Modify Y axis labels in circular Manhattan plot, and display all signal.lines above highest threshold

[fmazzarotto]

Dear Lilin,
thanks a lot (and congratulations) for developing such a useful package. I have 2 quick questions related to the plot above:

• how can I modify the Y axis (specifically, the black vertical axis with the 0,2,4,6,8 labels)? More in detail, I am unable to change the size of the labels (cex.lab does not seem to work) or their position (I'd prefer having the 0 and the 8 aligned with the respective circles, like the other labels). If these changes are not possible, I would maybe remove the axis, but I am currently unable to do it without removing also the gray grid circles (which I would like to keep).
• Is there a way to create the gray signal lines for all highlighted points, including those between the red and the orange thresholds?

The code that I used is the following:

CMplot(sumstats_clean,plot.type="c",r=0.5,H=2,cex=0.35,threshold=c(5E-8,5E-6),threshold.col=c("red","darkorange3"),amplify=F,highlight=c("rs73125698","rs637963","rs59515125","rs1406447","rs11983675","rs12606558","rs12954992","rs7069590","rs1789250","rs11250166","rs12495100","rs7118149","rs7948935","rs9588277","rs12586818","rs7087272"),outward=T,cir.chr.h=0.15,file="jpg",dpi=300,chr.labels=seq(1,22),file.name = "test_r0.5_H2_cex0.35_thres")

Thanks very much
Best regards

[YinLiLin]

Dear @fmazzarotto ,

Thank you for using CMplot.
Please try the latest version on GitHub (source the online script in R), the parameter "axis.cex" can work on the size of labels, and sorry that the positions are fixed, it's not available to adjust the position of labels for users. Regarding the gray signal lines, CMplot only draws the lines for the points which exceed the smallest threshold, thus if you would like to highlight all the signals, just use one threshold (5E-6) instead.

Best,
Lilin