methylation and demethylation manhattan points

[LandiMi2]

Hey, @YinLiLin Awesome package with colourful plots!

I am using this package to plot differential methylation. I have points that are hypermethylated (positive values) and de-methylated (negative values) as seen below. I have drawn a manhattan plot with these and now I was to highlight significant points separate colours, say green from + and red for - to see how they are distributed in the chromosomes

meth.site  chr    start    pvalue   meth.diff
  1:         1 Chr1      161 0.7348564   4.6153846
  2:         2 Chr1      310 0.9769043   0.4444444
  3:         3 Chr1      311 0.9322884  -1.8633540
  4:         4 Chr1      500 0.4369119  -9.6774194 

is this possible with this package?

[YinLiLin]

Thank you for using CMplot. may i know whether you plan to plot those two differential methylations in one axis or separated axis?

[LandiMi2]

@YinLiLin on the one axis

[LandiMi2]

@YinLiLin or even what flag should I use to have separate axis top and bottom

[YinLiLin]

you can try "CMplot(,..., multracks=TRUE)", but at this case, please remember to adjust 'pvalue' to 'meth.diff' scale by "-log10()" function prior to plotting.