panel.fun = function(x, y) {
#         circos.lines(c(0, 0 + mm_x(5)), c(0.5, 0.5), col = "blue")
#     })
# circos.par(track.margin = c(0, mm_h(2)))
# circos.track(ylim = c(0, 1), track.height = cm_h(1),
#     panel.fun = function(x, y) {
#         xcenter = get.cell.meta.data("xcenter")
#         circos.lines(c(xcenter, xcenter), c(0, cm_y(1)), col = "red")
#     })
# circos.par(track.margin = c(0, mm_h(5)))
# circos.track(ylim = c(0, 1), track.height = inch_h(1),
#     panel.fun = function(x, y) {
#         line_length_on_x = cm_x(1*sqrt(2)/2)
#         line_length_on_y = cm_y(1*sqrt(2)/2)
#         circos.lines(c(0, line_length_on_x), c(0, line_length_on_y), col = "orange")
#     })
# circos.clear()
convert_x = function(
    x, 
    unit = c("mm", "cm", "inches"),
    sector.index = get.cell.meta.data("sector.index"),
    track.index = get.cell.meta.data("track.index"),
    h = get.cell.meta.data("ycenter", sector.index = sector.index, 
        track.index = track.index)) {
    convert_unit_in_data_coordinate(x, unit = unit, sector.index = sector.index, 
        track.index = track.index, h = h, direction = "x")
}

# == title
# Convert unit on x direction in data coordinate
#
# == param
# -... pass to `convert_x`.
#
# == details
# Please do not use this function. Use `mm_x`/`cm_x`/inches_x` instead.
#
ux = function(...) {
    convert_x(...)
}

# == title
# Convert unit on y direction in data coordinate
#
# == param
# -x a numeric vector
# -unit supported units, only "mm", "cm", "inches"
# -sector.index index for the sector where the conversion is applied
# -track.index index for the track where the conversion is applied
#
# == value
# A vector of numeric values which are measured in the specified data coordinate
#
# == seealso
# For pre-defined units, users can use `cm_y`, `mm_y` and `inches_y`.
#
# `convert_x` converts on x direction.
#
# https://jokergoo.github.io/circlize_book/book/circular-layout.html#convert-functions
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see example on `convert_x` page 
# NULL
convert_y = function(
    x, 
    unit = c("mm", "cm", "inches"),
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index()) {
    convert_unit_in_data_coordinate(x, unit = unit, sector.index = sector.index, 
        track.index = track.index, direction = "y")
}

# == title
# Convert unit on y direction in data coordinate
#
# == param
# -... pass to `convert_y`.
#
# == details
# Please do not use this function. Use `mm_y`/`cm_y`/inches_y` instead.
#
uy = function(...) {
    convert_y(...)
}

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)
}

# == title
# Convert unit on x direction in data coordinate
#
# == param
# -x The x-value in numeric.
# -sector.index Index of sector.
# -track.index Index of track.
# -... Pass to `convert_x`.
#
# == details
# See explanations in `convert_x` page.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see examples in `convert_x` page
# NULL
cm_x = function(x, sector.index = get.current.sector.index(),
    track.index = get.current.track.index(), ...) {
    convert_x(x, unit = "cm", sector.index = sector.index, track.index = track.index, ...)
}

# == title
# Convert unit on y direction in data coordinate
#
# == param
# -y The y-value in numeric.
# -sector.index Index of sector.
# -track.index Index of track.
#
# == details
# See explanations in `convert_y` page.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see examples in `convert_y` page
# NULL
cm_y = function(y, sector.index = get.current.sector.index(),
    track.index = get.current.track.index()) {
    convert_y(y, unit = "cm", sector.index = sector.index, track.index = track.index)
}

# == title
# Convert units
#
# == param
# -h The height in numeric.
#
# == details
# See explanations in `convert_length` page.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see examples in `convert_length` page
# NULL
cm_h = function(h) {
    convert_length(h, unit = "cm")
}

# == title
# Convert unit on x direction in data coordinate
#
# == param
# -x The x-value in numeric.
# -sector.index Index of sector.
# -track.index Index of track.
# -... Pass to `convert_x`.
#
# == details
# See explanations in `convert_x` page.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see examples in `convert_x` page
# NULL
mm_x = function(x, sector.index = get.current.sector.index(),
    track.index = get.current.track.index(), ...) {
    convert_x(x, unit = "mm", sector.index = sector.index, track.index = track.index, ...)
}

