Hi Luis,
Ah yes, that paper. I was rather shocked at what it implied :( People are
still using dynamite plots, for heaven's sake! See
http://biostat.mc.vanderbilt.edu/wiki/Main/DynamitePlots for some comments.
I see Jim has given you one way to do the plots you want. Here is another way
using the ggplot2 package. You will probably have to install the package. The
code below covers the 2B:2D plots.
####=======Install
ggplot2==================install.packages("ggplot2")
###======== plot desired graphs=================library(ggplot2)
dat1 <- data.frame(x1 = rep("A", 4) , x2 = rep("B",
4), y1 = 5:8, y2 = 10:13)
p <- ggplot()
p1 <- p + geom_segment( aes(x = x1, y = y1, xend = x2, yend = y2)) +
geom_point(aes(x1, y1, colour = "blue", size = 2)) +
geom_point(aes(x2, y2, colour = "red", size = 2))
p1
p2 <- p1 + theme (legend.position = "none") +
xlab("Treatment") + ylab("Change Score")
p2
###======== end=================
We could have all the commands in one statement but it is easier to write the
code this way to help in debugging (damn typos1) and so I left it to help you
see what is happening.
For the lower plots, in ggplot2, you should have a look at geom_dotplot() . Here
is an interesting demo of it in use. I like the addition of the median line in
particular.
http://rstudio-pubs-static.s3.amazonaws.com/1406_947a49f2d7914dad8b0fd050a9df9858.html
John Kane
Kingston ON Canada
> -----Original Message-----
> From: luysgarcia at gmail.com
> Sent: Mon, 4 May 2015 04:52:51 -0300
> To: r-help at r-project.org
> Subject: [R] Fwd: Question about paired plotting
>
> Hello R experts,
>
> I just found a new paper which shows the proper way (according to the
> authors) to show data, specially paired. I am very interested in
> presenting
> this kind of data, specially the scatter plott. I have found a way to
> present it using this link:
>
>
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1002128#pbio.1002128.s007
>
> Nevertheless, I wanted to know if you know some example which allows me
> to
> produce a plot similar to the plots 2B-2D. I could do it by
"hand" but it
> was quite time consuming and required editing the pictures,
>
> Many thanks for any help you can provide!
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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 EARTH SCREENSAVER - Watch the Earth right on your desktop!
Dear John and Tim! Thanks a lot for your replies. This is just what I needed!! All the best for you!! 2015-05-04 13:58 GMT-03:00 John Kane <jrkrideau at inbox.com>:> Hi Luis, > Ah yes, that paper. I was rather shocked at what it implied :( People > are still using dynamite plots, for heaven's sake! See > http://biostat.mc.vanderbilt.edu/wiki/Main/DynamitePlots for some > comments. > I see Jim has given you one way to do the plots you want. Here is another > way using the ggplot2 package. You will probably have to install the > package. The code below covers the 2B:2D plots. > ####=======Install ggplot2==================> install.packages("ggplot2") > > ###======== plot desired graphs=================> library(ggplot2) > > dat1 <- data.frame(x1 = rep("A", 4) , x2 = rep("B", 4), y1 = 5:8, > y2 = 10:13) > > p <- ggplot() > p1 <- p + geom_segment( aes(x = x1, y = y1, xend = x2, yend = y2)) + > geom_point(aes(x1, y1, colour = "blue", size = 2)) + > geom_point(aes(x2, y2, colour = "red", size = 2)) > p1 > > p2 <- p1 + theme (legend.position = "none") + > xlab("Treatment") + ylab("Change Score") > p2 > > ###======== end=================> > We could have all the commands in one statement but it is easier to write > the code this way to help in debugging (damn typos1) and so I left it to > help you see what is happening. > > For the lower plots, in ggplot2, you should have a look at geom_dotplot() > . Here is an interesting demo of it in use. I like the addition of the > median line in particular. > > > http://rstudio-pubs-static.s3.amazonaws.com/1406_947a49f2d7914dad8b0fd050a9df9858.html > > > > > John Kane > Kingston ON Canada > > > > -----Original Message----- > > From: luysgarcia at gmail.com > > Sent: Mon, 4 May 2015 04:52:51 -0300 > > To: r-help at r-project.org > > Subject: [R] Fwd: Question about paired plotting > > > > Hello R experts, > > > > I just found a new paper which shows the proper way (according to the > > authors) to show data, specially paired. I am very interested in > > presenting > > this kind of data, specially the scatter plott. I have found a way to > > present it using this link: > > > > > http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1002128#pbio.1002128.s007 > > > > Nevertheless, I wanted to know if you know some example which allows me > > to > > produce a plot similar to the plots 2B-2D. I could do it by "hand" but it > > was quite time consuming and required editing the pictures, > > > > Many thanks for any help you can provide! > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > 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 EARTH SCREENSAVER - Watch the Earth right on your desktop! > Check it out at http://www.inbox.com/earth > > >[[alternative HTML version deleted]]
