[R] ggplot2 reorder factors for faceting
Dear List
I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted my
data by 'infection' of which I have four. These four infections break down into
two types and I would like to reorder the 'infection' column of my data to
reflect this.
Toy example below:
library(ggplot2)
# test data for ggplot reordering
genes - (rep (c(rep('a',4), rep('b',4), rep('c',4), rep('d',4), rep('e',4),
rep('f',4)) ,4))
fcData - rnorm(96)
times - rep(rep(c(2,6,24,48),6),4)
infection - c(rep('InfA', 24), rep('InfB', 24), rep('InfC', 24), rep('InfD',
24))
infType - c(rep('M', 24), rep('D',24), rep('M', 24), rep('D', 24))
# data is long format for ggplot2
plotData - as.data.frame(cbind(genes, as.numeric(fcData), as.numeric(times),
infection, infType))
hp2 - ggplot(plotData, aes(factor(times), genes)) + geom_tile(aes(fill =
scale(as.numeric(fcData + facet_wrap(~infection, ncol=4)
# set scale
hp2 - hp2 + scale_fill_gradient2(name=NULL, low=#0571B0, mid=#F7F7F7,
high=#CA0020, midpoint=0, breaks=NULL, labels=NULL, limits=NULL,
trans=identity)
# set up text (size, colour etc etc)
hp2 - hp2 + labs(x = Time, y = ) + scale_y_discrete(expand = c(0, 0)) +
opts(axis.ticks = theme_blank(), axis.text.x = theme_text(size = 10, angle =
360, hjust = 0, colour = grey25), axis.text.y = theme_text(size=10, colour =
'gray25'))
hp2 - hp2 + theme_bw()
In the resulting plot I would like infections infA and infC plotted next to
each other and likewise for infB and infD. I have a column in the data -
infType - which I could use to reorder the infection column but so far I have
no luck getting this to work.
Could someone give me a pointer to the best way to reorder the infection factor
and accompanying data into the order I would like?
Best
iain
sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6
loaded via a namespace (and not attached):
[1] digest_0.5.0 tools_2.13.2
__
R-help@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.
Re: [R] ggplot2 reorder factors for faceting
Hi, Iain-
You might want to have a look at
?relevel
i.e. plotData$infection-relevel(plotData$infection, ref = 'InfC')
Ken
On 11/08/11, Iain Gallagher wrote:
Dear List
I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted
my data by 'infection' of which I have four. These four infections break down
into two types and I would like to reorder the 'infection' column of my data
to reflect this.
Toy example below:
library(ggplot2)
# test data for ggplot reordering
genes - (rep (c(rep('a',4), rep('b',4), rep('c',4), rep('d',4), rep('e',4),
rep('f',4)) ,4))
fcData - rnorm(96)
times - rep(rep(c(2,6,24,48),6),4)
infection - c(rep('InfA', 24), rep('InfB', 24), rep('InfC', 24), rep('InfD',
24))
infType - c(rep('M', 24), rep('D',24), rep('M', 24), rep('D', 24))
# data is long format for ggplot2
plotData - as.data.frame(cbind(genes, as.numeric(fcData), as.numeric(times),
infection, infType))
hp2 - ggplot(plotData, aes(factor(times), genes)) + geom_tile(aes(fill =
scale(as.numeric(fcData + facet_wrap(~infection, ncol=4)
# set scale
hp2 - hp2 + scale_fill_gradient2(name=NULL, low=#0571B0, mid=#F7F7F7,
high=#CA0020, midpoint=0, breaks=NULL, labels=NULL, limits=NULL,
trans=identity)
# set up text (size, colour etc etc)
hp2 - hp2 + labs(x = Time, y = ) + scale_y_discrete(expand = c(0, 0)) +
opts(axis.ticks = theme_blank(), axis.text.x = theme_text(size = 10, angle =
360, hjust = 0, colour = grey25), axis.text.y = theme_text(size=10, colour
= 'gray25'))
hp2 - hp2 + theme_bw()
In the resulting plot I would like infections infA and infC plotted next to
each other and likewise for infB and infD. I have a column in the data -
infType - which I could use to reorder the infection column but so far I have
no luck getting this to work.
Could someone give me a pointer to the best way to reorder the infection
factor and accompanying data into the order I would like?
Best
iain
sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6
loaded via a namespace (and not attached):
[1] digest_0.5.0 tools_2.13.2
__
R-help@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.
__
R-help@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.
Re: [R] ggplot2 reorder factors for faceting
Dear Iain,
RSiteSearch(ggplot2 reorder, restrict = c(Rhelp10, Rhelp08)) gives you
the solution.
Best regards,
Thierry
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
Namens Iain Gallagher
Verzonden: dinsdag 8 november 2011 12:51
Aan: r-help
Onderwerp: [R] ggplot2 reorder factors for faceting
Dear List
I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted my
data by 'infection' of which I have four. These four infections break down
into
two types and I would like to reorder the 'infection' column of my data to
reflect
this.
