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

13 messages · stephen sefick, ONKELINX, Thierry, Anna Zakrisson +1 more

Original
stephen sefick
# 
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:
ONKELINX, Thierry
# 
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

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~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

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~ 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
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John Kane
# 
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
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John Kane
# 
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
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John Kane
# 
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
____________________________________________________________
FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop!
John Kane
# 
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
____________________________________________________________
FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop!