Publication quality figures from R....

I have been preparing figures for Suliman's revised manuscript.
This has been a bit of an R learning curve as I have had to prepare the figures in a publication quality format.

However, I have done it and it's progress.

Firstly a list of resources that give some good tips and info:

• http://blog.revolutionanalytics.com/2009/01/10-tips-for-making-your-r-graphics-look-their-best.html
• http://www.cookbook-r.com/Graphs/Output_to_a_file/
• http://thinkdatavis.com/2013/06/05/how-to-make-nice-boxplots-with-r/
• http://www.statmethods.net/advgraphs/axes.html 

So the key bit of code is as follows:

>ppi=600    #pixels per square inch

>png("boxplot_20140602.png", width=6*ppi, height=5*ppi, res=ppi)  

              #this creates the output file and adds information about size and resolution  

>boxplot(P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, 

               frame=FALSE,   #suppresses the frame

               las =2,                 #turns the labels sideways

               names = c("Patient 1","Patient 2","Patient 3","Patient 4","Patient 5","Patient 6","Patient 7","Patient 8","Patient 9","Patient 10","Patient 11","Patient 12"), 

               yaxt="n",             #suppresses the y axis

               ylab = expression(bold("Relative iTRAQ signal")))

>axis(2, 

         0:4,

         labels=formatC(seq(0,4, by=1)), 

        las=1, 

        xpd=NA)  # allows the axis to go outside of the graph area and plot "0" and "4"

   #  This creates a new axis. 

   # R won't usually let the axis go outside the 'graph area'.

>dev.off()

    #very important command that tells R that you are finished plotting; otherwise your graph will not show up.

Some key concepts:

    This generates PNG files but similar commands are also available for PDFs, SVGs and others. VERY POWERFUL. 

    Increasing the resolution makes the lines thicker and the text more distinct. 

I used PNG to put into Powerpoint. 

Need to learn more about colour.