SNP density plot

[deepti100rao]

I have two questions for generating rectangular SNP density plot:

1. Is it necessary to give SNP numbers in the first column? Are serial numbers taken like 1, 2, 3.. or does it have to be SNP1, SNP2...?

2. Is there a limit on the input file size?

[YinLiLin]

Yes, the order of columns should be exactly the same with the tutorial data (i.e., id, chr, pos, p). There are no mandatory format requirements for the SNP names, any values are acceptable. Theoretically, no limitation on the file size or the number of SNPs for CMplot, but it is restricted by the memory size of your computer.

[deepti100rao]

The package worked seamlessly. Thanks! I am attaching a picture of my plots side by side using two different references. Since the colour coding is sort of relative, I am not able to see a comparison in SNP density between the two references, which is what I want. Can I get the darkest green for numbers 1000-2000, and so on for example? Can you help with this?

On Thu, Aug 24, 2023, 6:40 AM Lilin Yin @.***> wrote:

Yes, the order of columns should be exactly the same with the tutorial data (i.e., id, chr, pos, p). There are no mandatory format requirements for the SNP names, any values are acceptable. Theoretically, no limitation on the file size or the number of SNPs for CMplot, but it is restricted by the memory size of your computer.

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[deepti100rao]

In fact, I must add that the reference genome used in the case of the plot on the right is closer to the query genome and fewer SNPs were called against it compared to the one on the left. But, the plot depicts the opposite. Seeking your help in fine-tuning this. Thanks a lot in advance!

On Thu, Aug 24, 2023 at 12:12 PM Deepti Rao @.***> wrote:

The package worked seamlessly. Thanks! I am attaching a picture of my plots side by side using two different references. Since the colour coding is sort of relative, I am not able to see a comparison in SNP density between the two references, which is what I want. Can I get the darkest green for numbers 1000-2000, and so on for example? Can you help with this?

On Thu, Aug 24, 2023, 6:40 AM Lilin Yin @.***> wrote:

Yes, the order of columns should be exactly the same with the tutorial data (i.e., id, chr, pos, p). There are no mandatory format requirements for the SNP names, any values are acceptable. Theoretically, no limitation on the file size or the number of SNPs for CMplot, but it is restricted by the memory size of your computer.

— Reply to this email directly, view it on GitHub https://github.com/YinLiLin/CMplot/issues/103#issuecomment-1690838771, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCC5QE7GPE5UJJ3YCGZTEL3XW2SW5ANCNFSM6AAAAAA33I53KM . You are receiving this because you authored the thread.Message ID: @.***>

[YinLiLin]

Thank you for the feedback. In the latest version, there is a parameter 'bin.breaks=c(min, max, step)' can be used to set the colors, you can set the same 'bin.breaks' for two plots, then it would be comparable on colors between plots.

[deepti100rao]

Thanks to you for your prompt response! I could generate the plots as per my need!

On Thu, Aug 24, 2023, 2:07 PM Lilin Yin @.***> wrote:

Thank you for the feedback. In the latest version, there is a parameter 'bin.breaks=c(min, max, step)' can be used to set the colors, you can set the same 'bin.breaks' for two plots, then it would be comparable on colors between plots.

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