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ANGSD / angsd

Program for analysing NGS data.
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visualizing the 2D-SFS #567

Closed yangwukaidi closed 1 year ago

yangwukaidi commented 1 year ago

hi. How do I visualize the 2D-SFS produced by this software? According to MFumagalli's tutorial (https://github.com/mfumagalli) . I try to get 2 D-SFS using the following script, Rscript $NGSTOOLS/Scripts/plot2DSFS.R Results/LWK.PEL.sfs LWK-PEL 10-10 But I failed, and I got a strange picture. As follows 1680575567157 How can these problems be solved? I get 2D-SFS file with only one row in it. Is that correct? Look forward to your reply! Thanks!

ANGSD commented 1 year ago

Plotting the 2dsfs can be abit tricky and will likely require some tweaking since it is visualized as a heatmap. It should indeed be one row, this is a flattened matrix. If you want to validate correctness of dimension you can convert to a matrix and look at the 1d marginals.

On 4 Apr 2023, at 04.34, yangwukaidi @.***> wrote:

hi. How do I visualize the 2D-SFS produced by this software? According to MFumagalli's tutorial (https://github.com/mfumagalli) . I try to get 2 D-SFS using the following script, Rscript $NGSTOOLS/Scripts/plot2DSFS.R Results/LWK.PEL.sfs LWK-PEL 10-10 But I failed, and I got a strange picture. As follows https://user-images.githubusercontent.com/127917612/229671814-fba48e22-15e6-4d27-a343-a91db5e8f235.png How can these problems be solved? I get 2D-SFS file with only one row in it. Is that correct? Look forward to your reply! Thanks!

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