Is it possible to represent the frequencies of two samples in the same .html browser?

[Coracollar]

Hi,
I was wondering whether besides the option of representing one pair of methylation frequencies and calls per .html, there was an option to generate a methylation html browser that shows the frequencies of two samples at the same time to compare them.

Thanks

[wdecoster]

I'm not sure if I understand what exactly you are hoping to get. Could you take a look at the examples and see if the plot you want is there?

[Coracollar]

Yes! The forth plot. El jue., 27 feb. 2020 21:35, Wouter De Coster <notifications@github.com> escribió:

…

I'm not sure if I understand what exactly you are hoping to get. Could you take a look at the examples <https://gigabaseorgigabyte.wordpress.com/2020/02/18/methplotlib-examples/> and see if the plot you want is there? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#21?email_source=notifications&email_token=ANZ7PMDKZRDDW5RK4ARNTYDRE6JM7A5CNFSM4K4PWRWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEND2VDA#issuecomment-591899276>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANZ7PMHVHJAJWBPW5S67NNDRE6JM7ANCNFSM4K4PWRWA> .

[wdecoster]

You'll get that if you just use two or more frequency files as input, and do not use the --split option.

If you add raw methylation likelihoods together with the frequencies then the tracks will be split automatically. I don't think I have a good way around that at the moment.

[Coracollar]

I have tried that but obtained: (methplot) [coracollar@spartan-login2 CORT13]$ methplotlib -m /data/cephfs/punim1048/allbarcoded/CORT/CORT13/chr11_cort13_calls_R.tsv \

/data/cephfs/punim1048/allbarcoded/CORT/CORT13/chr11_cort13_frec_R.tsv \

/data/cephfs/punim1048/allbarcoded/Control/C3/chr11_methylation_calls_R.tsv \

/data/cephfs/punim1048/allbarcoded/Control/C3/chr11_methylation_frec_R.tsv \

-n calls frequencies calls frequencies \ -w chr11:11,928,499-12,039,420

Traceback (most recent call last): File "/home/coracollar/anaconda3/envs/methplot/bin/methplotlib", line 10, in <module> sys.exit(main()) File "/home/coracollar/anaconda3/envs/methplot/lib/python3.7/site-packages/methplotlib/methplotlib.py", line 25, in main qc_plots(meth_data, window, qcpath=args.qcfile, outpath=args.outfile) File "/home/coracollar/anaconda3/envs/methplot/lib/python3.7/site-packages/methplotlib/methplotlib.py", line 177, in qc_plots full = data[0].join(data[1:]).dropna(how="any", axis="index") File "/home/coracollar/.local/lib/python3.7/site-packages/pandas/core/frame.py", line 7209, in join other, on=on, how=how, lsuffix=lsuffix, rsuffix=rsuffix, sort=sort File "/home/coracollar/.local/lib/python3.7/site-packages/pandas/core/frame.py", line 7248, in _join_compat frames, axis=1, join="outer", verify_integrity=True, sort=sort File "/home/coracollar/.local/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 281, in concat sort=sort, File "/home/coracollar/.local/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 452, in __init__ self.new_axes = self._get_new_axes() File "/home/coracollar/.local/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 517, in _get_new_axes for i in range(ndim) File "/home/coracollar/.local/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 517, in <listcomp> for i in range(ndim) File "/home/coracollar/.local/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 572, in _get_concat_axis self._maybe_check_integrity(concat_axis) File "/home/coracollar/.local/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 582, in _maybe_check_integrity "{overlap!s}".format(overlap=overlap) ValueError: Indexes have overlapping values: Index(['frequencies'], dtype='object')

…

On Fri, Feb 28, 2020 at 7:39 AM Wouter De Coster ***@***.***> wrote: You'll get that if you just use two or more frequency files as input, and do not use the --split option. If you add raw methylation likelihoods together with the frequencies then the tracks will be split automatically. I don't think I have a good way around that at the moment. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#21?email_source=notifications&email_token=ANZ7PMCKTU2LJHZOZX3OS5DRFAQINA5CNFSM4K4PWRWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENF3YQI#issuecomment-592165953>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANZ7PMEVVXRQNRNNJJ47Z43RFAQINANCNFSM4K4PWRWA> .

[wdecoster]

The cause here is that you reuse the same name for the datasets. It would be prevented if you would use e.g. frequencies1 and frequencies2:

methplotlib -m /data/cephfs/punim1048/allbarcoded/CORT/CORT13/chr11_cort13_calls_R.tsv \
 /data/cephfs/punim1048/allbarcoded/CORT/CORT13/chr11_cort13_frec_R.tsv \
/data/cephfs/punim1048/allbarcoded/Control/C3/chr11_methylation_calls_R.tsv \
/data/cephfs/punim1048/allbarcoded/Control/C3/chr11_methylation_frec_R.tsv \
 -n calls frequencies1 calls frequencies2 \
 -w chr11:11,928,499-12,039,420

And that's also not what I told you to do if you want a plot with overlapping frequency tracks. You should then do the following command with just frequencies:

methplotlib -m /data/cephfs/punim1048/allbarcoded/CORT/CORT13/chr11_cort13_frec_R.tsv \
/data/cephfs/punim1048/allbarcoded/Control/C3/chr11_methylation_frec_R.tsv \
 -n calls frequencies1 calls frequencies2 \
 -w chr11:11,928,499-12,039,420

As I said:

If you add raw methylation likelihoods together with the frequencies then the tracks will be split automatically. I don't think I have a good way around that at the moment.

If you include CALL files you won't get overlapping frequencies. That's just how the code is implemented at the moment.