Changes in circlize 0.4.10

Add circos.barplot(), circos.boxplot() and circos.violin()

circos.barplot(), circos.boxplot() and circos.violin() are used inside the panel.fun. Please note the values on x-axes are the integer indices of bars, boxes or violins for which xlim should be properly set in circos.initialize().

par(mfrow = c(1, 2))
circos.initialize(fa = letters[1:4], xlim = c(0, 10))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    value = runif(10)
    circos.barplot(value, 1:10 - 0.5, col = 1:10)
})
circos.track(ylim = c(-1, 1), panel.fun = function(x, y) {
    value = runif(10, min = -1, max = 1)
    circos.barplot(value, 1:10 - 0.5, col = ifelse(value > 0, 2, 3))
})
circos.clear()

circos.initialize(fa = letters[1:4], xlim = c(0, 10))
circos.track(ylim = c(0, 4), panel.fun = function(x, y) {
    value = matrix(runif(10*4), ncol = 4)
    circos.barplot(value, 1:10 - 0.5, col = 2:5)
})

circos.clear()

par(mfrow = c(1, 2))
circos.initialize(fa = letters[1:4], xlim = c(0, 10))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    for(pos in seq(0.5, 9.5, by = 1)) {
        value = runif(10)
        circos.boxplot(value, pos)
    }
})
circos.clear()

circos.initialize(fa = letters[1:4], xlim = c(0, 10))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    value = replicate(runif(10), n = 10, simplify = FALSE)
    circos.boxplot(value, 1:10 - 0.5, col = 1:10)
})

circos.clear()

par(mfrow = c(1, 2))
circos.initialize(fa = letters[1:4], xlim = c(0, 10))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    for(pos in seq(0.5, 9.5, by = 1)) {
        value = runif(10)
        circos.violin(value, pos)
    }
})
circos.clear()

circos.initialize(fa = letters[1:4], xlim = c(0, 10))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    value = replicate(runif(10), n = 10, simplify = FALSE)
    circos.violin(value, 1:10 - 0.5, col = 1:10)
})

circos.clear()

Physical units

In the older versions, the widths/heights/lengths are specified by convert_x()/convert_y()/convert_height() functions, however, the function names are not straightforward. Now there are following functions that control the physical size:

• mm_x()/cm_x()/inch_x(): on x-axes in the cells.
• mm_y()/cm_y()/inch_y(): on y-axes in the cells.
• mm_h()/cm_h()/inch_h(): control the height of track and the gap between tracks.

See the following example:

fa = letters[1:10]
circos.par(cell.padding = c(0, 0, 0, 0), track.margin = c(0, 0))
circos.initialize(fa, 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")
    })
set_track_gap(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")
    })
set_track_gap(mm_h(5))
circos.track(ylim = c(0, 1), track.height = inch_h(0.5),
    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()

Set gaps between tracks

In the older version, you need to set track.height parameter either in circos.par() or in circos.track() to control the space between tracks. Now there is a new set_track_gap() function which simplifies the setting of gaps between two tracks. With the mm_h()/cm_h()/inch_h() functions, it is very easy to set the gaps with physical units.

circos.initialize(fa = letters[1:10], xlim = c(0, 1))
circos.track(ylim = c(0, 1))
set_track_gap(mm_h(2)) # 2mm
circos.track(ylim = c(0, 1))
set_track_gap(cm_h(0.5)) # 0.5cm
circos.track(ylim = c(0, 1))

circos.clear()

gap.degree with names

circos.par() is aimed to be designed to be independent to the number or the order of sectors, however, there is an exception. The gap.degree parameter controls the spaces between two neighbouring sectors. When it is set as a scalar, the gap is the same to every two neighbouring sectors and it works fine. It can also be a vector which has the same length as the number of sectors and it can cause problems:

1. When you change the order of the sectors, you also need to manually change the order of gap.degree.
2. in chordDiagram() function, by default the tiny sectors are removed to improve the visualization, which means, the gap.degree should be adjusted.
3. Also in chordDiagram(), sometimes it is not very straightforward to find out the order of sectors, thus, it is difficult to set a proper gap.degree.

Now, from version 0.4.10, the value of gap.degree can be set as a named vector where the names are the names of the sectors. In this case, the gap.degree vector can be automatically reordered or subsetted according to the sector ordering in the plot.

Multi-group Chord diagram

Please see https://jokergoo.github.io/2020/06/08/multiple-group-chord-diagram/. An example is

Circular Heatmaps

Please see https://jokergoo.github.io/2020/05/21/make-circular-heatmaps/. An example is