Trouble making a ggmsa alignment plot

Question

[andre.arrudalima]

I'm having trouble making an ggmsa alignment plot. I want to do a figure just like this:

I already have my alignment in .fasta. Here's part of it

> At5g01950 |626-899 
FSSSTLVGRGGYGKVYRGVLSDN-TVAAIKRAD--EGSLQ-GEKEFLNEIELLSRLHHRN
LVSLIGYCDEESE-QMLVYEFMSNGTLRDWLSAK--GKESLSFGMRIRVALGAAKGILYL
HTEANPPVFHRDIKASNILLDPNFNAKVADFGLSRLAPVLEDEEDVPKHVSTVVRGTPGY
LDPEYFLTHKLTDKSDVYSIGVVFLELLTGMHAISHGK---------NIVREVKTAEQRD
-------MMVSLIDKRME-PW----SMESVEKFAALALRCSHDSPEMRPGMAEVVKELES
L---------L
> HPCA1 |631-905 
FSEANDVGGGGYGKVYRGILPNG-QLIAIKRAQ--QGSLQ-GGLEFKTEIELLSRVHHKN
VVRLLGFCFDRNE-QMLVYEYISNGSLKDSLSGK--SGIRLDWTRRLKIALGSGKGLAYL
HELADPPIIHRDIKSNNILLDENLTAKVADFGLSKLVGDPEK-----THVTTQVKGTMGY
LDPEYYMTNQLTEKSDVYGFGVVLLELLTGRSPIERGKYVVREVK--TKMNKSRSLYD--
--------LQELLDTTIIASSG---NLKGFEKYVDLALRCVEEEGVNRPSMGEVVKEIEN
I---------M
> THE1 |510-783 
FDESSLLGVGGFGRVYKGTLEDG-TKVAVKRGN--PRSEQ-GMAEFRTEIEMLSKLRHRH
LVSLIGYCDERSE-MILVYEYMANGPLRSHLYGA--DLPPLSWKQRLEICIGAARGLHYL
HTGASQSIIHRDVKTTNILLDENLVAKVADFGLSKTGPSLDQ-----THVSTAVKGSFGY
LDPEYFRRQQLTEKSDVYSFGVVLMEVLCCRPALN--PVLPREQV--NIAEWAMAWQKKG
-------LLDQIMDSNLTGKV----NPASLKKFGETAEKCLAEYGVDRPSMGDVLWNLEY
A----------

I think I was able to import it to R with

fasta_file_path <- "path/to/your/file.fasta"

, since fasta_file_path appears in Enviroment.

But now I dont know how to go on. If I follow the steps as specified in this site http://yulab-smu.top/ggmsa/articles/ggmsa.html

I get this error:

Error in if (freq1 > 0.9 && freq2 > 0) { : 


 absent value where TRUE/FALSE is necessary (free translation here)

Please help me solving this problem.

Thank you

Answer 1

[alslonik]

To make ggmsa work you need to upload your fasta as BioStrings object:

lbrary(BioStrings)
llibrary(ggmsa)

your_fasta = readAAStringSet("path/to/your/file.fasta")
ggmsa(your_fasta, 300, 350, color = "Clustal", font = "DroidSansMono", char_width = 0.5, seq_name = TRUE )`

They somehow skipped the BioStrings step on their "Getting started" page.