R help - Mar 2013 - Ggplot2: Moving legend, change fill and removal of space between plots when using grid.arrange() possible use of facet_grid?

Hi,

# For publications, I am not allowed to repeat the axes. I have tried to 
remove the axes using:
# yaxt="n", but it did not work. I have not understood how to do this
in
ggplot2. Can you help me?
# I also do not want loads of space between the graphs (see below script 
with Dummy Data). 
# If I could make it look like the examples on the (nice) examples page:
# http://www.ling.upenn.edu/~joseff/rstudy/summer2010_ggplot2_intro.html
# using the facet_grid(), I would be very very happy.

# I also do not want the gemoetric points to be filled and the
fill="white"
commande
# does not seem to work - why? and are there alternatives?

#Furthermore, I would like to add legends to inside the plot area instead of 
on the side. Like when you use plotrix() and brkdn.plot:
legend("topright", c("A", "B"), pch=c(0,1),
bg="white",
       lty = 1:2, cex=1, bty="n")
# This did not work in ggplot2. What are my alternatives. I have extensively 
searched the internet and have I missed something obvious, it was due to     
   # tiredness and not to lazyness. 

# 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)))


# Splitting data into 3 data frames (based on factor1)
# If I could do this using for example facet_wrap() or facet_grid(), I would 
be very
# happy! I have tried but failed that method.

DataAB <- mydata[(mydata$factor1) %in% c("A", "B"), ]
DataCD <- mydata[(mydata$factor1) %in% c("C", "D"), ]
DataEF <- mydata[(mydata$factor1) %in% c("E", "F"), ]
DataAB
library(plyr)
library(ggplot2)

#Plot: levels A and B:
# Summary (means etc)
SummAB  <-   ddply(DataAB, .(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))))
SummAB
p1  <-  ggplot(SummAB, aes(factor3, mean, 
                               colour = factor1, group = factor1, 
                               shape = factor1)) + 
  geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
             position = "dodge", width = 0.3, size=3) +  
  geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
  geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
                position = "dodge", color = "black",
size=0.3) +
  theme_bw() +
  ylab(expression(paste("my measured stuff"))) + 
  xlab("factor3") + ggtitle("") + 
  labs(color = "factor1", shape = "factor1", group =
"factor1",
       linetype = "factor1")
p1

#Plot: levels C and D:
# Summary (means etc)
SummCD  <-   ddply(DataCD, .(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))))

p2  <-  ggplot(SummCD, aes(factor3, mean, 
                           colour = factor1, group = factor1, 
                           shape = factor1)) + 
  geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
             position = "dodge", width = 0.3, size=3) +  
  geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
  geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
                position = "dodge", color = "black",
size=0.3) +
  theme_bw() +
  ylab(expression(paste("my measured stuff"))) + 
  xlab("factor3") + ggtitle("") + 
  labs(color = "factor1", shape = "factor1", group =
"factor1",
       linetype = "factor1")
p2

#Plot: levels C and D:
# Summary (means etc)
SummEF  <-   ddply(DataEF, .(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))))

p3  <-  ggplot(SummEF, aes(factor3, mean, 
                           colour = factor1, group = factor1, 
                           shape = factor1)) + 
  geom_point(aes(shape=factor(factor1)), color="black",
fill="white", #Why
is the fill commando not working?
             position = "dodge", width = 0.3, size=3) +  
  geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
  geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
                position = "dodge", color = "black",
size=0.3) +
  theme_bw() +
  ylab(expression(paste("my measured stuff"))) + 
  xlab("factor3") + ggtitle("") + 
  labs(color = "factor1", shape = "factor1", group =
"factor1",
       linetype = "factor1")
p3

ary(gridExtra)
sidebysideplot <- grid.arrange(p1, p2, p3, ncol=2)


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]]

Look at the function melt and use the factor columns as id variables.  
You should be able to do what you want with facet_grid. I have found 
inkscape useful to build legends and modify axes labels.  I know this is 
only a partial answer, but I hope this helps.

