Question

I have a semi-melted data frame that looks like this:

head(final_melt)

   Group       Source variable   value
 Control Whole Kidney     MZF1 0.23879
 Control Whole Kidney     MZF1 0.49381
 Control Whole Kidney     MZF1 0.40827
 Control Whole Kidney     MZF1 0.55548
 Control Whole Kidney     MZF1 0.34664
 Control Whole Kidney     MZF1 0.68102

Group has two levels (Control and Disease), source has 4 levels (Whole Kidney, Glomerulus, Tubulointerstitium, and HK-2 + TGF-B). variable also has four levels (TFAP2A, MZF1, YY1, SP1).
I would like to do something like the following in a loop

d = subset(final_melt, final_melt$Source=="Whole Kidney")
qplot(data=d, Group, value, facets=.~variable, geom="boxplot")
pdf("Whole Kideny.pdf")
dev.off()

While I know I could just say facets=Source~variable, the individual plots end up being too small to be informative. So I need to plot one level of the Source factor at a time.
The problem is I can’t even get the pdf() function to work. It creates a file, with the correct name, but when I try to open it adobe says There was an error opening the file, and that it is already open in another application (why I added the dev.off(), but that didn’t seem to do anything).

Any help is appreciated.
Cheers,
Davy.

Answer 1

1. Open a graphics device (pdf(), png() etc.)
2. Create and print your ggplot or lattice graphic.
3. Call dev.off().
4. …..?
5. Profit.

In that order.