# == title
# Convert unit on y direction in data coordinate
#
# == param
# -y The y-value in numeric.
# -sector.index Index of sector.
# -track.index Index of track.
#
# == details
# See explanations in `convert_y` page.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see examples in `convert_y` page
# NULL
mm_y = function(y, sector.index = get.current.sector.index(),
    track.index = get.current.track.index()) {
    convert_y(y, unit = "mm", sector.index = sector.index, track.index = track.index)
}

# == title
# Convert units
#
# == param
# -h The height in numeric.
#
# == details
# See explanations in `convert_length` page.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see examples in `convert_length` page
# NULL
mm_h = function(h) {
    convert_length(h, unit = "mm")
}

# == title
# Convert unit on x direction in data coordinate
#
# == param
# -x The x-value in numeric.
# -sector.index Index of sector.
# -track.index Index of track.
# -... Pass to `convert_x`.
#
# == details
# See explanations in `convert_x` page.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see examples in `convert_x` page
# NULL
inches_x = function(x, sector.index = get.current.sector.index(),
    track.index = get.current.track.index(), ...) {
    convert_x(x, unit = "inches", sector.index = sector.index, track.index = track.index, ...)
}

# == title
# Convert unit on y direction in data coordinate
#
# == param
# -y The y-value in numeric.
# -sector.index Index of sector.
# -track.index Index of track.
#
# == details
# See explanations in `convert_y` page.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see examples in `convert_y` page
# NULL
inches_y = function(y, sector.index = get.current.sector.index(),
    track.index = get.current.track.index()) {
    convert_y(y, unit = "inches", sector.index = sector.index, track.index = track.index)
}

# == title
# Convert units
#
# == param
# -h The height in numeric.
#
# == details
# See explanations in `convert_length` page.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# # see examples in `convert_length` page
# NULL
inches_h = function(h) {
    convert_length(h, unit = "inches")
}

# == title
# Convert unit on x direction in data coordinate
#
# == param
# -... pass to `inches_x`.
#
# == details
# This function is the same as `inches_x`.
inch_x = function(...) {
    inches_x(...)
}
# == title
# Convert unit on y direction in data coordinate
#
# == param
# -... pass to `inches_y`
#
# == details
# This function is the same as `inches_y`.
inch_y = function(...) {
    inches_y(...)
}

# == title
# Convert units
#
# == param
# -... pass to `inches_h`
#
# == details
# This function is the same as `inches_h`.
inch_h = function(...) {
    inches_h(...)
}

stop_wrap = function(...) {
    x = paste0(...)
    x = paste(strwrap(x), collapse = "\n")
    stop(x, call. = FALSE)
}

warning_wrap = function(...) {
    x = paste0(...)
    x = paste(strwrap(x), collapse = "\n")
    warning(x, call. = FALSE)
}

message_wrap = function(...) {
    x = paste0(...)
    x = paste(strwrap(x), collapse = "\n")
    message(x)
}

validate_data_frame = function(x) {
    if(inherits(x, "data.frame")) {
        return(as.data.frame(x))
    } else if(inherits(x, "GRanges")) {
        x = as.data.frame(x)
        return(x[, -(4:5), drop = FALSE])
    } else {
        oe = try(x <- as.data.frame(x))
        if(inherits(oe, "try-error")) {
            stop_wrap("The input should be a data frame or an object that can be converted to a data frame.")
        }
        return(x)
    }
}


roundrect_pos = function(xleft, ybottom, xright, ytop, radius = 0.1, 
  asp = NULL, plot = FALSE) {

  if(is.null(asp)) {
    pin = par("pin")
    usr = par("usr")
    asp = pin[1]/pin[2] * (usr[4] - usr[3])/(usr[2] - usr[1])
  }

  convert_y_1 = function(y, asp) {
    y/asp
  }

  covnert_y_2 = function(y, asp) {
    y*asp
  }

  if(xleft > xright) {
    foo = xleft
    xleft = xright
    xright = foo
  }
  if(ybottom > ytop) {
    foo = ybottom
    ybottom = ytop
    ytop = foo
  }

  ytop = convert_y_1(ytop, asp)
  ybottom = convert_y_1(ybottom, asp)

  w = abs(xright - xleft)
  h = abs(ytop - ybottom)
  r = radius*min(w, h)

  x = NULL
  y = NULL

  # left top 180 -> 90
  df = polar2Cartesian(cbind(seq(180, 90, length.out = 20), rep(r,20)))
  x = c(x, df[, 1] + xleft + r)
  y = c(y, df[, 2] + ytop - r)

  x = c(x, xleft + r, xright - r)
  y = c(y, ytop, ytop)