Toy example below:
library(ggplot2)
# test data for ggplot reordering
genes - (rep (c(rep('a',4), rep('b',4), rep('c',4), rep('d',4), rep('e',4),
rep('f',4)) ,4))
fcData - rnorm(96) times - rep(rep(c(2,6,24,48),6),4) infection -
c(rep('InfA',
24), rep('InfB', 24), rep('InfC', 24), rep('InfD', 24)) infType - c(rep('M',
24),
rep('D',24), rep('M', 24), rep('D', 24))
# data is long format for ggplot2
plotData - as.data.frame(cbind(genes, as.numeric(fcData), as.numeric(times),
infection, infType))
hp2 - ggplot(plotData, aes(factor(times), genes)) + geom_tile(aes(fill =
scale(as.numeric(fcData + facet_wrap(~infection, ncol=4)
# set scale
hp2 - hp2 + scale_fill_gradient2(name=NULL, low=#0571B0, mid=#F7F7F7,
high=#CA0020, midpoint=0, breaks=NULL, labels=NULL, limits=NULL,
trans=identity)
# set up text (size, colour etc etc)
hp2 - hp2 + labs(x = Time, y = ) + scale_y_discrete(expand = c(0, 0)) +
opts(axis.ticks = theme_blank(), axis.text.x = theme_text(size = 10, angle =
360,
hjust = 0, colour = grey25), axis.text.y = theme_text(size=10, colour =
'gray25'))
hp2 - hp2 + theme_bw()
In the resulting plot I would like infections infA and infC plotted next to
each
other and likewise for infB and infD. I have a column in the data - infType -
which
I could use to reorder the infection column but so far I have no luck getting
this
to work.
Could someone give me a pointer to the best way to reorder the infection
factor
and accompanying data into the order I would like?
Best
iain
sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C [11]
LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods [8]
base
other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6
loaded via a namespace (and not attached):
[1] digest_0.5.0 tools_2.13.2
__
R-help@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.
__
R-help@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.
Re: [R] ggplot2 reorder factors for faceting
Hi:
(1) Here is one way to reorganize the levels of a factor:
plotData[['infection']] - factor(plotData[['infection']],
levels = c('InfA', 'InfC', 'InfB', 'InfD'))
Do this ahead of the call to ggplot(), preferably after plotData is defined.
relevel() resets the baseline category of a factor, but here you want
to make multiple changes.
(2) You probably want a better title for the legend. Assuming you want
'Scale' as the title, you can add the following to labs:
labs(..., fill = 'Scale')
HTH,
Dennis
On Tue, Nov 8, 2011 at 3:51 AM, Iain Gallagher
iaingallag...@btopenworld.com wrote:
Dear List
I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted
my data by 'infection' of which I have four. These four infections break down
into two types and I would like to reorder the 'infection' column of my data
to reflect this.
Toy example below:
library(ggplot2)
# test data for ggplot reordering
genes - (rep (c(rep('a',4), rep('b',4), rep('c',4), rep('d',4), rep('e',4),
rep('f',4)) ,4))
fcData - rnorm(96)
times - rep(rep(c(2,6,24,48),6),4)
infection - c(rep('InfA', 24), rep('InfB', 24), rep('InfC', 24), rep('InfD',
24))
infType - c(rep('M', 24), rep('D',24), rep('M', 24), rep('D', 24))
# data is long format for ggplot2
plotData - as.data.frame(cbind(genes, as.numeric(fcData), as.numeric(times),
infection, infType))
hp2 - ggplot(plotData, aes(factor(times), genes)) + geom_tile(aes(fill =
scale(as.numeric(fcData + facet_wrap(~infection, ncol=4)
# set scale
hp2 - hp2 + scale_fill_gradient2(name=NULL, low=#0571B0, mid=#F7F7F7,
high=#CA0020, midpoint=0, breaks=NULL, labels=NULL, limits=NULL,
trans=identity)
# set up text (size, colour etc etc)
hp2 - hp2 + labs(x = Time, y = ) + scale_y_discrete(expand = c(0, 0)) +
opts(axis.ticks = theme_blank(), axis.text.x = theme_text(size = 10, angle =
360, hjust = 0, colour = grey25), axis.text.y = theme_text(size=10, colour
= 'gray25'))
hp2 - hp2 + theme_bw()
In the resulting plot I would like infections infA and infC plotted next to
each other and likewise for infB and infD. I have a column in the data -
infType - which I could use to reorder the infection column but so far I have
no luck getting this to work.
Could someone give me a pointer to the best way to reorder the infection
factor and accompanying data into the order I would like?
Best
iain
sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6
loaded via a namespace (and not attached):
[1] digest_0.5.0 tools_2.13.2
__
R-help@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.
__
R-help@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.
