Question

I have a simple csv file containing 2 columns of numbers with the headers “Colli_On” and “Colli_Off”. I have written a simple Rscript which passes 3 arguments – file name and column names – and would like to produce a Bland Altman plot. However I get the following error message

> Error in plot.window(...) : need finite 'xlim' values
Calls: baplot ... do.call -> plot -> plot.default -> localWindow -> plot.window
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf

Where am I going wrong?

   #!/usr/bin/Rscript
# -*- mode: R =*-

#script passes 3 arguments filename and 2 columns and does bland altman analysis
#Example BA /home/moadeep/Data/sehcat.csv Colli_on Colli_off

args <- commandArgs(TRUE)
mydata <- read.csv(file=args[1],head=TRUE,sep="\t")

baplot = function(x,y){

  bamean = (x+y)/2
  badiff = (y-x)

  plot(badiff~bamean, pch=20, xlab="mean", ylab="difference")
# in the following, the deparse(substitute(varname)) is what retrieves the
# name of the argument as data
  title(main=paste("Bland-Altman plot of collimator x and y\n",
    deparse(substitute(x)), "and", deparse(substitute(y)),
    "standardized"), adj=".5")
#construct the reference lines on the fly: no need to save the values in new 
# variable names
  abline(h = c(mean(badiff), mean(badiff)+1.96 * sd(badiff),
    mean(badiff)-1.96 * sd(badiff)), lty=2)
} 

pdf(file="test.pdf")
baplot(mydata$args[2],mydata$argss[3])
dev.off()

Answer 1

The problem is with this line:

baplot(mydata$args[2],mydata$argss[3])

Let’s not even mention the typo… When you ask for mydata$args[2], R looks for a column named “args” in your data.frame. Obviously, there is no such column so you get NULL. The programmatic way of extracting columns from a data.frame is using [. The correct syntax should be:

baplot(mydata[args[2]],mydata[args[3]])

That should fix your problem.

(Also note that the [ operator, unlike $, will throw an error if you are trying to extract a column that does not exist: a preferable feature IMHO.)