Can the code of a R package be changed? How?

Question

[Antonio R. Franco]

I am using limma, and in representing a volcano plot, it turn out that the gene systematic gene I want to highlight is truncated..

If I revise the code (shown below) I can see that the highlighted gene comes from a substring with a maximum of 8 digits.

This observation lead me to ask if it is possible to make minor changes in the code present in the R package, and how this can be accomplished.

In my case, I can change all the systematic gene names, or change that 8 by a different value

> volcanoplot
function (fit, coef = 1, highlight = 0, names = fit$genes$ID, 
    xlab = "Log Fold Change", ylab = "Log Odds", pch = 16, cex = 0.35, 
    ...) 
{
    if (!is(fit, "MArrayLM")) 
        stop("fit must be an MArrayLM")
    if (is.null(fit$lods)) 
        stop("No B-statistics found, perhaps eBayes() not yet run")
    x <- as.matrix(fit$coef)[, coef]
    y <- as.matrix(fit$lods)[, coef]
    plot(x, y, xlab = xlab, ylab = ylab, pch = pch, cex = cex, 
        ...)
    if (highlight > 0) {
        if (is.null(names)) 
            names <- 1:length(x)
        names <- as.character(names)
        o <- order(y, decreasing = TRUE)
        I <- o[1:highlight]
        text(x[i], y[i], labels = substring(names[i], 1, 8), 
            cex = 0.8, col = "blue")
    }
    invisible()
}
<environment: namespace:limma>

Answer 1

[Sukhi Singh]

You can always have the source and can directly change the files. Either repack and install the custom new package via command line

R CMD INSTALL package

or use the powerful updated editing capabilities within R. Check for function trace

Check this post on SO for more options.

[Giovanni M Dall'Olio]

You can also use the devtools package for easier debugging.

First, install the devtools and load it with library(devtools). Then, activate the development mode with dev_mode(). This will allow you to recompile and reinstall new packages without altering your main R installation. Then, use install_local("path to modified limma package") to install it again.

[Antonio R. Franco]

This answer fulfill everything I need and even more. Thank you

[David Quigley]

If that's the case, please mark the answer as accepted. That way the respondent gets credit and other readers can see this question has a satisfactory answer already.

[bioyas]

Hello,

I read this thread and I found it really useful. I am going to modify an r package too. I was wondering how can I recompile it through Rstudio. I have downloaded the source code of package and I have modified it. I am not sure how to source it or recompile it in Rstudio?

Thanks for your help

[Antonio R. Franco]

I don't think you can permanently change and/or compile a package using RStudio.. There are many books and references in the web to learn about it