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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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visualisation output #85

Closed magdaliput closed 1 week ago

magdaliput commented 2 months ago

Hi, I have two problems concerning saving the plots. The first one is outcome of pat_fig. It is great that I can get all the samples on 1 plot, however, I would like to change the number of samples per row. I analyze 18 samples (3 replicates for each cell type) and would like to have 3 in row. The scripts generates plot with 5 samples per row. Is it possible to change this? cg00256374-cg02480840

The other issue I have is the vis command with .beta files (numbers representing % of methylation). The visualisation is great however I cant save the results to the file. The -o option is red, there are no warnings but no file is saved. Do you know what could be posibbly the problem? example code: wgbstools vis .beta -r chr19:1226523-1226535 -o test.png

Thanks in advance for answear and for awsome tools for analysis :) Cheers Magda

yonniejon commented 1 month ago

For the pat_fig you have col_wrap argument which defaults to 5. You can change it to 3.

yonniejon commented 1 month ago

about the beta vis - i am not sure if there is an alternative but vis command does not provide this option for saving output as an image.

magdaliput commented 1 month ago

For the pat_fig you have col_wrap argument which defaults to 5. You can change it to 3.

thank you for reply