mix.R

    ## Throw out the possibly empty members.
    really_okind <- okind[m$qa$ms[irows, ]$qa_pass]
    m$qa$ms[which(qa_pass),ms2_sel:=.(mapply(function (spl,inds,ms1rt) {
        rtdiff <- sapply(spl[inds],function (x) abs(x$rt-ms1rt))
        closest <- which.min(rtdiff)
        inds[[closest]]
    },
    spec,
    really_okind,
    ms1_rt,
    SIMPLIFY=T))]

    m    
}

gen_mz_err_f <- function(entry,msg) {
    eppm <- grab_unit(entry,"ppm")
    eda <- grab_unit(entry,"Da")
    shinyscreen:::assert(xor(is.na(eda), is.na(eppm)), msg = msg)
    if (is.na(eda)) function(mz) eppm*1e-6*mz else function (mz) eda
}


gen_rt_err <- function(entry,msg) {
    em <- grab_unit(entry,"min")
    es <- grab_unit(entry,"s")
    shinyscreen:::assert(xor(is.na(em), is.na(es)), msg = msg)
    if (is.na(em)) es/60. else em
}

fig_path <- function(top,set,group,id,suff,ext="pdf") {
    base <- paste("plot",set,group,id,suff,sep="_")
    fn <- paste0(base,".",ext)
    fn <- gsub("\\[","",fn)
    fn <- gsub("\\]","",fn)
    fn <- gsub("\\+","p",fn)
    fn <- gsub("-","m",fn)
    if (!is.null(top)) file.path(top,fn) else fn
}

get_coord_lim <- function(new,def) {
    if (is.null(new)) return(def)
    res <- new
    if (length(new[[1]])==0) res[[1]]<-def[[1]]
    if (length(new[[2]])==0) res[[2]]<-def[[2]]
    res
}



gen_base_ms1_plot_tab <- function(summ,ms1_spec) {
    
    ident <- c("set",
               "adduct",
               "tag",
               "ID",
               "mz",
               "Files")
    
    res <- summ[ms1_spec,c(.SD,
                           list(rt_peak=i.ms1_rt,
                                eicMS1=lapply(i.eicMS1,list))),
                           .SDcols=ident,
                           on=BASE_KEY,
                nomatch=NULL]
    setkeyv(res,cols=BASE_KEY)
    res
}
plot_decor <- function(m,islog,all_labels,legend_name) {
    textf <- ggplot2::element_text

    ## Logarithmic, or linear y axis?
    scale_y <- if (shiny::isTruthy(islog))
                       ggplot2::scale_y_log10 else ggplot2::scale_y_continuous

    rt_new_lim <- c(rt_in_min(m$conf$figures$rt_min),
                    rt_in_min(m$conf$figures$rt_max))
    rt_lim <- get_coord_lim(rt_new_lim,DEFAULT_RT_RANGE)

    my_theme <- function (...) ggplot2::theme()

    getpal <- colorRampPalette(RColorBrewer::brewer.pal(8,"Dark2"))
    
    col_all_vals <- getpal(length(all_labels))
    names(col_all_vals) <- all_labels
    scale_colour <- function(breaks, labels, ...) ggplot2::scale_colour_manual(values = col_all_vals,
                                                                               breaks = breaks,
                                                                               labels = labels,
                                                                               name = legend_name,...)
    
    my_coord <- ggplot2::coord_cartesian(xlim = rt_lim)

    function(plot,breaks,labels) plot + my_coord + scale_colour(breaks=breaks,
                                                                labels=labels) + scale_y() + my_theme() 
}


plot_eic_ms1 <- function(df,style_fun,plot_label) {
    mk_leg_lab<-function(tag,rt) {if (length(tag) > 0) paste(tag,"; rt= ",formatC(rt,format='f',digits=RT_DIGITS)," min",sep='') else character(0)}

    mz <- df[,unique(mz)]
    tbl <- df[,.(verb_labs=mk_leg_lab(plot_label,rt_peak),plot_label),
              by=c("plot_label","rt_peak")]
    verb_labs <- tbl[,verb_labs]
    labs <- tbl[,plot_label]
    df[,plot_label:=factor(plot_label)]
    style_fun(ggplot2::ggplot(df,ggplot2::aes(x=rt,y=intensity,colour=plot_label)),
              breaks=labs,
              labels=verb_labs) +
        ggplot2::geom_line(key_glyph=KEY_GLYPH) +
        ggplot2::labs(x=CHR_GRAM_X,
                      y=CHR_GRAM_Y)
}