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Custom Plot - means, SD & 5th-95th% (Plotmeans or Boxplot)?

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Custom Plot - means, SD & 5th-95th% (Plotmeans or Boxplot)?

Steven
Any help with this problem would be greatly appreciated:

I need to produce a custom plot i haven't come across in R. Basically, I want to show means, 1st standard deviation and 5th and 95th percentiles visually, using something resembling a boxplot. Is it possible to completely customize a boxplot so that it shows means as the bar (instead of, not as well as medians), standard deviations at the hinges (instead of IQR) and 5th & 95th percentiles at the brackets? The plotmeans function (ggplots) allows means to be plotted, but it seems only with confidence intervals, not 5th and 95th percentiles, and also without hinges (for standard deviations). I've searched the forums and various books and have drawn a blank on this. Thanks.

Steve

~~~~~~~~~~~~~~~~
Steve Worthington
Ph.D. Candidate
New York Consortium
in Evolutionary Primatology
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Re: Custom Plot - means, SD & 5th-95th% (Plotmeans or Boxplot)

hadley wickham
It's fairly simple to set up something like this for ggplot2:

install.packages("ggplot2")
library(ggplot2)

library(ggplot2)

q5 <- function(data) {
 q <- function(p) unname(quantile(data$y, p))
 data.frame(min = q(0.05), max = q(0.95))
}

ggplot(diamonds, aes(x = cut, y = price)) +
stat_summary(fun="mean_sdl", geom="crossbar", mult=1) +
stat_summary(fun="q5", geom="linerange")

(see Hmisc::smean.sdl for more details on the first summary function).

Although from this example you can see that that choice of summary
statistics probably isn't the best.  You can read more about
stat_summary (and ggplot2 in general) at
http://had.co.nz/ggplot2/stat_summary.html.

Hadley

On 2/17/08, Stropharia <[hidden email]> wrote:

>
> Any help with this problem would be greatly appreciated:
>
> I need to produce a custom plot i haven't come across in R. Basically, I
> want to show means, 1st standard deviation and 5th and 95th percentiles
> visually, using something resembling a boxplot. Is it possible to completely
> customize a boxplot so that it shows means as the bar (instead of, not as
> well as medians), standard deviations at the hinges (instead of IQR) and 5th
> & 95th percentiles at the brackets? The plotmeans function (ggplots) allows
> means to be plotted, but it seems only with confidence intervals, not 5th
> and 95th percentiles, and also without hinges (for standard deviations).
> I've searched the forums and various books and have drawn a blank on this.
> Thanks.
>
> Steve
>
> ~~~~~~~~~~~~~~~~
> Steve Worthington
> Ph.D. Candidate
> New York Consortium
> in Evolutionary Primatology
> --
> View this message in context:
> http://www.nabble.com/Custom-Plot---means%2C-SD---5th-95th--%28Plotmeans-or-Boxplot%29--tp15537706p15537706.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] 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.
>


--
http://had.co.nz/

______________________________________________
[hidden email] 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.
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Re: Custom Plot - means, SD & 5th-95th% (Plotmeans or Boxplot)

David Winsemius
[hidden email] wrote in
news:[hidden email]:

> It's fairly simple to set up something like this for ggplot2:
>
> install.packages("ggplot2")
> library(ggplot2)
>
> library(ggplot2)
>
> q5 <- function(data) {
>  q <- function(p) unname(quantile(data$y, p))
>  data.frame(min = q(0.05), max = q(0.95))
> }
>
> ggplot(diamonds, aes(x = cut, y = price)) +
> stat_summary(fun="mean_sdl", geom="crossbar", mult=1) +
> stat_summary(fun="q5", geom="linerange")

On WXP with R2.6.1, and version 0.5.7 of ggplot2, ggplott threw an
error whose second line stated that:
'variable "stat_q5" of mode "function" was not found'

So I defined stat_q5 with the same function code as q5 above and the
plot appeared.

I have a follow on ggplot2 question for which I have not found the
correct terms for a successful search: how does one change the
background fill for the plots? I really would like something other than
grey backgrounds and they seem to be the default.

--
David Winsemius

 

>
> (see Hmisc::smean.sdl for more details on the first summary
> function).
>
> Although from this example you can see that that choice of summary
> statistics probably isn't the best.  You can read more about
> stat_summary (and ggplot2 in general) at
> http://had.co.nz/ggplot2/stat_summary.html.
>
> Hadley
>
> On 2/17/08, Stropharia <[hidden email]> wrote:
>>
>> Any help with this problem would be greatly appreciated:
>>
>> I need to produce a custom plot i haven't come across in R.
>> Basically, I want to show means, 1st standard deviation and 5th and
>> 95th percentiles visually, using something resembling a boxplot. Is
>> it possible to completely customize a boxplot so that it shows
>> means as the bar (instead of, not as well as medians), standard
>> deviations at the hinges (instead of IQR) and 5th & 95th
>> percentiles at the brackets? The plotmeans function (ggplots)
>> allows means to be plotted, but it seems only with confidence
>> intervals, not 5th and 95th percentiles, and also without hinges
>> (for standard deviations). I've searched the forums and various
>> books and have drawn a blank on this. Thanks.
>>
>> Steve
>>
>> ~~~~~~~~~~~~~~~~
>> Steve Worthington
>> Ph.D. Candidate
>> New York Consortium
>> in Evolutionary Primatology
>> --
>> View this message in context:
>> http://www.nabble.com/Custom-Plot---means%2C-SD---5th-95th--%28Plotm
>> eans-or-Boxplot%29--tp15537706p15537706.html Sent from the R help
>> mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> [hidden email] 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.
>>
>
>

______________________________________________
[hidden email] 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.
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Re: Custom Plot - means, SD & 5th-95th% (Plotmeans or Boxplot)

Gabor Grothendieck
In reply to this post by Steven
Using builtin dataset stackloss try this:

f <- function(x) replace(quantile(x, c(5, 25, 50, 75, 95)/100), 3, mean(x))
bxp(list(stats = sapply(stackloss, f), n = stackloss, names = names(stackloss)))

and see ?bxp and ?boxplot

On Feb 17, 2008 9:17 PM, Stropharia <[hidden email]> wrote:

>
> Any help with this problem would be greatly appreciated:
>
> I need to produce a custom plot i haven't come across in R. Basically, I
> want to show means, 1st standard deviation and 5th and 95th percentiles
> visually, using something resembling a boxplot. Is it possible to completely
> customize a boxplot so that it shows means as the bar (instead of, not as
> well as medians), standard deviations at the hinges (instead of IQR) and 5th
> & 95th percentiles at the brackets? The plotmeans function (ggplots) allows
> means to be plotted, but it seems only with confidence intervals, not 5th
> and 95th percentiles, and also without hinges (for standard deviations).
> I've searched the forums and various books and have drawn a blank on this.
> Thanks.
>
> Steve
>
> ~~~~~~~~~~~~~~~~
> Steve Worthington
> Ph.D. Candidate
> New York Consortium
> in Evolutionary Primatology
> --
> View this message in context: http://www.nabble.com/Custom-Plot---means%2C-SD---5th-95th--%28Plotmeans-or-Boxplot%29--tp15537706p15537706.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] 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.
>

______________________________________________
[hidden email] 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.
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