R/facet_msa.R

In YuLab-SMU/ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

##' The MSA would be plot in a field that you set.

##' @title segment MSA
##' @param field a numeric vector of the field size.
##' @return ggplot layers
##' @examples
##' library(ggplot2)
##' f <- system.file("extdata/sample.fasta", package="ggmsa")
##' # 2 fields
##' ggmsa(f, end = 120, font = NULL, color="Chemistry_AA") + 
##'   facet_msa(field = 60)
##' # 3 fields
##' ggmsa(f, end = 120, font = NULL,  color="Chemistry_AA") + 
##'   facet_msa(field = 40)
##' @export
##' @author Lang Zhou
facet_msa <- function(field) {
    structure(list(field = field),
              class = "facet_msa"
              )
}

facet_data <- function(msaData, field) {

    if(min(msaData$position) > 1){
        pos_reset <- msaData$position - min(msaData$position)
        pos_reset[pos_reset == 0] <- 1
    }else {
        pos_reset <- msaData$position
    }
    msaData$facet <- pos_reset %/% field


    msaData[(pos_reset %% field) == 0, "facet"] <- 
        msaData[(pos_reset %% field) == 0, "facet"] - 1

    return(msaData)

}