Epinano differr warning

[rania-o]

Hello, Each time I use Epinano_DiffErr.R, I get this warning :

1: ggrepel: 23 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
2: ggrepel: 42 unlabeled data points (too many overlaps). Consider increasing max.overlaps

Please, can you tell me what this means ? and how to increase these overlaps ? and if I do, will it enhance the modif detection ?

Rania

[enovoa]

Hi @rania-o - have you tried the test data of the repo? Thanks

[rania-o]

Hi @enovoa Thank you for your fast reply. No I didn't use it with the test data of the repo, but I used with other test data and it worked well without the warning.

[enovoa]

Please share reproducible command line with input data to be able to reproduce the error, because we have never encountered it. Thank you!

[Huanle]

Hi @enovoa Thank you for your fast reply. No I didn't use it with the test data of the repo, but I used with other test data and it worked well without the warning.

Hi @rania-o ,

Have you sorted it out? If you haven't, do you mind sharing your input data?

Best, Huanle

[rania-o]

Hi @Huanle , @enovoa

Sorry for my late reply. No, I didn't sorted it out, but as I already mentioned I do get results with the warning. Our data is too big to transfer it to you. On the other hand, I got the warning also by testing the data provided by Drummer in their github, here is the command I used:

Rscript /home/rania/softs/EpiNano/Epinano_DiffErr.R -k exome.Ad5.UNMOD.plus_strand.per.site.csv -w exome.Ad5.MOD.plus_strand.per.site.csv -o epinano_results_001_deviance_4_t -f sum_err -p -t 4 -d 0.01

You can find the *.csv files of the command Epinano_Variants.py.

Thank you, Rania exome.Ad5.UNMOD.plus_strand.per.site.csv

exome.Ad5.MOD.plus_strand.per.site.csv

[Huanle]

Hi @rania-o ,

It is an alarming emitted by ggrepel, which repels away texts, labels and data points. But when there are too many overlaps between the above mentioned elements, it relseases the warning message you have seen.

It wont affect the analysis. If you are annoyed by the warning message, you can add ggrepel.max.overlaps = Inf (this suppresses the warning msg globally) to the script.

Hope this helps.

Cheers - Huanle