CMplot

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Hello, Much apprecitated for excellent software. I met a error warning about chromosome number. I used scaffolds as chromosomes to draw manhaton plot, total of 3000 scaffolds. I get this warning as following:

Warning message: In max(numeric.chr, na.rm = TRUE) : no non-missing arguments to max; returning -Inf Could you help me check how I can figure out this error? Thanks, Fuyou

Hi Fuyou,

Thank you for using CMplot. This warning doesn't affect the plotting, did you check the plotted results? are they fine?

Best, Lilin

Hi Lilin, I think it is good. Do you have suggestions that the chromosome number and tag are not presented in x axis? Because I have more than 3000 scaffolds. I only want to show the significant dots. Thanks, Fuyou

Hi Fuyou,

I have tweaked the script. You may try to assign a character vector with unique chromosome labels (for example: mychr=unique(yourdata[,2])) to the parameter 'chr.labels', and remain the chromosome labels of your interest, but replace the labels of no interest with NA (for example: mychr[c(yourindex)]=NA). With the setting above, CMplot will only show a fraction of chromosome labels. Please source the online script and try again.

Best, Lilin