Stephen

On Wed 06 Mar 2013 06:32:42 AM CST, Anna Zakrisson
wrote:
>
> Hi,
>
> # For publications, I am not allowed to repeat the axes. I have tried to
> remove the axes using:
> # yaxt="n", but it did not work. I have not understood how to do
this in
> ggplot2. Can you help me?
> # I also do not want loads of space between the graphs (see below script
> with Dummy Data).
> # If I could make it look like the examples on the (nice) examples page:
> # http://www.ling.upenn.edu/~joseff/rstudy/summer2010_ggplot2_intro.html
> # using the facet_grid(), I would be very very happy.
>
> # I also do not want the gemoetric points to be filled and the 
> fill="white"
> commande
> # does not seem to work - why? and are there alternatives?
>
> #Furthermore, I would like to add legends to inside the plot area 
> instead of
> on the side. Like when you use plotrix() and brkdn.plot:
> legend("topright", c("A", "B"), pch=c(0,1),
bg="white",
> lty = 1:2, cex=1, bty="n")
> # This did not work in ggplot2. What are my alternatives. I have 
> extensively
> searched the internet and have I missed something obvious, it was due to
> # tiredness and not to lazyness.
>
> # 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)))
>
>
> # Splitting data into 3 data frames (based on factor1)
> # If I could do this using for example facet_wrap() or facet_grid(), I 
> would
> be very
> # happy! I have tried but failed that method.
>
> DataAB <- mydata[(mydata$factor1) %in% c("A", "B"),
]
> DataCD <- mydata[(mydata$factor1) %in% c("C", "D"),
]
> DataEF <- mydata[(mydata$factor1) %in% c("E", "F"),
]
> DataAB
> library(plyr)
> library(ggplot2)
>
> #Plot: levels A and B:
> # Summary (means etc)
> SummAB <- ddply(DataAB, .(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))))
> SummAB
> p1 <- ggplot(SummAB, aes(factor3, mean,
> colour = factor1, group = factor1,
> shape = factor1)) +
> geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
> position = "dodge", width = 0.3, size=3) +
> geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
> geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
> position = "dodge", color = "black", size=0.3) +
> theme_bw() +
> ylab(expression(paste("my measured stuff"))) +
> xlab("factor3") + ggtitle("") +
> labs(color = "factor1", shape = "factor1", group =
"factor1",
> linetype = "factor1")
> p1
>
> #Plot: levels C and D:
> # Summary (means etc)
> SummCD <- ddply(DataCD, .(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))))
>
> p2 <- ggplot(SummCD, aes(factor3, mean,
> colour = factor1, group = factor1,
> shape = factor1)) +
> geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
> position = "dodge", width = 0.3, size=3) +
> geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
> geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
> position = "dodge", color = "black", size=0.3) +
> theme_bw() +
> ylab(expression(paste("my measured stuff"))) +
> xlab("factor3") + ggtitle("") +
> labs(color = "factor1", shape = "factor1", group =
"factor1",
> linetype = "factor1")
> p2
>
> #Plot: levels C and D:
> # Summary (means etc)
> SummEF <- ddply(DataEF, .(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))))
>
> p3 <- ggplot(SummEF, aes(factor3, mean,
> colour = factor1, group = factor1,
> shape = factor1)) +
> geom_point(aes(shape=factor(factor1)), color="black",
fill="white", #Why
> is the fill commando not working?
> position = "dodge", width = 0.3, size=3) +
> geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
> geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
> position = "dodge", color = "black", size=0.3) +
> theme_bw() +
> ylab(expression(paste("my measured stuff"))) +
> xlab("factor3") + ggtitle("") +
> labs(color = "factor1", shape = "factor1", group =
"factor1",
> linetype = "factor1")
> p3
>
> ary(gridExtra)
> sidebysideplot <- grid.arrange(p1, p2, p3, ncol=2)
>
>
> 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 at su.se
> Tel work: +49-(0)3091541281
> Mobile: +49-(0)15777374888
> LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
>
>>
>> <((((??>`???. . ??? `???. .??? `???. . ><((((??>`???. .
??? `???. .???
>
> `???. .><((((??>`???. . ??? `???. .??? `???. .><((((??>
>
> [[alternative HTML version deleted]]
>
>
>
> ______________________________________________
> R-help at 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.

Dear Anna,

Is this what you would like?

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$Grouping <- c("AB", "AB", "CD",
"CD", "EF", "EF")[Summ$factor1]
Summ$factor1bis <- c("0", "1", "0",
"1", "0", "1")[Summ$factor1]

ggplot(Summ, aes(factor3, mean, group = factor1bis, shape = factor1bis, linetype
= factor1bis, 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_bw() +
ylab(expression(paste("my measured stuff"))) +
xlab("factor3") +
labs(shape = "factor1", group = "factor1", linetype =
"factor1")

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
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 Anna Zakrisson
Verzonden: woensdag 6 maart 2013 13:33
Aan: r-help at r-project.org
Onderwerp: [R] Ggplot2: Moving legend, change fill and removal of space between
plots when using grid.arrange() possible use of facet_grid?

