[R] boxplot - code for labeling outliers - any suggestions for improvements?

Thu Jan 27 21:57:37 CET 2011

Try:

library(TeachingDemos)

plot(Sepal.Length~Sepal.Width, data=iris)

tmp.y <- iris$Sepal.Length
for( i in unique(iris$Sepal.Width) ) {
	tmp <- iris$Sepal.Width == i
	tmp.y[ tmp ] <- spread.labs( tmp.y[tmp], .6*strheight('A'),
		maxiter=1000 )
}

# optional
with(iris, segments(Sepal.Width, Sepal.Length, Sepal.Width+0.025, tmp.y) )

with(iris, text(Sepal.Width+0.05, tmp.y, seq_along(tmp.y), cex=.5 ) )

There is also thigmophobe.labels in the plotrix package which is simpler and works well for some plots

Also look at dynIdentify (Windows only) and TkIdentify (all platforms) in the TeachingDemosp package for a way to interactively place the labels (little more work, but labels end up where you think they look best).

I have experimented with spreading simultaneously in 2 directions, but what works well for one case does lousy in another and what ends up working for the other doesn't work in the first case.

But I would argue against labeling all the points in a plot of that many points, they make it too busy and distract more than help.  HWidentify (windows) and HTKidentify (all platforms) in TeachingDemos give another option.  Sometimes just using different colors/symbols/etc. for groups of points gives more useful information than labels.

Hope this helps,

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111

> -----Original Message-----
> From: Kevin Wright [mailto:kw.stat at gmail.com]
> Sent: Thursday, January 27, 2011 10:27 AM
> To: Tal Galili
> Cc: Greg Snow; r-help at r-project.org
> Subject: Re: [R] boxplot - code for labeling outliers - any suggestions
> for improvements?
> 
> My colleagues that use one of the .Net languages/libraries can make
> scatter plots that look better than R's because they have better
> spreading of the labels.
> 
> If someone could spread this labels on the following graph, I would be
> impressed.
> 
> plot(Sepal.Length~Sepal.Width, data=iris)
> with(iris,text(Sepal.Width, Sepal.Length, 1:nrow(iris), cex=.5))
> 
> Kevin
> 
> 
> On Thu, Jan 27, 2011 at 9:52 AM, Tal Galili <tal.galili at gmail.com>
> wrote:
> > Thanks again for the pointer to spread.labs Greg.
> >
> > I implemented it into the function and also extended it to deal with
> > formulas so it could behave just like boxplot.
> > Code and examples are available here:
> > http://www.r-statistics.com/2011/01/how-to-label-all-the-outliers-in-
> a-boxplot/
> >
> > I'd be happy for any suggestions on how to improve it.
> >
> > Best,
> > Tal
> >
> >
> >
> > ----------------Contact
> > Details:-------------------------------------------------------
> > Contact me: Tal.Galili at gmail.com |  972-52-7275845
> > Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il
> (Hebrew) |
> > www.r-statistics.com (English)
> > ---------------------------------------------------------------------
> -------------------------
> >
> >
> >
> >
> > On Thu, Jan 27, 2011 at 1:09 AM, Greg Snow <Greg.Snow at imail.org>
> wrote:
> >
> >> For the last point (cluttered text), look at spread.labels in the
> plotrix
> >> package and spread.labs in the TeachingDemos package (I favor the
> later, but
> >> could be slightly biased as well).  Doing more than what those 2
> functions
> >> do becomes really complicated really fast.
> >>
> >> --
> >> Gregory (Greg) L. Snow Ph.D.
> >> Statistical Data Center
> >> Intermountain Healthcare
> >> greg.snow at imail.org
> >> 801.408.8111
> >>
> >>
> >> > -----Original Message-----
> >> > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> >> > project.org] On Behalf Of Tal Galili
> >> > Sent: Wednesday, January 26, 2011 4:05 PM
> >> > To: r-help at r-project.org
> >> > Subject: [R] boxplot - code for labeling outliers - any
> suggestions for
> >> > improvements?
> >> >
> >> > Hello all,
> >> > I wrote a small function to add labels for outliers in a boxplot.
> >> > This function will only work on a simple boxplot/formula command
> (e.g:
> >> > something like boxplot(y~x)).
> >> >
> >> > Code + example follows in this e-mail.
> >> >
> >> > I'd be happy for any suggestions on how to improve this code, for
> >> > example:
> >> >
> >> >    - Handle boxplot.matrix (which shouldn't be too hard to do)
> >> >    - Handle cases of complex functions (e.g: boxplot(y~a*b))
> >> >    - Handle cases where there are many outliers leading to a
> clutter of
> >> > text
> >> >    (to this I have no idea how to systematically solve)
> >> >
> >> >
> >> > Best,
> >> > Tal
> >> > ------------------------------
> >> >
> >> >
> >> > # the function
> >> > boxplot.add.outlier.text <- function(DATA, x_name, y_name,
> label_name)
> >> > {
> >> >
> >> >
> >> > boxplot.outlier.data <- function(xx, y_name)
> >> > {
> >> >  y <- xx[,y_name]
> >> > boxplot_range <- range(boxplot.stats(y)$stats)
> >> > ss <- (y < boxplot_range[1]) | (y > boxplot_range[2])
> >> >  return(xx[ss,])
> >> > }
> >> >
> >> > require(plyr)
> >> > txt_to_run <- paste("ddply(DATA, .(",x_name,"),
> boxplot.outlier.data,
> >> > y_name
> >> > = y_name)", sep = "")
> >> >  ourlier_df <- eval(parse(text = txt_to_run))
> >> > # head(ourlier_df)
> >> >  txt_to_run <- paste("formula(",y_name,"~", x_name,")")
> >> >  formu <- eval(parse(text = txt_to_run))
> >> > boxdata <- boxplot(formu , data = DATA, plot = F)
> >> >  boxdata_group_name <- boxdata$names[boxdata$group]
> >> > boxdata_outlier_df <- data.frame(group = boxdata_group_name, y =
> >> > boxdata$out, x = boxdata$group)
> >> >  for(i in seq_len(dim(boxdata_outlier_df)[1]))
> >> > {
> >> >  ss <- (ourlier_df[,x_name]  %in% boxdata_outlier_df[i,]$group) &
> >> > (ourlier_df[,y_name] %in% boxdata_outlier_df[i,]$y)
> >> > current_label <- ourlier_df[ss,label_name]
> >> >  temp_x <- boxdata_outlier_df[i,"x"]
> >> > temp_y <- boxdata_outlier_df[i,"y"]
> >> >  text(temp_x, temp_y, current_label,pos=4)
> >> > }
> >> >
> >> > list(boxdata_outlier_df = boxdata_outlier_df,
> ourlier_df=ourlier_df)
> >> > }
> >> >
> >> > # example:
> >> > boxplot(decrease ~ treatment, data = OrchardSprays, log = "y", col
> =
> >> > "bisque")
> >> > boxplot.add.outlier.text(OrchardSprays, "treatment", "decrease",
> >> > "colpos")
> >> >
> >> >
> >> >
> >> >
> >> > ----------------Contact
> >> > Details:-------------------------------------------------------
> >> > Contact me: Tal.Galili at gmail.com |  972-52-7275845
> >> > Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il
> (Hebrew)
> >> > |
> >> > www.r-statistics.com (English)
> >> > ------------------------------------------------------------------
> -----
> >> > -----------------------
> >> >
> >> >       [[alternative HTML version deleted]]
> >> >
> >> > ______________________________________________
> >> > 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.
> >>
> >
> >        [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > 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.
> >
> 
> 
> 
> --
> Kevin Wright