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YinLiLin / CMplot

📊 Circular and Rectangular Manhattan Plot
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out or chromosomes number! #27

Open sunnycqcn opened 4 years ago

sunnycqcn commented 4 years ago

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

YinLiLin commented 4 years ago

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

sunnycqcn commented 4 years ago

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

YinLiLin commented 4 years ago

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