Arguments, Plots, Outputs and Lines of best fit in R

Question

I have several questions to do with handling some data in R:

1. I am using this statement: detailsTable <- read.table(file=commandArgs()[6], header=TRUE, col.names=c("a", "b", "c", "d", "e")) and it seems that the table is not being loaded correctly... but if I specify the path of the file I am loading excplicitly then all goes well. What am I doing wrong?

2. I plot the data contained in that table mentioned above. How do I save the plot (eg: plot.savePDF("plot.pdf")) to a PDF file?

3. How could I redirect the output of, for example, cor(detailsTable$a, detailsTable$b) to a file? and how do I write a simple string to a file. eg: "Correlation of the data: " + cor(...)

4. How do I plot the line of best fit on an existing plot?

All of this is in R.

Many thanks to anyone who can help,

ExtremeCoder

Answer 1

How to save the plot you're producing depends on which plotting system you're using. Assuming it's base graphics, you need to start a pdf graphics device, then plot to it.

pdf(file = "path/file.pdf", width = 5, height = 5)
...
#plotting commands here
...
dev.off()

Answer 2

I plot the data contained in that table mentioned above. How do I save the plot (eg: plot.savePDF("plot.pdf")) to a PDF file?

 pdf("filename.pdf")
 plot(...)
 dev.off()

How could I redirect the output of, for example, cor(detailsTable$a, detailsTable$b) to a file? and how do I write a simple string to a file. eg: "Correlation of the data: " + cor(...)

check the write.table manual page (?write.table)

How do I plot the line of best fit on an existing plot?

x <- 1:10
y <- 2 * x + runif(10) 
plot (x, y, pch=20)
fit <- glm(y~x)
coefs <- coef(fit)
abline(coefs, lwd=2, col='red')
# Or also, without finding the coefficients
abline(fit, lwd=2, col='red')

Answer 3

You can redirect output using sink().