Closed shivamgupta0791 closed 2 years ago
Please provide a minimal example that exhibits this behavior.
Hi Gavin,
Hope you are doing well.
Thank you so much for replying.
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
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)
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.
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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.
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.
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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.
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