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YinLiLin / CMplot

📊 Circular and Rectangular Manhattan Plot
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How can I draw no-p-value trait? #69

Open Maximus0212 opened 2 years ago

Maximus0212 commented 2 years ago

Hi Lilin,

I'm very thank you for developing this tool.

I want to draw a Circular Manhattan plot between p-value and no p-value.

for example,

SNP CHR BP trait1 trait2 trait3 1_1273278 1 1273278 0 0 0.14624 1_1274242 1 1274242 9.38e-01 0 0.387652 1_1274350 1 1274350 0 0 0.233855 1_1276410 1 1276410 0 0 0.257981 1_1276459 1 1276459 0 0 0.22406 1_1276478 1 1276478 0 0 0.224091 1_1276812 1 1276812 9.42e-01 0 0.38066 1_1278237 1 1278237 9.43e-01 0 0.377236 1_1279428 1 1279428 0 0 0.0799209 1_1280014 1 1280014 9.12e-01 0 0.210048 1_1280519 1 1280519 8.01e-01 0 0.371235

I want to draw a Manhattan plot for traits with p-value and Blank for traits with no-p-value.

But, the CMplot P-value input is only (0,1). So, the above table is an error.

How can I draw ???

YinLiLin commented 2 years ago

Hi, you can try to adjust the columns representing p-values into '-log10' scale prior to using CMplot, and keep the columns containing non-pvalues unchanged, then plot the adjusted data with a parameter LOG10=FALSE.