R/color_by_conservation.R

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

color_increment <- function(conservation_visibility){
    lapply(seq_len(nrow(conservation_visibility)), function(i){
        color_ramp <- 
            colorRampPalette(colors = 
                                 c(conservation_visibility[i,"color"], 
                                   "#ffffff"))
        
        color_change <- 
            rev(color_ramp(100))[conservation_visibility[i,"visibility"]]
        return(color_change)
        }) %>% unlist 

}


color_visibility <- function(y){
    #options(digits = 2)
    #on.exit()
    conser_data <- bar_data(y)
    conser_data$visibility <- 
        conser_data$Freq / length(levels(y[[1]])) %>% round(2)
    conser_data$visibility <- conser_data$visibility * 100
    names(conser_data)[3] <- "position"
    y_filter <- y[c(-1,-3)] 
    conser_ready <- merge(conser_data, y_filter)
    y$color <- color_increment(conser_ready)
    return(y)
}