Im using see.geens from the maSigPro package and one of the outputs is the figure attached. The legend text is too small and the colors I would like to invert to have the mutant in red... or change it to blue.

I would like to make the output plots better to include in a publication

out.groups <- see.genes(get.groups$sig.genes$mutantvscontrol, color.mode = "gray", 
                    newX11 = FALSE, k = 6, cex = 6, cex.xaxis = 1)

If I try "cex.legend" it gives the following error:

    Error in PlotProfiles(data = dat[cut == i, ], repvect = repvect, main = i,  :  
unused argument (cex.legend = 2)

Hi Itzel,

The error is because cex.legend was only used in IsoPlot but not in see.genes. However, as we are working improving plots, we have updated see.genes and with the new version you could use cex.legend. Also you can decide eliminating lines in legend (lty.legend=NULL by default) or not (lty.legend=1). You can also change colors choosing the codes of the desired colors, example col = c(1,2,3) for 3 groups, draw thicker lines with lwd=2 ...

You can download the new version in https://github.com/mjnueda/maSigPro. There are also other changes: newX11 and cex.xaxis have been removed. For instance:

out.groups <- see.genes(get.groups$sig.genes$mutantvscontrol, color.mode = "gray", k = 6, cex = 1, cex.axis = 1, cex.legend = 0.5, lwd=1.5, pch=19)

MJNueda