Omar Wagih comments

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                                            Omar Wagih

Trimming adapter sequence with Ns

In my case it’s just a 3’ sequencing adapter

Logo Range

If your input is sequences you can just subset your specific positions/indexes that you want, and set the x-axis tick labels of your ggplot object > On Jul 4, 2021,...

Change numbers on the x-axis of logos

This is a ggplot question rather than a ggseqlogo question. ggseqlogo just builds on top of ggplot. A quick Google will show you how to change axis labels in ggplot2...

Hi Claire, ggseqlogo returns a ggplot object which you can extend with ggplot in whatever way you want including [geom_errorbar](https://ggplot2.tidyverse.org/reference/geom_linerange.html) ``` ggseqlogo(seqs) + geom_errorbar(data=df, aes(x, y, ymin, ymax)) ``` should...

secondary structure not rendering when no HELIX/SHEET in pdb file

Hi Marco, Thanks for your reply. I did indeed update PDB to include predictions DSSM, but I would rather use the original PDB files so this helps a lot, even...

sequence logo with phosphorylated amino acids

Did you try the custom alphabets, see https://omarwagih.github.io/ggseqlogo/ Otherwise, can you post a reproducible example

<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as of ggplot2 3.3.4

Thanks for reporting. Nothing you need to worry about in this version but this will probably break in future versions. I'll address this soon.

Glitch or Feature? Either methods do not represent the true distribution of an allele when gaps are involved

Can you share example data for me to be able to fully reproduce?

about fix length

@pariswu1988 you can use the `msa` package: https://bioconductor.org/packages/release/bioc/html/msa.html to pre-align your sequences.

Omar Wagih