Hi,

# For publications, I am not allowed to repeat the axes. I have tried to
remove the axes using:
# yaxt="n", but it did not work. I have not understood how to do this
in
ggplot2. Can you help me?
# I also do not want loads of space between the graphs (see below script
with Dummy Data).
# If I could make it look like the examples on the (nice) examples page:
# http://www.ling.upenn.edu/~joseff/rstudy/summer2010_ggplot2_intro.html
# using the facet_grid(), I would be very very happy.

# I also do not want the gemoetric points to be filled and the
fill="white"
commande
# does not seem to work - why? and are there alternatives?

#Furthermore, I would like to add legends to inside the plot area instead of
on the side. Like when you use plotrix() and brkdn.plot:
legend("topright", c("A", "B"), pch=c(0,1),
bg="white",
       lty = 1:2, cex=1, bty="n")
# This did not work in ggplot2. What are my alternatives. I have extensively
searched the internet and have I missed something obvious, it was due to
   # tiredness and not to lazyness.

# 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)))


# Splitting data into 3 data frames (based on factor1)
# If I could do this using for example facet_wrap() or facet_grid(), I would
be very
# happy! I have tried but failed that method.

DataAB <- mydata[(mydata$factor1) %in% c("A", "B"), ]
DataCD <- mydata[(mydata$factor1) %in% c("C", "D"), ]
DataEF <- mydata[(mydata$factor1) %in% c("E", "F"), ]
DataAB
library(plyr)
library(ggplot2)

#Plot: levels A and B:
# Summary (means etc)
SummAB  <-   ddply(DataAB, .(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))))
SummAB
p1  <-  ggplot(SummAB, aes(factor3, mean,
                               colour = factor1, group = factor1,
                               shape = factor1)) +
  geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
             position = "dodge", width = 0.3, size=3) +
  geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
  geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
                position = "dodge", color = "black",
size=0.3) +
  theme_bw() +
  ylab(expression(paste("my measured stuff"))) +
  xlab("factor3") + ggtitle("") +
  labs(color = "factor1", shape = "factor1", group =
"factor1",
       linetype = "factor1")
p1

#Plot: levels C and D:
# Summary (means etc)
SummCD  <-   ddply(DataCD, .(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))))

p2  <-  ggplot(SummCD, aes(factor3, mean,
                           colour = factor1, group = factor1,
                           shape = factor1)) +
  geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
             position = "dodge", width = 0.3, size=3) +
  geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
  geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
                position = "dodge", color = "black",
size=0.3) +
  theme_bw() +
  ylab(expression(paste("my measured stuff"))) +
  xlab("factor3") + ggtitle("") +
  labs(color = "factor1", shape = "factor1", group =
"factor1",
       linetype = "factor1")
p2

#Plot: levels C and D:
# Summary (means etc)
SummEF  <-   ddply(DataEF, .(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))))

p3  <-  ggplot(SummEF, aes(factor3, mean,
                           colour = factor1, group = factor1,
                           shape = factor1)) +
  geom_point(aes(shape=factor(factor1)), color="black",
fill="white", #Why
is the fill commando not working?
             position = "dodge", width = 0.3, size=3) +
  geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
  geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
                position = "dodge", color = "black",
size=0.3) +
  theme_bw() +
  ylab(expression(paste("my measured stuff"))) +
  xlab("factor3") + ggtitle("") +
  labs(color = "factor1", shape = "factor1", group =
"factor1",
       linetype = "factor1")
p3

ary(gridExtra)
sidebysideplot <- grid.arrange(p1, p2, p3, ncol=2)


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 at su.se
Tel work: +49-(0)3091541281
Mobile: +49-(0)15777374888
LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
><((((??>`???. . ??? `???. .??? `???. . ><((((??>`???. . ???
`???. .???
`???. .><((((??>`???. . ??? `???. .??? `???. .><((((??>

        [[alternative HTML version deleted]]

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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.

For the simplist of the issues use  scale_shape(solid = FALSE) to get hollow
points
 Using your data (below) this seems to work
p1  <-  ggplot(SummAB, aes(factor3, mean,
          colour = factor1, group = factor1,shape = factor1)) + 
        scale_y_continuous(guide_legend(legend.position=c(4 ,6))) +
       scale_shape(solid = FALSE) + guides(colour = guide_legend(title.position
= "right")) +
       geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
        position = "dodge", width = 0.3, size=3) +
       geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
       geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
                position = "dodge", color = "black",
size=0.3) +
      theme_bw() +
       ylab(expression(paste("my measured stuff"))) +
       xlab("factor3") + ggtitle("") +
      labs(color = "factor1", shape = "factor1", group =
"factor1",
       linetype = "factor1")
p1

