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

[Anna Zakrisson]

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: a...@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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