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YuLab-SMU / ggmsa

:traffic_light: Visualizing publication-quality multiple sequence alignment using ggplot2
http://yulab-smu.top/ggmsa
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Error in .Call2 with DNAbin #19

Open bbvdhoorn opened 3 years ago

bbvdhoorn commented 3 years ago

Hi,

Whenever I try to use ggmsa, I get the following error code: Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 48 (char '0') not in lookup table.

I use ggsma on a DNAbin object. What am I doing wrong?

Best, Berry

nyzhoulang commented 3 years ago

Hi Berry,

Thanks for your feedback!

We have fixed the error that the DNAbin or AAbin cannot be read by ggmsa(). This error will no longer occur in the dev version.

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("YuLab-SMU/ggmsa")

Best, Lang Zhou, YuLab member

bbvdhoorn commented 3 years ago

Dear Lang,

Thanks for your respons.

Are you sure it should be solved? I still get an error, even when I remove the pacakage and reinstall it with the code below. Is that really the development version?

The script: ggmsa(refseq.bin, seq_name = TRUE, color='Chemistry_AA', char_width = 0.5) + facet_msa(field = 100)

The error code: Error in $<-.data.frame(*tmp*, "name", value = integer(0)) : replacement has 0 rows, data has 144261

Best, Berry

Op vr 2 apr. 2021 om 09:25 schreef Lang Chau @.***>:

Hi Berry,

Thanks for your feedback!

We have fixed the error that the DNAbin or AAbin cannot be read by ggmsa(). This error will no longer occur in the dev version.

if (!requireNamespace("devtools", quietly=TRUE)) install.packages("devtools") devtools::install_github("YuLab-SMU/ggmsa")

Best, Lang Zhou, YuLab member

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nyzhoulang commented 3 years ago

Hi Berry,

The error code: Error in $<-.data.frame(*tmp*, "name", value = integer(0)) :

I can't repeat the error from our DNAbin or AAbin object.They can run well in my tests.

library(ape) library(ggmsa)

nt_sequence <- system.file("extdata", "LeaderRepeat_All.fa", package = "ggmsa") protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa") DNA.bin <- read.FASTA(nt_sequence, type = "DNA") AA.bin <- read.FASTA(protein_sequences, type = "AA") class(DNA.bin) class(AA.bin)

ggmsa(DNA.bin, end = 50, seq_name = F, font = NULL,color = "Chemistry_NT") ggmsa(AA.bin,start = 200,end = 250, seq_name = F,font = NULL) ggmsa(AA.bin, start = 0,end = 150,seq_name = TRUE, color='Chemistry_AA',char_width = 0.5) + facet_msa(field = 50)

The dev version number is shown as 0.0.6-1 if you have installed it correctly. If this error still occurs, could you please send us a reproducible example that you use to run the ggmsa? (nyzhoulang@gmail.com)

Thanks much, Lang