-----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:>
-----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