John Kane
Kingston ON Canada

> -----Original Message-----
> From: anna at ecology.su.se
> Sent: Wed, 06 Mar 2013 13:32:42 +0100
> To: r-help at r-project.org
> Subject: [R] Ggplot2: Moving legend, change fill and removal of space
> between plots when using grid.arrange() possible use of facet_grid?
> 
> Hi,
> 
> # For publications, I am not allowed to repeat the axes. I have tried to
> remove the axes using:
> # yaxt="n", but it did not work. I have not understood how to do
this in
> ggplot2. Can you help me?
> # I also do not want loads of space between the graphs (see below script
> with Dummy Data).
> # If I could make it look like the examples on the (nice) examples page:
> # http://www.ling.upenn.edu/~joseff/rstudy/summer2010_ggplot2_intro.html
> # using the facet_grid(), I would be very very happy.
> 
> # I also do not want the gemoetric points to be filled and the
> fill="white"
> commande
> # does not seem to work - why? and are there alternatives?
> 
> #Furthermore, I would like to add legends to inside the plot area instead
> of
> on the side. Like when you use plotrix() and brkdn.plot:
> legend("topright", c("A", "B"), pch=c(0,1),
bg="white",
>        lty = 1:2, cex=1, bty="n")
> # This did not work in ggplot2. What are my alternatives. I have
> extensively
> searched the internet and have I missed something obvious, it was due to
>    # tiredness and not to lazyness.
> 
> # 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)))
> 
> 
> # Splitting data into 3 data frames (based on factor1)
> # If I could do this using for example facet_wrap() or facet_grid(), I
> would
> be very
> # happy! I have tried but failed that method.
> 
> DataAB <- mydata[(mydata$factor1) %in% c("A", "B"),
]
> DataCD <- mydata[(mydata$factor1) %in% c("C", "D"),
]
> DataEF <- mydata[(mydata$factor1) %in% c("E", "F"),
]
> DataAB
> library(plyr)
> library(ggplot2)
> 
> #Plot: levels A and B:
> # Summary (means etc)
> SummAB  <-   ddply(DataAB, .(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))))
> SummAB
> p1  <-  ggplot(SummAB, aes(factor3, mean,
>                                colour = factor1, group = factor1,
>                                shape = factor1)) +
>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
>              position = "dodge", width = 0.3, size=3) +
>   geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
>                 position = "dodge", color = "black",
size=0.3) +
>   theme_bw() +
>   ylab(expression(paste("my measured stuff"))) +
>   xlab("factor3") + ggtitle("") +
>   labs(color = "factor1", shape = "factor1", group =
"factor1",
>        linetype = "factor1")
> p1
> 
> #Plot: levels C and D:
> # Summary (means etc)
> SummCD  <-   ddply(DataCD, .(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))))
> 
> p2  <-  ggplot(SummCD, aes(factor3, mean,
>                            colour = factor1, group = factor1,
>                            shape = factor1)) +
>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
>              position = "dodge", width = 0.3, size=3) +
>   geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
>                 position = "dodge", color = "black",
size=0.3) +
>   theme_bw() +
>   ylab(expression(paste("my measured stuff"))) +
>   xlab("factor3") + ggtitle("") +
>   labs(color = "factor1", shape = "factor1", group =
"factor1",
>        linetype = "factor1")
> p2
> 
> #Plot: levels C and D:
> # Summary (means etc)
> SummEF  <-   ddply(DataEF, .(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))))
> 
> p3  <-  ggplot(SummEF, aes(factor3, mean,
>                            colour = factor1, group = factor1,
>                            shape = factor1)) +
>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
> #Why
> is the fill commando not working?
>              position = "dodge", width = 0.3, size=3) +
>   geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
>                 position = "dodge", color = "black",
size=0.3) +
>   theme_bw() +
>   ylab(expression(paste("my measured stuff"))) +
>   xlab("factor3") + ggtitle("") +
>   labs(color = "factor1", shape = "factor1", group =
"factor1",
>        linetype = "factor1")
> p3
> 
> ary(gridExtra)
> sidebysideplot <- grid.arrange(p1, p2, p3, ncol=2)
> 
> 
> 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 at su.se
> Tel work: +49-(0)3091541281
> Mobile: +49-(0)15777374888
> LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
> 
> ><((((B:>`b?". . b?" `b?". .b?" `b?". .
><((((B:>`b?". . b?" `b?". .b?"
> `b?". .><((((B:>`b?". . b?" `b?". .b?"
`b?". .><((((B:>
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at 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.
____________________________________________________________
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Placing a legend.  

 z <- ggplot(mtcars, aes(wt, mpg, colour = factor(cyl))) + geom_point()
  z + theme(legend.position = c(.5, .5))
  
Currently this does not appear to work in RStudio but seems fine if I use gedit
or if I run R in a terminal session.

