R icenReg package: Move plot legend for ic_np fit

Question

I need to create a plot that compares interval censored survival curves for three species. I am able to generate a plot that shows all three curves using the ic_np function in the icenReg package in R. When I plot the output of this ic_np fit using base R plot(), a legend appears in the bottom left corner.

This example from the icenReg package documentation yields a similar figure:

library(icenReg)
data(miceData)
fit <- ic_np(cbind(l, u) ~ grp, data = miceData) #Stratifies fit by group
plot(fit)

However, having the caption in the bottom left covers the most interesting comparison of my survival curves, so I would like to move the legend to the top right.

I have seen this question about setting a legend position for basic plots in base R. Answers to this question seem to assume that I can generate a plot without the legend, but I have not been able to do that.

I have also seen this question about adding a legend to other types of survival analysis that do not seem to generate a legend by default, but I have not been able to implement these methods with interval censored data.

I have read that I can't move a legend that has already been added to a plot, but I don't know how to generate this particular plot without a legend so that I can add one back in where I want it (top right).

How can I either (a) generate this plot of interval censored Kaplan-Meier survival curves using ic_np without a legend -- maybe using some hidden parameter of plot() -- OR (b) generate this figure using a different plotting device, assuming the plot legend is then moveable?

score 3 · Accepted Answer · answered Mar 13 '18 at 00:20

There doesn't seem to be a help page in the package for the plot function so you need to determine the class of the fit-object and look at the code:

class(fit)
#[1] "ic_npList"
#attr(,"package")
#[1] "icenReg"

 plot.ic_npList
#Error: object 'plot.ic_npList' not found

So it's not exported and we need to dig deeper (not suprising since exported functions do need to have help pages.)

 getAnywhere(plot.ic_npList)
#-----------
A single object matching ‘plot.ic_npList’ was found
It was found in the following places
  registered S3 method for plot from namespace icenReg
  namespace:icenReg
with value

function (x, fitNames = NULL, lgdLocation = "bottomleft", ...) 
{
    addList <- list(xlim = x$xRange, ylim = c(0, 1), xlab = "time", 
        ylab = "S(t)", x = NA)
    dotList <- list(...)
   #.........
#..........
    legend(lgdLocation, legend = grpNames, col = cols, lty = 1)
}
<bytecode: 0x7fc9784fa660>
<environment: namespace:icenReg>

So there is a location parameter for the legend placement and the obvious alternative to try is:

plot(fit, lgdLocation = "topright")

As of version 2.0.8, you can also exclude the legend with `plot_legend = F` — Cliff AB, Jul 18 '18 at 04:41

R icenReg package: Move plot legend for ic_np fit

1 Answers1