Hi everyone (again),
before you all start screaming that the reordering of factors has been 
discusse on several threads and is not particular to ggplot2, hear me out.
I can easily reorder my x-axis factor in facet.grid() in ggplot2. What I 
cannot reorder are the factors represented on the strips. I can see that the 
graphs are changing, so I am afraid of what it is I am doing. Why is ggplot2 
not changin the strip labels if indeed the factor-order has been changed? 
or have I missed to add code defining the factor-labels in the strips. I 
have not found such code as it has been done automatically from my dataframe 
using facet.grid() previously. I am simply afraid of displaying the wrong 
things without noticing it.
Here is my code and comments:

I want to have my factor 1 in the order: "F", "E", "C", "D", "A", "B" 
instead of alphabetical. My normal methods do not work.

with kind regards
Anna Zakrisson

# Some dummy data:
mydata<- data.frame(factor1 = factor(rep(LETTERS[1:6], each = 80)),
                    factor2 = factor(rep(c(1:5), each = 16)),
                    factor3 = factor(rep(c(1:4), each = 4)),
                    var1 = rnorm(120, mean = rep(c(0, 3, 5), each = 40),
                                 sd = rep(c(1, 2, 3), each = 20)),
                    var2 = rnorm(120, mean = rep(c(6, 7, 8), each = 40),
                                 sd = rep(c(1, 2, 3), each = 20)))

# Trying to change the order of my factor1 (same method works for factor3,
# which is on th x-axis). Factor1 (A-F) is represented on the different 
facets
# and the factor1 labels can be read off the strips:
mydata$factor1 <- factor(mydata$factor1, 
                       levels=c("F", "E", "C", "D", "A", "B"), 
                       order=T)

# summarizing the data with factor1 and factor3:
Summ  <-   ddply(mydata, .(factor3,factor1), summarize,
                 mean = mean(var1, na.rm = FALSE),
                 sdv = sd(var1, na.rm = FALSE),
                 se = 1.96*(sd(var1, na.rm=FALSE)/sqrt(length(var1))))
Summ$Grouping <- c("F", "E", "C", "D", "A", "B")[Summ$factor1]

# Trying to order factor 1 accordingly:
Summ$factor1 <- factor(Summ$factor1, 
                       levels=c("F", "E", "C", "D", "A", "B"), 
                       order=T)


# plotting:
ggplot(Summ, aes(factor3, mean, group = factor1,
                 ymin = mean - sdv , ymax = mean + sdv)) +
  geom_point(position = position_dodge(width = 0.25), size = 3) +
  geom_line(position = position_dodge(width = 0.25)) +
  geom_errorbar(width = 0.3, position = position_dodge(width = 0.25), size = 
0.3) +
  facet_wrap(~Grouping, ncol = 2) +
  theme(strip.background = element_blank()) +
  scale_shape(solid = FALSE)+
  theme_bw() +
  ylab(expression(paste("my measured stuff"))) +
  xlab("factor3") +
  theme(legend.position="none")+
  labs(shape = "factor1", group = "factor1", linetype = "factor1")

# What I find really scary is that when excluding the parts:
mydata$factor1 <- factor(mydata$factor1, 
                         levels=c("F", "E", "C", "D", "A", "B"), 
                         order=T)
Summ$factor1 <- factor(Summ$factor1, 
                       levels=c("F", "E", "C", "D", "A", "B"), 
                       order=T)
# I actually get a different plot than had I not reordered the factors. 
# The labels are however still the same. How do I solve this?



### But if I change the factor order for factor 3 (on the x-axis) it works! 
I get
# a different factor order!
Summ$factor1 <- factor(Summ$factor1, 
                       levels=c("4", "2", "3", "1"), 
                       order=T)


ggplot(Summ, aes(factor3, mean, group = factor1,
                 ymin = mean - sdv , ymax = mean + sdv)) +
  geom_point(position = position_dodge(width = 0.25), size = 3) +
  geom_line(position = position_dodge(width = 0.25)) +
  geom_errorbar(width = 0.3, position = position_dodge(width = 0.25), size = 
0.3) +
  facet_wrap(~Grouping, ncol = 2) +
  theme(strip.background = element_blank()) +
  scale_shape(solid = FALSE)+
  theme_bw() +
  ylab(expression(paste("my measured stuff"))) +
  xlab("factor3") +
  theme(legend.position="none")+
  labs(shape = "factor1", group = "factor1", linetype = "factor1")


Anna Zakrisson Braeunlich
PhD student

Department of Ecology Environment and Plant Sciences
Stockholm University
Svante Arrheniusv. 21A
SE-106 91 Stockholm
Sweden

Lives in Berlin.
For paper mail:
Katzbachstr. 21
D-10965, Berlin - Kreuzberg
Germany/Deutschland

E-mail: anna.zakrisson@su.se
Tel work: +49-(0)3091541281
Mobile: +49-(0)15777374888
LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b

><((((º>`•. . • `•. .• `•. . ><((((º>`•. . • `•. .• 
`•. .><((((º>`•. . • `•. .• `•. .><((((º>

	[[alternative HTML version deleted]]

