Two solutions with errorbars
library(ggplot2)
#option 1
lowCI <- function(x){mean(x) + qt(0.025, length(x) - 1) * sd(x) /
sqrt(length(x))}
highCI <- function(x){mean(x) + qt(0.975, length(x) - 1) * sd(x) /
sqrt(length(x))}
ggplot(mtcars, aes(x = factor(round(wt)), y = mpg, colour = factor(am)))
+ geom_boxplot() + geom_point(stat = "summary", fun.y = mean, position =
position_dodge(width = 0.75)) + geom_errorbar(stat = "summary", fun.ymin
= lowCI, fun.ymax = highCI, position = position_dodge(width = 0.75),
linetype = 2)
#option2
mtcars$fwt <- factor(round(mtcars$wt))
MeanCI <- ddply(mtcars, c("fwt", "am"), function(z){
with(z, mean(mpg) + qt(c(low = 0.025, mean = 0.5, high = 0.975),
length(mpg) - 1) * sd(mpg) / sqrt(length(mpg)))
})
ggplot(mtcars, aes(x = fwt, y = mpg, colour = factor(am))) +
geom_boxplot() + geom_point(data = MeanCI, aes(y = mean), position =
position_dodge(width = 0.75)) + geom_errorbar(data = MeanCI, aes(ymin =
low, ymax = high), position = position_dodge(width = 0.75), linetype =
2)
------------------------------------------------------------------------
----
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.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
________________________________
Van: Tal Galili [mailto:tal.gal...@gmail.com]
Verzonden: woensdag 12 augustus 2009 12:48
Aan: ONKELINX, Thierry
CC: r-help@r-project.org
Onderwerp: Re: [R] A function for plotting a boxplot with added dot and
bars (formean and SE) - please help improve my code
Thanks Thierry,
I didn't know about that, it's always nice to see different ways of
doing things.
Question: How would you add the bars ?
Hope to see more interesting replies,
Tal
On Wed, Aug 12, 2009 at 1:29 PM, ONKELINX, Thierry
<thierry.onkel...@inbo.be> wrote:
This can be done much easier and transparent with ggplot2
library(ggplot2)
ggplot(mtcars, aes(x = factor(round(wt)), y = mpg, colour =
factor(am)))
+ geom_boxplot() + geom_point(stat = "summary", fun.y = "mean",
position
= position_dodge(width = 0.75))
HTH,
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.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be
no more
than asking him to perform a post-mortem examination: he may be
able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer
does not
ensure that a reasonable answer can be extracted from a given
body of
data.
~ John Tukey
-----Oorspronkelijk bericht-----
Van: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org]
Namens Tal Galili
Verzonden: woensdag 12 augustus 2009 11:48
Aan: r-help@r-project.org
Onderwerp: [R] A function for plotting a boxplot with added dot
and bars
(formean and SE) - please help improve my code
Hello people,
A while back I wanted to plot boxplots with interactions that
will have
a dot for the mean of the sample + bars for the SE.
After searching for some code, I found something that did it for
one
level, but couldn't find something that will allow for
interactions the
way the original boxplot does.
After playing with the original code, I found a way for allowing
the
boxplot code to introduce interactions to it. The price for that
was
that I was forced to use a little different syntax for the
function then
that of the original boxplot. In order to use the function, one
must use
lists for the function input arguments, and until now I didn't
find a
way for doing the same task from a formula input.
So for example, the original boxplot will be written like this:
boxplot(y ~ A*B)
Where as my function will look like this:
boxplot.2(y , list(A,B) )
In this e-mail I am giving away the code for:
1) helping out others searching for this solution. and
2) in hope to have more experienced R programmers come by and
improve on
this code (by, for example, removing the for loop in it, or
allowing to
use a formula instead of a list input)
Here is the code:
boxplot.2 <- function(fo.head, list.fo.tail = list(1),
print.mean = T,
plot.CI = T, add.mean.sd.to.boxplot.names = T, plot.round.factor
= 2
,...) {
require(gplots)
tmp <- split(fo.head , list.fo.tail)
means <- sapply(tmp, mean)
stdev <- sqrt(sapply(tmp, var)) #IS right - because of the
sqrt !!!
<- sqrt(sapply(tmp, var)) # was var, I changed it to sd
n <- sapply(tmp,length)
ciw <- qt(0.975, n-1) * stdev / sqrt(n)
old.names = attributes(tmp)$names
length.of.names = length(old.names)
new.names = as.list(old.names)
for(i in c(1:length.of.names))
{
new.names[[i]] <- paste(old.names[i], " (",
round(means[i],plot.round.factor) ,",",
round(ciw[i],plot.round.factor)
,")", sep = "")
}
if(add.mean.sd.to.boxplot.names)
{
if(length(list.fo.tail) == 1)
{
sub.text = paste("mean:", round(means,3),
"(SE:",round(ciw,3), " ; N:" ,n, ")")
boxplot(tmp, xlab = sub.text, cex.axis = min(1,
mean(c(1,12/
max(nchar(new.names)) )) ), ...)
} else {
boxplot(tmp, names = new.names, cex.axis = min(1,
mean(c(1,12/
max(nchar(new.names)) )) ), ...)
}
} else { boxplot(tmp, ...) } # else - make boxplot without
them
# adding the points and the bars
points(means, col = 'red', pch = 19)
if(require(gplots) & plot.CI) {
plotCI(x=means, uiw=ciw, col="white", barcol="blue",
xaxt="n" , add = T)
}
if(print.mean) {
small.mean.and.se.table <-
rbind(round(means,3),round(ciw,3), n)
rownames(small.mean.and.se.table) <- c("means:", "SE's:",
"N")
print(t(small.mean.and.se.table))
}
} # <-- end boxplot3
# Here is a small example:
data(mtcars)
head(mtcars)
attach(mtcars)
boxplot.2(mpg , list(round(wt), am) , data = mtcars, las = 2)
Hope this will benefit others, and also hope that others will
improve on
this code and give it back to the community, Tal galili
--
----------------------------------------------
My contact information:
Tal Galili
Phone number: 972-50-3373767
FaceBook: Tal Galili
My Blogs:
http://www.r-statistics.com/
http://www.talgalili.com
http://www.biostatistics.co.il
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible
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Dit bericht en eventuele bijlagen geven enkel de visie van de
schrijver weer
en binden het INBO onder geen enkel beding, zolang dit bericht
niet bevestigd is
door een geldig ondertekend document. The views expressed in
this message
and any annex are purely those of the writer and may not be
regarded as stating
an official position of INBO, as long as the message is not
confirmed by a duly
signed document.
--
----------------------------------------------
My contact information:
Tal Galili
Phone number: 972-50-3373767
FaceBook: Tal Galili
My Blogs:
http://www.r-statistics.com/
http://www.talgalili.com
http://www.biostatistics.co.il
Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in this message
and any annex are purely those of the writer and may not be regarded as stating
an official position of INBO, as long as the message is not confirmed by a duly
signed document.
______________________________________________
R-help@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.
