Reorganize and optimize peak-gene diagnostic plots
As discussed today, let's revamp the peak-gene diagnostic plots. To start with, just use readRDS to load in an existing GRN, and then simply take a look at the (internal) function .plotDiagnosticPlots_peakGene_all
and follow the code there. Execute the beginning until the first plots are produced and from there, you can start to re-arrange and optimize. No errors should be thrown; if, let me know, been there.
Notes:
- I added a
addOptionalPlots
parameter today so we can omit some plots unless asked for - gray / white vs colors: your judgment, we can discuss together what looks better
- Usage of the
patchwork
package seems like a good idea, let's try that - Let's try a QQ plot instead of the current density plot for the correlation coefficient, comparing real vs random
- Let's also make terminology identical and clear in the legends, plot title, axis etc
- I add things if they come to mind