I can't find Cripavirus.fasta

[aimer-entropy]

Hello, when I run the code in the tutorial here: cripavirus_msa <- system.file("extdata", "Cripavirus.fasta", package = "ggmsa") I couldn't find the Cripavirus.fasta Where could I get it?

[nyzhoulang]

Hi @aimer-entropy,

We updated the data for this example, so you can use the following code to repeat it (ggmsa ver >= 1.0.0):

library(ggplot2)

RF03120_msa<- system.file("extdata", "Rfam", "RF03120.fasta", package = "ggmsa")
RF03120_ss <- system.file("extdata", "Rfam", "RF03120_SS.txt", package = "ggmsa")

RF_arc <- readSSfile(RF03120_ss, type = "Vienna" )

p <- ggmsa(RF03120_msa, 
             font = NULL, 
             color = "Chemistry_NT", 
             seq_name = F, 
             show.legend = F, 
             border = NA) +
  geom_helix(helix_data = RF_arc) + 
  theme(axis.text.y = element_blank())
p

RF03120_msa<- system.file("extdata", "Rfam", "RF03120.fasta", package = "ggmsa") corresponds to cripavirus_msa <- system.file("extdata", "Cripavirus.fasta", package = "ggmsa") above.

Thanks for your feedback! Lang

[aimer-entropy]

Thank you for your help. It works now.