Mirrored plot in plotHicSquare for interchromosomal interactions

[catroro]

Hello,

I’m encountering an issue while using plotHicSquare to visualize interchromosomal interactions from a .hic file that contains all chromosomes.

When plotting two different chromosomes, the output seems to show the interaction matrix twice — once in the expected orientation, and once mirrored or rotated (perpendicular). I've tried using both half = "top" and half = "bottom"

Please let me know if I'm doing something wrong

Thanks in advance for your help — and for maintaining such a great tool!

plot.pdf

The code I'm using:

mydata <- "./filtered.hic"
pageCreate(
    width = 10, height = 10, default.units = "inches",
    showGuides = FALSE, xgrid = 0, ygrid = 0
)

inter <- plotHicSquare(data = mydata,
                chrom = "4",
                chromstart = 1,
                chromend = 200000000,
                altchrom = "14",
                altchromstart = 1,
                altchromend = 200000000,
                assembly = "hg38", 
                x = 3.5, y = 3.5, 
                colorTrans = "log",
                resolution = 500000,
                width = 2.5, 
                height = 2.5,
                half = "top")

annoGenomeLabel(
    plot = inter, scale = "Mb", axis = "y",
    x = 3.25, y = 3.5,
    just = c("right", "top")
)
annoGenomeLabel(
    plot = inter, scale = "Mb", axis = "x",
    x = 3.25, y = 3.5,
    just = c("left", "bottom")
)