Re: [R] ggplot2 boxplot confusion

From: ONKELINX, Thierry <Thierry.ONKELINX_at_inbo.be>
Date: Wed, 27 Feb 2008 15:25:55 +0100

Chris,

1.
This will make more sense.

ggplot(mydata, aes(y = VALUE, x = SERIES)) + geom_boxplot() + facet_grid(.~ ID)

2.
Now I think I understand want you want. I'm affraid that won't be easy because you're trying to mix continuous variables with categorical ones on the same scale. A density plot has two continuous scales: VALUE and it's density. The boxplot has a continuous scale (VALUE) and the other is categorical. Maybe Hadley knows a solution for your problem.

Thierry




ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx_at_inbo.be
www.inbo.be

Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney

-----Oorspronkelijk bericht-----
Van: r-help-bounces_at_r-project.org [mailto:r-help-bounces_at_r-project.org] Namens Chris Friedl
Verzonden: woensdag 27 februari 2008 15:08 Aan: r-help_at_r-project.org
Onderwerp: Re: [R] ggplot2 boxplot confusion

Thanks Thierry.

But this leads to a couple more questions if you don't mind.

  1. I tried to extend your example to a grid by the facet_grid command with the aim of getting a boxplot of VALUE according to two factors SERIES and ID. However whatever syntax I use give me an error. For example:

ggplot(mydata, aes(y = VALUE, x = factor(1))) + geom_boxplot() + scale_x_discrete("") +facet_grid(SERIES ~ ID)

Error: position_dodge requires the following missing aesthetics: x

I tried x=c(SERIES, ID) etc etc but they failed.

Yet I know I can get a grid of density plots with qplot as follows:

ggplot(mydata, aes(x = VALUE, y = ..density..)) + geom_density() + facet_grid(ID ~ SERIES)

Yet it doesn't work if I say geom_boxplot.

I hope you can help me understand where I've gone wrong.

2. On your point about overlaying box and density plots, I'm not sure I understand. I thought a a boxplot is just a particular view of a density function, showing median, interquartile range etc. The "vertical" scale is
the same as the density functions "horizontal" scale, isn't it? For example
in the dummy dataset above:

summary(mydata$VALUE)

    Min. 1st Qu. Median Mean 3rd Qu. Max. -2.54400 -0.64690 0.07417 0.08289 0.77830 2.75900

and

ggplot(mydata, aes(x = VALUE, y = ..density..)) + geom_density() shows a density plot that shows features on the x-axis that are visually close to
the summary features.

My intent was to plot density because the box plot doesn't reveal shape details such as multiple modes, and to augment with a narrow boxplot to show
some density features such as the position of the median, IQR etc.

Or perhaps I've completely misunderstood your point (highly likely I think).

Thanks again for your help. Much appreciated.

ONKELINX, Thierry wrote:
>
> Chris,
>
> 1.
>
> This code will give you the boxplot that you want.
>
> library(ggplot2)
> series <- c('C2','C4','C8','C10','C15','C20')
> ids <- c('ID1','ID2','ID3')
> mydata <-
> data.frame(SERIES=rep(series,30),ID=rep(ids,60),VALUE=rnorm(180))
> ggplot(mydata, aes(y = VALUE, x = factor(1))) + geom_boxplot() +
> scale_x_discrete("")
>
> But the real power of ggplot2 is when you want a boxplot for each
> category:
>
> ggplot(mydata, aes(y = VALUE, x = series)) + geom_boxplot()
>
>
> 2.
> Overlaying boxplots and density plots seems a bad idea to me as both
> plots are likey to have a different scale.
>
> HTH,
>
> Thierry
>
>

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