  # right top 90 -> 0
  df = polar2Cartesian(cbind(seq(90, 0, length.out = 20), rep(r,20)))
  x = c(x, df[, 1] + xright - r)
  y = c(y, df[, 2] + ytop - r)

  x = c(x, xright, xright)
  y = c(y, ytop - r, ybottom + r)

  # bottom right 0 - (-90)
  df = polar2Cartesian(cbind(seq(0, -90, length.out = 20), rep(r,20)))
  x = c(x, df[, 1] + xright - r)
  y = c(y, df[, 2] + ybottom + r)

  x = c(x, xright - r, xleft + r)
  y = c(y, ybottom, ybottom)

  # bottom left 270 - 180
  df = polar2Cartesian(cbind(seq(270, 180, length.out = 20), rep(r,20)))
  x = c(x, df[, 1] + xleft + r)
  y = c(y, df[, 2] + ybottom + r)

  x = c(x, xleft, xleft)
  y = c(y, ybottom + r, ytop - r)

  y = covnert_y_2(y, asp)

  if(plot) plot(x, y, type = "l")

  return(list(x = x, y = y))
}

# plot(c(-2, -1), c(-2, -1))
# foo = roundrect_pos(-2, -2, -1, -1)
# lines(foo$x, foo$y)


# plot(c(-4, -1), c(-2, -1))
# foo = roundrect_pos(-4, -2, -1, -1)
# lines(foo$x, foo$y)



stack_text = function(x, text, margin = 0.2, 
    strwidth = strwidth, strheight = strheight, ...) {

    tw = sapply(text, strwidth, ...)
    th = sapply(text, strheight, ...)

    e = min(c(tw, th))*margin

    tw = tw + e

    x1 = x - tw/2
    x2 = x + tw/2
    ind = seq_along(x)

    od = order(x1)
    tw = tw[od]
    x1 = x1[od]
    x2 = x2[od]
    ind = ind[od]

    lt = list()

    i_lt = 1
    while(length(x1)) {
        v = ind[1]
        x_right = x2[1]

        ind_used = 1
        for(i in seq_along(x1)[-1]) {
            if(x1[i] >= x_right) {
                v = c(v, ind[i])
                x_right = x2[i]
                ind_used = c(ind_used, i)
            }
        }
        x1 = x1[-ind_used]
        x2 = x2[-ind_used]
        ind = ind[-ind_used]

        lt[[i_lt]] = v

        i_lt = i_lt + 1

    }

    lt
}


circos.strwidth = function(text, ..., 
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    h = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)[1]) {

    chars = strsplit(text, "")
        
    nlabel = length(text)
    strw = lapply(chars, strwidth, ...) # width of every character in text
    
    strw = sapply(strw, function(w) {
        w2 = convert_unit_in_data_coordinate(w, unit = "canvas", direction = "x",
            sector.index = sector.index, track.index = track.index, h = h)
        sum(w2)
    })

    strw
}

circos.strheight = function(text, ..., 
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index()) {

    strh = lapply(text, strheight, ...)
    
    strh = sapply(strh, function(w) {
        w2 = convert_unit_in_data_coordinate(w, unit = "canvas", direction = "y",
            sector.index = sector.index, track.index = track.index)
        max(w2)
    })

    strh
}

circos.strAscent = function(text, cex = par("cex"), font = par("font"), family = par("family"),
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index()) {

    sapply(text, function(t) {
        gb = textGrob(t, gp = gpar(cex = cex, fontface = font, fontfamily = family))
        h = grobAscent(gb)
        h = convertHeight(h, "mm", valueOnly = TRUE)
        mm_y(h, sector.index = sector.index, track.index = track.index)
    })
}

circos.strDescent = function(text, cex = par("cex"), font = par("font"), family = par("family"),
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index()) {

    sapply(text, function(t) {
        gb = textGrob(t, gp = gpar(cex = cex, fontface = font, fontfamily = family))
        h = grobDescent(gb)
        h = convertHeight(h, "mm", valueOnly = TRUE)
        mm_y(h, sector.index = sector.index, track.index = track.index)
    })
}

