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YinLiLin / CMplot

📊 Circular and Rectangular Manhattan Plot
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p values should be at range of (0, 1). #112

Open ssieub opened 8 months ago

ssieub commented 8 months ago

CMplot(x,plot.type="q",threshold=0.05) Error in CMplot(x, plot.type = "q", threshold = 0.05) : p values should be at range of (0, 1). The p-values of my data are all between 0 and 1, but the code runs with an error

YinLiLin commented 8 months ago

Please update to the latest version and have a try again.

ssieub commented 8 months ago

It's version 4.3.3 now.

ssieub commented 8 months ago

图片

YinLiLin commented 8 months ago

Could you please provide a screenshot for a head of your data? Thanks.

ssieub commented 8 months ago

X-芽期相对盐害率.txt Thanks
I've removed the blank lines at runtime x=fread("X-芽期相对盐害率.txt") x=x %>% drop_na(p) CMplot(x,plot.type = "q",threshold = 0.05) Error in CMplot(x, plot.type = "q", threshold = 0.05) : p values should be at range of (0, 1).

YinLiLin commented 8 months ago

the structure of your data doesn't fully meet the requirements. As the same with example datasets (see the README.md on GitHub), the first three columns are names, chromosome, position of SNPs respectively, the rest of columns are the pvalues of GWAS or effects of GS/GP for traits. Please adjust your data to be fully consistent with the example data prior plotting.