[Bug]: Incorrect labelling of the "Ratio of M and U Intensities" box plots

[lw371]

Contact Details

[email protected]

What happened?

In the produced html QC report the "Ratio of M and U Intensities" labelling of the box plots can sometimes be incorrect. For example for samples where I have genders of Male (M), Female (F), and fully methylated controls (C) the C plot is incorrectly labelled as 'M'.

How can the bug be reproduced?

No response

Relevant log output

No response

[sof202]

Code in question:

BrainFANS/array/DNAm/preprocessing/QC.rmd

Lines 268 to 282 in 169609f

	```{r, intensRatio, fig.width = 10, fig.height = 5, echo = FALSE}
	par(mfrow = c(1,1))
	par(mar = c(4,4,4,1))
	hist(QCmetrics$intens.ratio, xlab = "Ratio of M:U intensities", breaks = 25, main = "", col = "gray")
	for(i in 2:ncol(plotCols)){
	if(length(unique(plotCols[!is.na(QCmetrics$intens.ratio),i])) > 1){
	model<-lm(QCmetrics$intens.ratio ~ plotCols[,i])
	anova(model)
	legendDat<-legendParams[[i-1]]
	boxplot(QCmetrics$intens.ratio ~ plotCols[,i], col = legendDat[,2], names = legendDat[,1], xlab = "", ylab = "Ratio M:U", main = paste("Split by ", colnames(plotCols)[i]))
	title(main = paste("ANOVA P =", signif(anova(model)[1,5], 3)), line = 0.5, adj = 1)
	}
	}

[sof202]

I'm think that the order of legendParams is not guaranteed to be the same order as whatever the boxplot() function thinks to make with plotCols[[]]. Which causes the problem. I'm going to assume we can fix this by changing line 279 to:

boxplot(QCmetrics$intens.ratio ~ legendDat[,1], ...)

As this accomplishes the same thing, but ensures consistent ordering.