Trouble making a ggmsa alignment plot
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
• 1,235 views
•
link
updated
by
GenoMax
•
written
by
andre.arrudalima •
•
written
by
andre.arrudalima •
1 answer
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.
Log in to answer this question.