John Kane
Kingston ON Canada

> -----Original Message-----
> From: anna at ecology.su.se
> Sent: Wed, 06 Mar 2013 13:32:42 +0100
> To: r-help at r-project.org
> Subject: [R] Ggplot2: Moving legend, change fill and removal of space
> between plots when using grid.arrange() possible use of facet_grid?
> 
> Hi,
> 
> # For publications, I am not allowed to repeat the axes. I have tried to
> remove the axes using:
> # yaxt="n", but it did not work. I have not understood how to do
this in
> ggplot2. Can you help me?
> # I also do not want loads of space between the graphs (see below script
> with Dummy Data).
> # If I could make it look like the examples on the (nice) examples page:
> # http://www.ling.upenn.edu/~joseff/rstudy/summer2010_ggplot2_intro.html
> # using the facet_grid(), I would be very very happy.
> 
> # I also do not want the gemoetric points to be filled and the
> fill="white"
> commande
> # does not seem to work - why? and are there alternatives?
> 
> #Furthermore, I would like to add legends to inside the plot area instead
> of
> on the side. Like when you use plotrix() and brkdn.plot:
> legend("topright", c("A", "B"), pch=c(0,1),
bg="white",
>        lty = 1:2, cex=1, bty="n")
> # This did not work in ggplot2. What are my alternatives. I have
> extensively
> searched the internet and have I missed something obvious, it was due to
>    # tiredness and not to lazyness.
> 
> # 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)))
> 
> 
> # Splitting data into 3 data frames (based on factor1)
> # If I could do this using for example facet_wrap() or facet_grid(), I
> would
> be very
> # happy! I have tried but failed that method.
> 
> DataAB <- mydata[(mydata$factor1) %in% c("A", "B"),
]
> DataCD <- mydata[(mydata$factor1) %in% c("C", "D"),
]
> DataEF <- mydata[(mydata$factor1) %in% c("E", "F"),
]
> DataAB
> library(plyr)
> library(ggplot2)
> 
> #Plot: levels A and B:
> # Summary (means etc)
> SummAB  <-   ddply(DataAB, .(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))))
> SummAB
> p1  <-  ggplot(SummAB, aes(factor3, mean,
>                                colour = factor1, group = factor1,
>                                shape = factor1)) +
>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
>              position = "dodge", width = 0.3, size=3) +
>   geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
>                 position = "dodge", color = "black",
size=0.3) +
>   theme_bw() +
>   ylab(expression(paste("my measured stuff"))) +
>   xlab("factor3") + ggtitle("") +
>   labs(color = "factor1", shape = "factor1", group =
"factor1",
>        linetype = "factor1")
> p1
> 
> #Plot: levels C and D:
> # Summary (means etc)
> SummCD  <-   ddply(DataCD, .(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))))
> 
> p2  <-  ggplot(SummCD, aes(factor3, mean,
>                            colour = factor1, group = factor1,
>                            shape = factor1)) +
>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
>              position = "dodge", width = 0.3, size=3) +
>   geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
>                 position = "dodge", color = "black",
size=0.3) +
>   theme_bw() +
>   ylab(expression(paste("my measured stuff"))) +
>   xlab("factor3") + ggtitle("") +
>   labs(color = "factor1", shape = "factor1", group =
"factor1",
>        linetype = "factor1")
> p2
> 
> #Plot: levels C and D:
> # Summary (means etc)
> SummEF  <-   ddply(DataEF, .(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))))
> 
> p3  <-  ggplot(SummEF, aes(factor3, mean,
>                            colour = factor1, group = factor1,
>                            shape = factor1)) +
>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
> #Why
> is the fill commando not working?
>              position = "dodge", width = 0.3, size=3) +
>   geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
>                 position = "dodge", color = "black",
size=0.3) +
>   theme_bw() +
>   ylab(expression(paste("my measured stuff"))) +
>   xlab("factor3") + ggtitle("") +
>   labs(color = "factor1", shape = "factor1", group =
"factor1",
>        linetype = "factor1")
> p3
> 
> ary(gridExtra)
> sidebysideplot <- grid.arrange(p1, p2, p3, ncol=2)
> 
> 
> 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 at su.se
> Tel work: +49-(0)3091541281
> Mobile: +49-(0)15777374888
> LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
> 
> ><((((B:>`b?". . b?" `b?". .b?" `b?". .
><((((B:>`b?". . b?" `b?". .b?"
> `b?". .><((((B:>`b?". . b?" `b?". .b?"
`b?". .><((((B:>
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at 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.
____________________________________________________________
FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your
desktop!

