comparison lib.r @ 26:db6549f27ad1 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"

25:acc66e5c23d7

    par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))

    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
    names(group_colors) <- unique(xdata$sample_group)

    xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
    for (i in 1:nrow(featureDefinitions(xdata))) {
        mzmin = featureDefinitions(xdata)[i,]$mzmin
        mzmax = featureDefinitions(xdata)[i,]$mzmax
        plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
    }

    dev.off()
}

26:db6549f27ad1

    par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))

    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
    names(group_colors) <- unique(xdata$sample_group)
    col_per_samp <- as.character(xdata$sample_group)
    for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]}

    xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
    for (i in 1:nrow(featureDefinitions(xdata))) {
        mzmin = featureDefinitions(xdata)[i,]$mzmin
        mzmax = featureDefinitions(xdata)[i,]$mzmax
        plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=col_per_samp, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
    }

    dev.off()
}