Stacked barplot with two stacked bars besides each other - R-help

Tue, Jan 20, 2009 2:28 AM #

Hi,

I have a particular barplot I would like to generate, but I am having
trouble getting it to work.  What I would like is in effect two barplots
 with stacked bars merged into one.  For example,  I have two samples
(yoda1,yoda2) on which I measure whether two variables (var1,var2) are
present or absent for a number of measurements on that sample.

For each variable I can plot a barplot

I would like to join these together, so that for each sample there are
two stacked bars next to each other, one for var1 and the other for
var2.  I was thinking something like:

would work, but it didn't.

Any suggestions you could make would be great.

Dan

**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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Henrique Dallazuanna

Tue, Jan 20, 2009 2:50 AM #

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Daniel Brewer

Tue, Jan 20, 2009 3:03 AM #

Thanks.
That is definitely in the right direction, but firstly I would like
yoda1:var1 next to yoda1:var2, not as currently yoda1:var1, yoda2:var1,
yoda1:var2, yoda2:var2.  Additionally, I would like the gap between
samples to be greater than the gap between variables.

Many thanks

Dan

Henrique Dallazuanna wrote:

**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the a...{{dropped:2}}

Henrique Dallazuanna

Tue, Jan 20, 2009 3:31 AM #

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Daniel Brewer

Tue, Jan 20, 2009 4:22 AM #

Thanks Henrique.  Unfortunately, that gets us a step closer but it fails
to stack the individual bars, so instead of having a total of 10 for
each bar you get 7, 8, 9 & 5 (i.e. the largest for each var sample
pair).  I tried adding the stack=T option, but that stacks all of each
sample and you are left with two bars.  Any more ideas?

Appreciate your help

Dan

Henrique Dallazuanna wrote:

One option is to use lattice package:

library(lattice)
newVar <- cbind(stack(rbind(var1, var2)), Var = rep(c("var1", "var2"),
each = 2))
barchart(values ~ ind, groups = Var, data = newVar)


On Tue, Jan 20, 2009 at 9:03 AM, Daniel Brewer <daniel.brewer at icr.ac.uk
<mailto:daniel.brewer at icr.ac.uk>> wrote:

    Thanks.
    That is definitely in the right direction, but firstly I would like
    yoda1:var1 next to yoda1:var2, not as currently yoda1:var1, yoda2:var1,
    yoda1:var2, yoda2:var2.  Additionally, I would like the gap between
    samples to be greater than the gap between variables.

    Many thanks

    Dan

    Henrique Dallazuanna wrote:

    > Try this:
    >
    > barplot(cbind(as.matrix(var1), as.matrix(var2)), names.arg =

    LETTERS[1:4])

    >
    > On Tue, Jan 20, 2009 at 8:28 AM, Daniel Brewer

    <daniel.brewer at icr.ac.uk <mailto:daniel.brewer at icr.ac.uk>

    > <mailto:daniel.brewer at icr.ac.uk <mailto:daniel.brewer at icr.ac.uk>>>

    wrote:

    >
    >     Hi,
    >
    >     I have a particular barplot I would like to generate, but I am

    having

    >     trouble getting it to work.  What I would like is in effect

    two barplots

    >      with stacked bars merged into one.  For example,  I have two

    samples

    >     (yoda1,yoda2) on which I measure whether two variables

    (var1,var2) are

    >     present or absent for a number of measurements on that sample.
    >

    >     > var1 <- data.frame(yoda1=c(3,7), yoda2=c(1,9))
    >     > var2 <- data.frame(yoda1=c(8,2), yoda2=c(5,5))

    >
    >     For each variable I can plot a barplot
    >

    >     > barplot(as.matrix(var1))
    >     > barplot(as.matrix(var2))

    >
    >     I would like to join these together, so that for each sample

    there are

    >     two stacked bars next to each other, one for var1 and the

    other for

    >     var2.  I was thinking something like:
    >

    >     > barplot(list(as.matrix(var1),as.matrix(var2)))

    >
    >     would work, but it didn't.
    >
    >     Any suggestions you could make would be great.
    >
    >     Dan

**************************************************************

Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom

Tel: +44 (0) 20 8722 4109

Email: daniel.brewer at icr.ac.uk

**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the a...{{dropped:2}}

Hadley Wickham

Tue, Jan 20, 2009 5:35 AM #

On Tue, Jan 20, 2009 at 4:28 AM, Daniel Brewer <daniel.brewer at icr.ac.uk> wrote:

I'd start by storing your data in a single data frame, with all
information explicit:

var1$row <- 1:2
var1$var <- "one"
var2$row <- 1:2
var2$var <- "two"

vars <- rbind(var1, var2)

library(reshape)
df <- melt(vars, id = c("var", "row"))
names(df)[3] <- "yoda"
df

(In reality you'd give the variables informative names based on your
study design)

Then you're in a position to better describe and control what you
want.  With the data in this form, you could then use the ggplot2
package to display it:

library(ggplot2)
qplot(yoda, value, data = df, fill = factor(row), geom="bar", stat =
"identity", facets = ~ var)

This puts yoda on the x axis, colours the bars by the row and
separates the plot into two panels based on var.  It's trivial to
produce any other arrangement of the three variables.

qplot(var, value, data = df, fill = factor(row), geom="bar", stat =
"identity", facets = ~ yoda)
qplot(row, value, data = df, fill = yoda, geom="bar", stat =
"identity", facets = ~ var)
etc

Hadley

http://had.co.nz/