Replying to my own post RStudio is doing this fine once I had rebooted R.  I
must have had some strange stuff loaded that I had not realised was there.

John Kane
Kingston ON Canada

> -----Original Message-----
> From: jrkrideau at inbox.com
> Sent: Wed, 6 Mar 2013 11:16:28 -0800
> To: anna at ecology.su.se, r-help at r-project.org
> Subject: Re: [R] Ggplot2: Moving legend, change fill and removal of space
> between plots when using grid.arrange() possible use of facet_grid?
> 
> Placing a legend.
> 
>  z <- ggplot(mtcars, aes(wt, mpg, colour = factor(cyl))) + geom_point()
>   z + theme(legend.position = c(.5, .5))
> 
> Currently this does not appear to work in RStudio but seems fine if I use
> gedit or if I run R in a terminal session.
> 
> John Kane
> Kingston ON Canada
> 
> 
>> -----Original Message-----
>> From: anna at ecology.su.se
>> Sent: Wed, 06 Mar 2013 13:32:42 +0100
>> To: r-help at r-project.org
>> Subject: [R] Ggplot2: Moving legend, change fill and removal of space
>> between plots when using grid.arrange() possible use of facet_grid?
>> 
>> Hi,
>> 
>> # For publications, I am not allowed to repeat the axes. I have tried
to
>> remove the axes using:
>> # yaxt="n", but it did not work. I have not understood how to
do this in
>> ggplot2. Can you help me?
>> # I also do not want loads of space between the graphs (see below
script
>> with Dummy Data).
>> # If I could make it look like the examples on the (nice) examples
page:
>> #
http://www.ling.upenn.edu/~joseff/rstudy/summer2010_ggplot2_intro.html
>> # using the facet_grid(), I would be very very happy.
>> 
>> # I also do not want the gemoetric points to be filled and the
>> fill="white"
>> commande
>> # does not seem to work - why? and are there alternatives?
>> 
>> #Furthermore, I would like to add legends to inside the plot area
>> instead
>> of
>> on the side. Like when you use plotrix() and brkdn.plot:
>> legend("topright", c("A", "B"),
pch=c(0,1), bg="white",
>>        lty = 1:2, cex=1, bty="n")
>> # This did not work in ggplot2. What are my alternatives. I have
>> extensively
>> searched the internet and have I missed something obvious, it was due
to
>>    # tiredness and not to lazyness.
>> 
>> # 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)))
>> 
>> 
>> # Splitting data into 3 data frames (based on factor1)
>> # If I could do this using for example facet_wrap() or facet_grid(), I
>> would
>> be very
>> # happy! I have tried but failed that method.
>> 
>> DataAB <- mydata[(mydata$factor1) %in% c("A",
"B"), ]
>> DataCD <- mydata[(mydata$factor1) %in% c("C",
"D"), ]
>> DataEF <- mydata[(mydata$factor1) %in% c("E",
"F"), ]
>> DataAB
>> library(plyr)
>> library(ggplot2)
>> 
>> #Plot: levels A and B:
>> # Summary (means etc)
>> SummAB  <-   ddply(DataAB, .(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))))
>> SummAB
>> p1  <-  ggplot(SummAB, aes(factor3, mean,
>>                                colour = factor1, group = factor1,
>>                                shape = factor1)) +
>>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
>>              position = "dodge", width = 0.3, size=3) +
>>   geom_line(aes(linetype=factor1), color = "black", size =
0.5) +
>>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width =
0.3,
>>                 position = "dodge", color =
"black", size=0.3) +
>>   theme_bw() +
>>   ylab(expression(paste("my measured stuff"))) +
>>   xlab("factor3") + ggtitle("") +
>>   labs(color = "factor1", shape = "factor1", group
= "factor1",
>>        linetype = "factor1")
>> p1
>> 
>> #Plot: levels C and D:
>> # Summary (means etc)
>> SummCD  <-   ddply(DataCD, .(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))))
>> 
>> p2  <-  ggplot(SummCD, aes(factor3, mean,
>>                            colour = factor1, group = factor1,
>>                            shape = factor1)) +
>>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
>>              position = "dodge", width = 0.3, size=3) +
>>   geom_line(aes(linetype=factor1), color = "black", size =
0.5) +
>>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width =
0.3,
>>                 position = "dodge", color =
"black", size=0.3) +
>>   theme_bw() +
>>   ylab(expression(paste("my measured stuff"))) +
>>   xlab("factor3") + ggtitle("") +
>>   labs(color = "factor1", shape = "factor1", group
= "factor1",
>>        linetype = "factor1")
>> p2
>> 
>> #Plot: levels C and D:
>> # Summary (means etc)
>> SummEF  <-   ddply(DataEF, .(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))))
>> 
>> p3  <-  ggplot(SummEF, aes(factor3, mean,
>>                            colour = factor1, group = factor1,
>>                            shape = factor1)) +
>>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
>> #Why
>> is the fill commando not working?
>>              position = "dodge", width = 0.3, size=3) +
>>   geom_line(aes(linetype=factor1), color = "black", size =
0.5) +
>>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width =
0.3,
>>                 position = "dodge", color =
"black", size=0.3) +
>>   theme_bw() +
>>   ylab(expression(paste("my measured stuff"))) +
>>   xlab("factor3") + ggtitle("") +
>>   labs(color = "factor1", shape = "factor1", group
= "factor1",
>>        linetype = "factor1")
>> p3
>> 
>> ary(gridExtra)
>> sidebysideplot <- grid.arrange(p1, p2, p3, ncol=2)
>> 
>> 
>> 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 at su.se
>> Tel work: +49-(0)3091541281
>> Mobile: +49-(0)15777374888
>> LinkedIn:
>> http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
>> 
>> ><((((B:>`b?". . b?" `b?". .b?" `b?".
. ><((((B:>`b?". . b?" `b?". .b?"
>> `b?". .><((((B:>`b?". . b?" `b?".
.b?" `b?". .><((((B:>
>> 
>> 	[[alternative HTML version deleted]]
>> 
>> ______________________________________________
>> R-help at 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.
> 
> ____________________________________________________________
> FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on
> your desktop!
> 
> ______________________________________________
> R-help at 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.
____________________________________________________________
FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your
desktop!