Hi
With R there are usually several ways
Here is another one using lattice (I think it ships with R otherwise
install)
Reshape dat1 to long form and add a column for groups do give d2
d2 = structure(list(y = c(5L, 10L, 6L, 11L, 7L, 12L, 8L, 13L), x = c(1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L), gp = structure(c(1L, 1L, 2L, 2L,
3L, 3L, 4L, 4L), .Label = c("1", "2", "3",
"4"), class = "factor")), .Names
= c("y",
"x", "gp"), row.names = c(NA, -8L), class =
"data.frame")
library(lattice)
d2
library(lattice)
xyplot(y~x, data = d2,
groups = gp,
scales = list(x = list(at = 1:2,
labels= LETTERS[1:2])),
col = 1,
type = "b")
PS it makes it easier for every one if you send an example; even better
using dput
For windows
dput(d2, file= "clipboard")
and paste it into your email
Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mackay at northnet.com.au
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Luis
Fernando Garc?a
Sent: Tuesday, 5 May 2015 04:35
To: John Kane
Cc: r-help at r-project.org
Subject: Re: [R] Fwd: Question about paired plotting
Dear John and Tim!
Thanks a lot for your replies. This is just what I needed!!
All the best for you!!
2015-05-04 13:58 GMT-03:00 John Kane <jrkrideau at inbox.com>:
> Hi Luis,
> Ah yes, that paper. I was rather shocked at what it implied :( People
> are still using dynamite plots, for heaven's sake! See
> http://biostat.mc.vanderbilt.edu/wiki/Main/DynamitePlots for some
> comments.
> I see Jim has given you one way to do the plots you want. Here is another
> way using the ggplot2 package. You will probably have to install the
> package. The code below covers the 2B:2D plots.
> ####=======Install ggplot2==================>
install.packages("ggplot2")
>
> ###======== plot desired graphs=================> library(ggplot2)
>
> dat1 <- data.frame(x1 = rep("A", 4) , x2 =
rep("B", 4), y1 = 5:8,
> y2 = 10:13)
>
> p <- ggplot()
> p1 <- p + geom_segment( aes(x = x1, y = y1, xend = x2, yend = y2))
+
> geom_point(aes(x1, y1, colour = "blue", size = 2)) +
> geom_point(aes(x2, y2, colour = "red", size = 2))
> p1
>
> p2 <- p1 + theme (legend.position = "none") +
> xlab("Treatment") + ylab("Change
Score")
> p2
>
> ###======== end=================>
> We could have all the commands in one statement but it is easier to write
> the code this way to help in debugging (damn typos1) and so I left it to
> help you see what is happening.
>
> For the lower plots, in ggplot2, you should have a look at geom_dotplot()
> . Here is an interesting demo of it in use. I like the addition of the
> median line in particular.
>
>
>
http://rstudio-pubs-static.s3.amazonaws.com/1406_947a49f2d7914dad8b0fd050a9d
f9858.html>
>
>
>
> John Kane
> Kingston ON Canada
>
>
> > -----Original Message-----
> > From: luysgarcia at gmail.com
> > Sent: Mon, 4 May 2015 04:52:51 -0300
> > To: r-help at r-project.org
> > Subject: [R] Fwd: Question about paired plotting
> >
> > Hello R experts,
> >
> > I just found a new paper which shows the proper way (according to the
> > authors) to show data, specially paired. I am very interested in
> > presenting
> > this kind of data, specially the scatter plott. I have found a way to
> > present it using this link:
> >
> >
>
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.10021
28#pbio.1002128.s007> >
> > Nevertheless, I wanted to know if you know some example which allows
me
> > to
> > produce a plot similar to the plots 2B-2D. I could do it by
"hand" but
it> > was quite time consuming and required editing the pictures,
> >
> > Many thanks for any help you can provide!
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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 EARTH SCREENSAVER - Watch the Earth right on your desktop!
> Check it out at http://www.inbox.com/earth
>
>
>
[[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.