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YinLiLin / CMplot

📊 Circular and Rectangular Manhattan Plot
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Strange x-axis in my Manhattan plot #83

Open lebronzhong opened 1 year ago

lebronzhong commented 1 year ago

Hi, I want to draw a Manhattan plot in one chromosome, but I always get this strange style. Since cmplot cannot adjust "xlim", I want to ask how I can improve my image ?

Here is my data, code and plot:

My data: SNP CHR POS P Q rs317552747 1 171171186 0.257355 0.815110386978283 rs730957333 1 171171399 0.05990999 0.49651867882562 rs315124272 1 171171416 0.1514469 0.704036303186825 rs312590688 1 171172575 0.05764159 0.488092406988546 rs316971493 1 171172716 0.3928236 0.890057962406588 rs315421835 1 171172919 0.5634916 0.942154920675489 rs317897119 1 171174837 0.001948485 0.0645866447272067 ... rs314064314 1 171314163 0.4513443 0.911618505004523 rs315815464 1 171314260 0.4438239 0.90915176480257 1_171314387_A_G 1 171314387 0.1222877 0.656616978432227 1_171314394_C_T 1 171314394 0.1463708 0.696594952993791 1_171314541_C_G 1 171314541 0.1955836 0.75937198512281 1_171314606_T_C 1 171314606 0.06063531 0.499162063306579 1_171314614_T_G 1 171314614 0.04764708 0.447574918952535 focusing on the region on chr1 171Mb

My plot: Rectangular-Manhattan Q_test2

My code: CMplot(c, plot.type="m", col=c("grey30","grey60"), LOG10=TRUE, threshold=0.05,cex = 1, pch = 19, threshold.lty=2, threshold.lwd=1, threshold.col="black", chr.den.col=NULL, signal.col="#FF7F24", cex.axis=1,lwd.axis=2, signal.cex=1, signal.pch=19, file="pdf",memo="test3",dpi=350, width = 14,height = 6, file.output=TRUE)

YinLiLin commented 1 year ago

Thank you for the feedback, i will check the script for this issue.

YinLiLin commented 1 year ago

Hi, would you mind sending me your data at ylilin@163.com to debug this issue? Thanks.

Porfigc commented 2 months ago

I have same problem, Is there a solution to the problem?