Looking good.  I think the function in this post is what you want. It worked on
your code for me. 
http://stackoverflow.com/questions/13297155/add-floating-axis-labels-in-facet-wrap-plot
.

John Kane
Kingston ON Canada

> -----Original Message-----
> From: anna at ecology.su.se
> Sent: Thu, 07 Mar 2013 12:47:34 +0100
> To: thierry.onkelinx at inbo.be, r-help at r-project.org
> Subject: Re: [R] Ggplot2: Moving legend, change fill and removal of space
> between plots when using grid.arrange() possible use of facet_grid?
> 
> Hi,
> have managed to get rid of the facet labels (so do not spend your time
> explaining that to me). Tthere were some old code out there which did not
> work. My only remaining issue is how to add the axis labels to the plot
> without labels.
> Anna
> 
> 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$Grouping <- c("AB", "AB", "CD",
"CD", "EF", "EF")[Summ$factor1]
> Summ$factor1bis <- c("0", "1", "0",
"1", "0", "1")[Summ$factor1]
> 
> ggplot(Summ, aes(factor3, mean, group = factor1bis, shape = factor1bis,
> linetype = factor1bis, 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() +
>   theme(strip.background = element_blank())+
>   theme(strip.text.x = element_blank(),
>         strip.text.y = element_blank())+
>   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 at su.se
> Tel work: +49-(0)3091541281
> Mobile: +49-(0)15777374888
> LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
> 
> ><((((B:>`b?". . b?" `b?". .b?" `b?". .
><((((B:>`b?". . b?" `b?". .b?"
> `b?". .><((((B:>`b?". . b?" `b?". .b?"
`b?". .><((((B:>
> 
> -----Original Message-----
> From: "ONKELINX, Thierry" <Thierry.ONKELINX at inbo.be>
> To: Anna Zakrisson <anna at ecology.su.se>, "r-help at
r-project.org"
> <r-help at r-project.org>
> Date: Wed, 6 Mar 2013 13:36:00 +0000
> Subject: RE: [R] Ggplot2: Moving legend,   change fill and removal of
> space
> between   plots when using   grid.arrange() possible use of facet_grid?
> 
> Dear Anna,
> 
> Is this what you would like?
> 
> 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$Grouping <- c("AB", "AB", "CD",
"CD", "EF", "EF")[Summ$factor1]
> Summ$factor1bis <- c("0", "1", "0",
"1", "0", "1")[Summ$factor1]
> 
> ggplot(Summ, aes(factor3, mean, group = factor1bis, shape = factor1bis,
> linetype = factor1bis, 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_bw() +
> ylab(expression(paste("my measured stuff"))) +
> xlab("factor3") +
> labs(shape = "factor1", group = "factor1", linetype =
"factor1")
> 
> Best regards,
> 
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> and
> Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality
Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> 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 Anna Zakrisson
> Verzonden: woensdag 6 maart 2013 13:33
> Aan: r-help at r-project.org
> Onderwerp: [R] Ggplot2: Moving legend, change fill and removal of space
> between plots when using grid.arrange() possible use of facet_grid?
> 
> Hi,
> 
> # For publications, I am not allowed to repeat the axes. I have tried to
> remove the axes using:
> # yaxt="n", but it did not work. I have not understood how to do
this in
> ggplot2. Can you help me?
> # I also do not want loads of space between the graphs (see below script
> with Dummy Data).
> # If I could make it look like the examples on the (nice) examples page:
> # http://www.ling.upenn.edu/~joseff/rstudy/summer2010_ggplot2_intro.html
> # using the facet_grid(), I would be very very happy.
> 
> # I also do not want the gemoetric points to be filled and the
> fill="white"
> commande
> # does not seem to work - why? and are there alternatives?
> 
> #Furthermore, I would like to add legends to inside the plot area instead
> of
> on the side. Like when you use plotrix() and brkdn.plot:
> legend("topright", c("A", "B"), pch=c(0,1),
