Controlling our graphs...

The styles of graphs in journals vary a lot and can be quite different from the default style encoded by R or by most data analysis packages. An essential part of learning to control a piece of analysis software is expressing the graphs in the format that your discipline and your journals like.

One of the things that varies a lot is whether your graph has a box or not. Boxes are presented by default in R and many other programmes. Removing the boxes leave floating axis which is not in the style of the journal either.

Working through some of these things using the data from the LD50 graph previously:

Here is the default graph:

From the default code:

plot(data$nM, data$dead.cells, 
    )

Make the x-axis log tranformed, add limits and change symbols:

Here is the code:

# Add log axis, x and y limits and change the symbols
plot(data$nM, data$dead.cells, 
     log="x", # makes it a log plot
     pch=20, # gives small black dots instead of empty circles
     xlim= c(500, 10000),
     ylim= c(0,100),
    ) 

Key next step is to suppress everything except the points. It looks a very odd:

Here is the code:
plot(data$nM, data$dead.cells, 
     log="x", 
     pch=20,
     xlim= c(500, 10000),
     ylim= c(0,100),
     axes=FALSE, # suppresses the titles on the axes
     ann=FALSE, # suppresses the axes and the box  
  ) 


Now,  add back axis first:

Code:
axis(1, at=c(200, 500, 1000, 2500, 5000, 10000), # x-axis 
     lab=c("","0.5","1","2.5","5","10"), 
     lwd=2, # thicker lines
     pos=0)  # puts the x-axis at zero rather than floating 
axis(2, at=c(0, 20, 40, 60, 80,100), # y-axis
     lab=c("0", "20", "40", "60", "80", "100"), 
     lwd=2, 
     las=1) # turns the numbers so easier to read

Next, add titles (I like the Greek symbol in the x-axis):

Code:
title("Figure 1A", 
      xlab= expression(paste("Drug concentration (", mu, "M)")), 
      # not the word "micro"
      ylab= "Dead cells (% of cells)")

And a nice black fitted line:

Code:
# adds the fitted non-linear line 
lines(10^x,y, lty=1, lwd =2)

Finally, add the LD50 again:

using this code:
# add the LD50 in the legend which allows nice positioning. 
rp = vector('expression',1)
rp[1] = substitute(expression(LD50(microM) == MYVALUE), 
                   list(MYVALUE = format((10^m[3])/1000,dig=3)))[2]
legend('topleft', legend = rp, bty = 'n')


The full code for this script and the others mentioned in this blog are available on Github.

I used these resources to develop this script:

Quick R: http://www.statmethods.net/advgraphs/parameters.html

http://www.carlislerainey.com/2012/12/17/controlling-axes-of-r-plots/
Adding micro to the R plot: http://stackoverflow.com/questions/6044800/adding-greek-character-to-axis-title
Getting the x-axis where I wanted it: http://stackoverflow.com/questions/19581721/changing-x-axis-position-in-r-barplot