[BioC] Overlapping boxplots with transparency

Heidi Dvinge heidi at ebi.ac.uk
Wed Mar 2 23:25:51 CET 2011

Hi Fong,

> Hi,
> I am pretty stumped on how I can approach this problem.  Basically, I have
> two groups of boxplots which I would like to overlap on top of each other.
>  Each boxplot in a group represents a probeset's expression values.  So
> when
> I overlap them, I would like to see which probesets differ a great deal
> between the two groups.  I know that the boxplot function has a parameter
> add that when you set to TRUE it will just add the entire boxplot to the
> current graph which is what I want.  But sometimes the boxplots will just
> completely cover another boxplot.  What would be great is if I could set
> transparency, but there doesn't appear to be any parameters to set.
I'm not really sure why overlapping the boxes would be better than just
showing them side by side. However, you can define transparent colours
using e.g. adjustcolor() or the alpha parameter in rgb().

For example:
> boxplot(count ~ spray, data = InsectSprays, col=rgb(1,0.5,0.3, alpha=0.5))
> boxplot(count*1.1 ~ spray, data = InsectSprays, col=rgb(0.2,0.5,0.3,
alpha=0.5), add=TRUE)


> What I would like to do is demonstrated in the Affymetrix technical note:
> "Identifying and Validating Alternative Splicing Events" figure 15.
> Does anyone have any idea how I could do this?  Any help would be greatly
> appreciated.
> Fong
> 	[[alternative HTML version deleted]]
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