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gecrooks / weblogo

WebLogo 3: Sequence Logos redrawn
weblogo.threeplusone.com
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No reproducibility #123

Closed shivamgupta0791 closed 2 years ago

shivamgupta0791 commented 2 years ago

for sequences more than 10 K weblogo doesn't show consistency. Sometime it generates logo and sometimes it shows random error like sequences are different length

gecrooks commented 2 years ago

Please provide a minimal example that exhibits this behavior.

shivamgupta0791 commented 2 years ago

Hi Gavin,

Hope you are doing well.

Thank you so much for replying.

  1. If I am choosing a resolution of more than 3600, I am getting an inverted image of sequences. Please see the image (resolution-4000) attached.

      weblogo -f P200_S37-CDR3-Padded.fasta -D fasta -o P200-S37-CDR3-2

    -F jpeg -n 20 -s large --resolution 4000

  2. which option do I need to choose to see the sequences at the bottom (more mutation at one place) big and clear. Please see the attached image.(1_Li)

  3. How to give the desired seperation between two alphabets. I tried all the options mentioned in tutorial but could not change the separation distance. Please help me out with this issue.(2_Li)

With Regards Shivam Gupta

On Fri, 17 Dec 2021 at 07:58, Gavin Crooks @.***> wrote:

Please provide a minimal example that exhibits this behavior.

— Reply to this email directly, view it on GitHub https://github.com/WebLogo/weblogo/issues/123#issuecomment-996257806, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOWRHL4KOJHHHCI6APYKEQ3URJVHVANCNFSM5KCX2P3Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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gecrooks commented 2 years ago

A resolution of 4000 is enormous. I'd hazard a guess that Ghostscript is choking on the huge files you're generating. You should either generate a file in a vector format, such as PDF, or use a more reasonable resolution, e.g. 600.

shivamgupta0791 commented 2 years ago

Dear Gavin,

Hope this email finds you well.

Is there any option to change the distance between two stacks of logos to avoid overlapping among them?

[image: image.png]

Looking forward to your reply. Have a nice day ahead.

With Regards Shivam Gupta

On Wed, 29 Dec 2021 at 06:56, Gavin Crooks @.***> wrote:

A resolution of 4000 is enormous. I'd hazard a guess that Ghostscript is choking on the huge files you're generating. You should either generate a file in a vector format, such as PDF, or use a more reasonable resolution, e.g. 600.

— Reply to this email directly, view it on GitHub https://github.com/WebLogo/weblogo/issues/123#issuecomment-1002296927, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOWRHLZF25SBS3RD25YDEX3UTIXBHANCNFSM5KCX2P3Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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gecrooks commented 2 years ago

I cannot see any image, so I don't know how it is that stacks are overlapping.

There is a variable stack_margin that controls the gap between stacks. But it's only accessible via the API, not the command line or GUI.