Colour/fill palette order inconsistent between `spectra` plot types

[jackscanlan]

*.fl.png, *.ln.png and *.st.png plots have different palette orders and colour:value combinations for both the spectra-cn and spectra-asm plots. Below are examples for the spectra-cn plots:

Compare the scale_*_manual arguments between the plot_line/plot_fill and plot_stack functions in plot_spectra_cn.R, which I think it causing it:

plot_line <- function(dat, name, x_max, y_max, zero, cutoff) {
  ggplot(data=dat, aes(x=kmer_multiplicity, y=Count, group=dat[,1], colour=dat[,1])) +
    geom_line() +
    scale_color_manual(values = merqury_brw(dat[,1]), name="k-mer") +
    plot_zero_line(zero=zero) +
    plot_zero_fill(zero=zero) +
    plot_cutoff(cutoff) +
    theme_bw() +
    format_theme() +
    scale_y_continuous(labels=fancy_scientific) +
    coord_cartesian(xlim=c(0,x_max), ylim=c(0,y_max))
}

plot_fill <- function(dat, name, x_max, y_max, zero, cutoff) {
  ggplot(data=dat, aes(x=kmer_multiplicity, y=Count)) +
    geom_ribbon(aes(ymin=0, ymax=pmax(Count,0), fill=dat[,1], colour=dat[,1]), alpha=ALPHA, linetype=1) +
    plot_zero_fill(zero=zero) +
    plot_cutoff(cutoff) +
    theme_bw() +
    format_theme() +
    scale_color_manual(values = merqury_brw(dat[,1]), name="k-mer") +
    scale_fill_manual(values = merqury_brw(dat[,1]), name="k-mer") +
    scale_y_continuous(labels=fancy_scientific) +
    coord_cartesian(xlim=c(0,x_max), ylim=c(0,y_max))
}

plot_stack <- function(dat, name, x_max, y_max, zero, cutoff) {
  dat[,1]=factor(dat[,1], levels=rev(levels(dat[,1]))) #[c(4,3,2,1)] reverse the order to stack from read-only
  ggplot(data=dat, aes(x=kmer_multiplicity, y=Count, fill=dat[,1], colour=dat[,1])) +
    geom_area(size=LINE_SIZE , alpha=ALPHA) +
    plot_zero_stack(zero=zero) +
    plot_cutoff(cutoff) +
    theme_bw() +
    format_theme() +
    scale_color_manual(values = merqury_brw(dat[,1], direction=1), name="k-mer", breaks=rev(levels(dat[,1]))) +
    scale_fill_manual(values = merqury_brw(dat[,1], direction=1), name="k-mer", breaks=rev(levels(dat[,1]))) +
    scale_y_continuous(labels=fancy_scientific) +
    coord_cartesian(xlim=c(0,x_max), ylim=c(0,y_max))
}

Similar cause for the spectra-asm plots I imagine.