[R] introducing jitter in overlapping graphs using ggplots (plotmeans). Also sciplot.

[John Kane]

Hi Anna,
A small point -- there is no package called ggplots.  There is a package called gplots and one called ggplot2, which in earlier form was called ggplot.

To see what is happening I believe we need some sample data from  the three data  files or some mock-up data that matches your actual data in form.

 The easiest way to supply data  is to use the dput() function.  Example with your file named "testfile": 
dput(testfile) 
Then copy the output and paste into your email.  For large data sets, you can just supply a representative sample.  Usually, 
dput(head(testfile, 100)) will be sufficient.   

In this case it looks like we would want three dput results, one for each year.

John Kane
Kingston ON Canada


> -----Original Message-----
> From: anna at ecology.su.se
> Sent: Tue, 19 Feb 2013 12:38:25 +0100
> To: r-help at r-project.org
> Subject: [R] introducing jitter in overlapping graphs using ggplots
> (plotmeans). Also sciplot.
> 
> Hi,
> 
> I want to plot means with standard deviations of Total Nitrogen (TN)
> across
> 4 stations (S1-S4) and over 3 years (2007-2009). I want this plot in one
> panel.
> I do not want medians (bwplot, boxplot).
> 
> I have tried a few different packages and it seems that ggplots with
> plotmeans was the fastest (I am not extremely skilled in writing my own
> scripts). Unfortunately, there is no grouping argument in plotmeans().
> Therefore, I have overlaid three plots (plotting all stations witin
> year).
> However, as the graphs are exctly overlaid, it is not possible to
> distinguish the confidence intervals. How do I introduce jitter?
> Data2007, Data2008 and Data2009 are the dataframes with the data from
> that
> particular year including all the stations.
> 
> I have also tried lineplot.CI from the package sciplot and also there I
> am
> not able to introduce jitter. I have looked at the helpfiles.
> 
> 
> PACKAGE GGPLOT:
> 
> library(gplots)
> par(family="serif",font=1)
> plotmeans(TN ~ STATION,
>           data =Data2007,
>           bars=TRUE, p=0.95,
>           pch=1,
>           cex=0.8,
>           n.label=FALSE,
>           mean.labels=FALSE,
>           barwidth=1.5, barcol="black",
>           connect=TRUE,
>           xlab="Station",
>           ylab = expression(paste("TN (",mu, g~L^{-1}, ")")))
> par(new=T)
> plotmeans(TN ~ STATION,
>           data =Data2008,
>           bars=TRUE, p=0.95,
>           pch=2,
>           cex=0.8,
>           lty=2,
>           n.label=FALSE,
>           mean.labels=FALSE,
>           barwidth=1.5, barcol="black",
>           connect=TRUE,
>           na.action=na.exclude,
>           yaxt='n', ann=FALSE,
>           xaxt="n")
> par(new=T)
> plotmeans(TN ~ STATION,
>           data =Data2009,
>           bars=TRUE, p=0.95,
>           pch=3,
>           cex=0.8,
>           lty=3,
>           n.label=FALSE,
>           mean.labels=FALSE,
>           barwidth=1.5, barcol="black",
>           connect=TRUE,
>           na.action=na.exclude,
>           yaxt='n', ann=FALSE,
>           xaxt="n")
> 
> PACKAGE SCIPLOT:
> library(sciplot)
> lineplot.CI(response=TN, x.factor=STATION, group=YEAR,
>             ci.fun= function(x) c(mean(x)-sd(x), mean(x) + sd(x)),
>             data = Mydata,
>             xlab="Station",
>             ylab = expression(paste("TN(",mu, g~L^{-1}, ")")))
> 
> #here I have calculated the standard deviations instead of the default
> standard errors.
> 
> Thank you for taking your time. I have spent a long time trying to solve
> this and the frustration slowly approaches anger (in myself)  :-)
> 
> Yours sincerely
> 
> Anna Zakrisson Braeunlich
> PhD Student
> 
> Department of Systems Ecology
> Stockholm University
> Svante Arrheniusv. 21A
> SE-106 91 Stockholm
> 
> Lives in Berlin.
> For fast paper-mail responses, please use the below address:
> Katzbachstr. 21
> D-10965, Berlin - Kreuzberg
> Germany/Deutschland
> 
> E-mail: anna at ecology.su.se
> Tel work: +49-(0)3091541281
> Mobile: +49-(0)15777374888
> Web site: http://www.ecology.su.se/staff/personal.asp?id=163
> 
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