Tal Galili
2009-Aug-12 09:47 UTC
[R] A function for plotting a boxplot with added dot and bars (for mean 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]]
ONKELINX, Thierry
2009-Aug-12 10:29 UTC
[R] A function for plotting a boxplot with added dot and bars (formean and SE) - please help improve my code
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.Onkelinx at 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-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Tal Galili
Verzonden: woensdag 12 augustus 2009 11:48
Aan: r-help at 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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