## code copied from circos.genomicLabels()
refer_to_one_sector = function(sectors, x) {

    bed = data.frame(sectors = sectors, x = x, order = seq_along(x))
    od = order(bed[[1]], bed[[2]])
    bed = bed[od, , drop = FALSE]

    if(!circos.par$xaxis.clock.wise) {
        all_chr_vec = as.character(bed[, 1])
        bed[, 2] = .CIRCOS.ENV$.SECTOR.DATA[all_chr_vec, "max.value"] - bed[, 2] + .CIRCOS.ENV$.SECTOR.DATA[all_chr_vec, "min.value"]
        bed[, 3] = .CIRCOS.ENV$.SECTOR.DATA[all_chr_vec, "max.value"] - bed[, 3] + .CIRCOS.ENV$.SECTOR.DATA[all_chr_vec, "min.value"]
        bed[, 2:3] = bed[, 3:2]
        circos.par(xaxis.clock.wise = TRUE)
        on.exit(circos.par(xaxis.clock.wise = FALSE))
    }

    chr = get.all.sector.index()[1]
    sector_data = get.sector.data(chr)
    
    all_chr = unique(bed[, 1])
    rho = NULL
    for(cr in all_chr) {
        sub_bed = bed[bed[, 1] == cr, ]
        rho = c(rho, circlize(sub_bed[, 2], y = rep(1, nrow(sub_bed)), sector.index = cr)[, 1])
    }
    if(length(rho) == 0) {
        anchor = ((sector_data["start.degree"] + sector_data["end.degree"])/2 + 180) %% 360
    } else if(length(rho) == 1) {
        anchor = (rho + 180) %% 360
    } else {
        rho = sort(rho)
        rho = c(rho, rho[1] + 360)
        i = which.max(diff(rho))
        anchor = ((rho[i] + rho[i+1])/2) %% 360
    }

    # map all other chromosomes to the first chromosome
    chr_width = sector_data["start.degree"] - sector_data["end.degree"]
    # extend = (360 - chr_width)/chr_width
    # extend = c(0, extend)
    extend = numeric(2)
    s1 = sector_data["start.degree"] %% 360
    s2 = sector_data["end.degree"] %% 360
    # if the anchor in inside the first sector
    if(s1 < s2) { # the first sector go across theta = 0
        s1 = s1 + 360
    } 

    if(anchor >= s2 && anchor <= s1) { # anchor inside sector
        if(s1 - s2 > 180) {
            extend[1] = (abs(s1 - anchor) %% 360)/chr_width
            extend[2] = -(abs(s2 - anchor) %% 360)/chr_width
        } else {
            extend = (360 - chr_width)/chr_width
            extend = c(0, extend)
        }
    } else {
        extend[1] = ((anchor - s1) %% 360)/chr_width  # goes reverse clockwise
        extend[2] = ((s2 - anchor) %% 360)/chr_width  # goes clockwise
    }
    extend = abs(extend)

    if(0) segments(0, 0, cos(anchor/180*pi), sin(anchor/180*pi))

    # start.degree is always larger than end.degree
    new_chr_range = c(sector_data["start.degree"] + chr_width*extend[1], sector_data["end.degree"] - chr_width*extend[2])

    all_chr = unique(bed[, 1])
    bed2 = NULL
    for(cr in all_chr) {
        sub_bed = bed[bed[, 1] == cr, ]
        if(cr != chr) {
            dfx1 = circlize(sub_bed[, 2], y = rep(1, nrow(sub_bed)), sector.index = cr)
            
            l = dfx1[, 1] > new_chr_range[1] | dfx1[, 1] < new_chr_range[2]
            if(any(l)) dfx1[l, 1] = (dfx1[l, 1] - new_chr_range[2]) %% 360 + new_chr_range[2]
            x1 = reverse.circlize(dfx1, sector.index = chr)[, 1]
            
            sub_bed[, 2] = data.frame(start = x1)
        }
        bed2 = rbind(bed2, sub_bed)
    }
    bed2[, 1] = chr
    bed2
}