bg="white",
>        lty = 1:2, cex=1, bty="n")
> # This did not work in ggplot2. What are my alternatives. I have
> extensively
> searched the internet and have I missed something obvious, it was due to
>    # tiredness and not to lazyness.
> 
> # 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)))
> 
> 
> # Splitting data into 3 data frames (based on factor1)
> # If I could do this using for example facet_wrap() or facet_grid(), I
> would
> be very
> # happy! I have tried but failed that method.
> 
> DataAB <- mydata[(mydata$factor1) %in% c("A", "B"),
]
> DataCD <- mydata[(mydata$factor1) %in% c("C", "D"),
]
> DataEF <- mydata[(mydata$factor1) %in% c("E", "F"),
]
> DataAB
> library(plyr)
> library(ggplot2)
> 
> #Plot: levels A and B:
> # Summary (means etc)
> SummAB  <-   ddply(DataAB, .(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))))
> SummAB
> p1  <-  ggplot(SummAB, aes(factor3, mean,
>                                colour = factor1, group = factor1,
>                                shape = factor1)) +
>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
>              position = "dodge", width = 0.3, size=3) +
>   geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
>                 position = "dodge", color = "black",
size=0.3) +
>   theme_bw() +
>   ylab(expression(paste("my measured stuff"))) +
>   xlab("factor3") + ggtitle("") +
>   labs(color = "factor1", shape = "factor1", group =
"factor1",
>        linetype = "factor1")
> p1
> 
> #Plot: levels C and D:
> # Summary (means etc)
> SummCD  <-   ddply(DataCD, .(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))))
> 
> p2  <-  ggplot(SummCD, aes(factor3, mean,
>                            colour = factor1, group = factor1,
>                            shape = factor1)) +
>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
>              position = "dodge", width = 0.3, size=3) +
>   geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
>                 position = "dodge", color = "black",
size=0.3) +
>   theme_bw() +
>   ylab(expression(paste("my measured stuff"))) +
>   xlab("factor3") + ggtitle("") +
>   labs(color = "factor1", shape = "factor1", group =
"factor1",
>        linetype = "factor1")
> p2
> 
> #Plot: levels C and D:
> # Summary (means etc)
> SummEF  <-   ddply(DataEF, .(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))))
> 
> p3  <-  ggplot(SummEF, aes(factor3, mean,
>                            colour = factor1, group = factor1,
>                            shape = factor1)) +
>   geom_point(aes(shape=factor(factor1)), color="black",
fill="white",
> #Why
> is the fill commando not working?
>              position = "dodge", width = 0.3, size=3) +
>   geom_line(aes(linetype=factor1), color = "black", size = 0.5) +
>   geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3,
>                 position = "dodge", color = "black",
size=0.3) +
>   theme_bw() +
>   ylab(expression(paste("my measured stuff"))) +
>   xlab("factor3") + ggtitle("") +
>   labs(color = "factor1", shape = "factor1", group =
"factor1",
>        linetype = "factor1")
> p3
> 
> ary(gridExtra)
> sidebysideplot <- grid.arrange(p1, p2, p3, ncol=2)
> 
> 
> 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 at su.se
> Tel work: +49-(0)3091541281
> Mobile: +49-(0)15777374888
> LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
> 
> ><((((C?B:>`C"b?,B". . C"b?,B"
`C"b?,B". .C"b?,B" `C"b?,B". .
> ><((((C?B:>`C"b?,B". . C"b?,B"
`C"b?,B". .C"b?,B"
> `C"b?,B". .><((((C?B:>`C"b?,B". .
C"b?,B" `C"b?,B". .C"b?,B" `C"b?,B".
> .><((((C?B:>
> 
>         [[alternative HTML version deleted]]
> 
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> 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.
> 
> 	[[alternative HTML version deleted]]
> 
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