problem with circle.margin

[onmyojiyys]

NK T cells Monocytes B cells Plasma cells NK_pseudo pDCs 1 100 0 0 0 0 0 0 2 0 100 0 0 0 0 0 3 100 0 0 0 0 0 0 4 0 0 100 0 0 0 0 5 0 100 0 0 0 0 0 6 0 0 0 100 0 0 0 7 0 0 0 100 0 0 0 8 0 0 100 0 0 0 0 9 0 100 0 0 0 0 0 10 0 0 0 0 100 0 0 11 0 0 0 0 0 100 0 12 100 0 0 0 0 0 0 13 0 0 100 0 0 0 0 14 0 0 0 0 100 0 0 15 0 0 0 0 0 0 100 16 0 47 0 0 0 0 0

This is my data. When I use the following code to plot and save the image as a PNG, the margins of the image are quite large, with a lot of white space. I wonder if there is any way to address this issue. The 'circle.margin' does not seem to have a very good effect.

png('Circle.png'), width = 4, height = 4, res = 300, units = 'in') circos.par$circle.margin = c(0.1, 0.1, 0.001, 0.1) circos.par(gap.after = c(rep(3, nrow(plot_data)-1), 10, rep(3, ncol(plot_data)-1), 10)) chordDiagram(tdata, grid.col = use_color, preAllocateTracks = 2, annotationTrack = c("grid")) circos.track( track.index = 2, panel.fun = function(x, y) { circos.text( CELL_META$xcenter, CELL_META$ylim[1], CELL_META$sector.index, facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5), cex = 0.6) }, bg.border = NA ) circos.clear() dev.off()