Allelic plot sequence not visible
Closed this issue · 11 comments
Hi
I just updated to new version (2.214). Everything works but the sequence in allelic plot is missing.
Can you let me know what is going on and how I can fix the issue ?
Hi @AnkushAuradkar, Thanks for using CRISPResso.
I've never seen this before, and the allele plots work fine for others. I suspect it may be something with the pdf generation or the pdf viewer.
- What OS are you using to view the file?
- Does this happen in the PDF file as well as the png? (they should be the same)
- If you email the file to someone else is it viewable?
- Does this happen for every run (e.g. do you see a few letters for every allele plot, or are there some plots with all the letters, and others with no letters?)
I had the same issue. It happens for all the runs and in the PDF as well as the PNG format. Do you know how to fix it?
Hi @QiaoyanYang1211,
I've never seen this before, and the allele plots work fine for others. I suspect it may be something with the pdf generation or the pdf viewer.
- What OS are you using to view the file?
- Does this happen in the PDF file as well as the png? (they should be the same)
- If you email the file to someone else is it viewable?
- Does this happen for every run (e.g. do you see a few letters for every allele plot, or are there some plots with all the letters, and others with no letters?)
Hi @QiaoyanYang1211 and @AnkushAuradkar,
I have seen something similar on OS X using the default PDF viewer in Firefox. It would only happen at certain zoom levels (when I would change the zoom, letters would disappear/reappear). Would either you mind sharing the PDF or PNG files so that we can check them?
Hi @QiaoyanYang1211,
I've never seen this before, and the allele plots work fine for others. I suspect it may be something with the pdf generation or the pdf viewer.
- What OS are you using to view the file?
- Does this happen in the PDF file as well as the png? (they should be the same)
- If you email the file to someone else is it viewable?
- Does this happen for every run (e.g. do you see a few letters for every allele plot, or are there some plots with all the letters, and others with no letters?)
Hi kclem,
I am using the macOS Big Sur system.
It happens in all the PDF and png files.
No
I totally have 54 samples. They all look similar. Only a few letters for every allele plot were shown.
I have used CRISPRresso2 for analysis previously. It worked pretty well. But somehow, the old CRISPRresso2 version didn't work anymore, so I created a new environment and downloaded the package again. This time, all the other files look fine except for the plot of allels_frequency_around_gRNA.
del52-Heart-DNA-102.9.Alleles_frequency_table_around_sgRNA_TTGAAAGAATTCAGAATCAG.pdf
Hi @Colelyman
Attached the PDF and PNG files. Could you tell me how to fix it if you figure it out?
Thank you for providing the files; it certainly is strange ans doesn't look like what I have seen in the past. Would you be willing to share a small input file to see if I can reproduce the behavior on my machine? Also, if it isn't too much trouble could you run with the --debug flag and provide the log file? That my help us get to the bottom of the issue.
Previously, I was using Python version 3.11. However, I tried changing it to version 3.8 and the problem was resolved.
Thanks for the tip @AnkushAuradkar! Not sure why changing the Python version would make a difference (perhaps there were some other dependency versions that changed as well), but we will keep an eye on this.
@AnkushAuradkar @QiaoyanYang1211 I was able to reproduce this behavior and narrowed it down to occurring in matplotlib version 3.8.0 or greater. The fix for now (until we can figure out why version 3.8.0 is doing this) is to install version 3.7.2 or earlier.
Please let us know if you have any additional issues!