[R] ROCR package question

[Tobias Sing]

Waverley,

if you want to modify components of the ROCR plot, you need to direct
the parameters to the component functions by prefixing them with the
name of that component function. In your case, you should add
"boxplot.outline=FALSE" as follows:
plot(perf, avg= "vertical", spread.estimate="boxplot", boxplot.outline=FALSE)

That should solve your issue. Please see below for the full
explanation which is part of the ROCR reference.
You can read this either by typing help(package="ROCR"), or by looking
at the reference PDF, e.g. here:
http://rocr.bioinf.mpi-sb.mpg.de/ROCR.pdf

You may also want to have a look at the examples in this slide deck:
http://rocr.bioinf.mpi-sb.mpg.de/ROCR_Talk_Tobias_Sing.ppt

"Optional graphical parameters to adjust different components of the performance
plot. Parameters are directed to their target component by prefixing them with
the name of the component (component.parameter, e.g. text.cex).
The following components are available: xaxis, yaxis, coloraxis, box
(around the plotting region), points, text, plotCI (error bars), boxplot.
The names of these components are influenced by the R functions that are used
to create them. Thus, par(component) can be used to see which parameters
are available for a given component (with the expection of the three axes;
use par(axis) here). To adjust the canvas or the performance curve(s), the
standard plot parameters can be used without any prefix."

Good luck,
  Tobias



On Sat, Jul 25, 2009 at 7:38 PM, Waverley<waverley.paloalto at gmail.com> wrote:
> Thanks for the quick reply.  That is very clear for my question 1, 2.
>
> How about question 3? When I plot, is there way not to show the
> whisker plot outliers for evaluating the multiple runs?  I have tried
> to put the option from boxplot command outline=FALSE, however, it did
> not work.
>
> Can you help?
>
> Thanks again for your kind help.
>
>
>
>
>
>
> Waverley, see help('performance-class') for a description of the slots.
>
> Your AUCs will be in perf at y.values, which itself is a list (one list
> element per run).
>
> Thus, you can use functions like unlist or s/lapply to access them, e.g.
> mean(unlist(perf at y.values))
>
> Kind regards,
>  Tobias
>
> On Sat, Jul 25, 2009 at 5:44 PM, Waverley<waverley.paloalto at gmail.com> wrote:
>> Thanks for the reply.  I am not sure I am following:
>>
>> 1. for the sample code.  I tried perf at auc but get auc object not found
>> 2. I am SPECIFICALLY interested in the averaged auc value of the
>> multiple runs.  How to get that out?  I typed perf and it comes out as
>> a list.
>> 3. as for the plot using whisker plot to see the distribution of the
>> multiple runs, the outliers outside the whisker is very annoying.  How
>> to get rid of the "outline" which is outside the whisker?  I tried to
>> use boxplot option and put in the following plot code as an option
>> outline=FALSE and it did not work.
>>
>> Please help me with the specifics of the above 3 questions.  Use code
>> instead of description would be helpful.
>>
>> Thanks a lot in advance.
>>
>>
>>
>>>Waverley,
>>
>>>use @ (instead of $) to extract the slots from the performance object (it's S4 class system).
>>
>>>HTH,
>>>  Tobias
>>
>> On Sat, Jul 25, 2009 at 8:20 AM, Waverley<waverley.paloalto at gmail.com> wrote:
>>> I use ROCR to plot multiple runs' performance.  Using the sample code
>>> as example:
>>>
>>> # plot ROC curves for several cross-validation runs (dotted # in
>>> grey), overlaid by the vertical average curve and boxplots # showing
>>> the vertical spread around the average.
>>> data(ROCR.xval)
>>> pred <- prediction(ROCR.xval$predictions, ROCR.xval$labels) perf <-
>>> performance(pred,"tpr","fpr")
>>> plot(perf,col="grey82",lty=3)
>>> plot(perf,lwd=3,avg="vertical",spread.estimate="boxplot",add=TRUE)
>>>
>>> I can follow the code and plot without any problem.  However, I don't
>>> know how to extract the averaged ROC area under curve value.
>>>
>>> Can someone help?
>>>
>>> Thanks.
>>>
>>> --
>>> Waverley @ Palo Alto
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>> --
>> Waverley @ Palo Alto
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
> --
> Waverley @ Palo Alto
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>