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:

)

Make the x-axis

**log tranformed, add limits and**

**change**

**symbols**:

Here is the code:

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:

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:

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

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

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