Hi,
Just a quick question. I have a dataset that has been divided into
three groups. I would like to plot a density plot of the expression
levels for a particular gene for each group. Also I would like to
plot
the actual expression levels on a horizontal line under the density
line. I think this is a reasonably standard thing to do. How would I
go about doing this? Is there a function that simplifies this?
Many thanks
--
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
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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Daniel,
You can use the lattice package to create conditioned density plots
with a
dataframe as input and a model formula, e.g.
library(lattice)
densityplot(~height, data=singer)
A first principles approach would be to create a density plot with
enough
room to be able to add the expression points using the points
'function'
e.g.
n <- 1000
x <- rnorm(n)
plot(density(x), ylim=c(-0.05, 0.4))
points(x, jitter(rep(0, n)) + par()$usr[3]/2)
The jitter function is adding random noise and appears to have a BUG
in it,
if the input vector is a negative scalar or vector of the same
negative
value. It returns NaN e.g.
> jitter(-1)
[1] NaN
> jitter(-(1:2))
[1] -0.811903 -1.806600
> jitter(rep(0,5))
[1] 0.006074348 0.002293362 -0.019214007 0.010290299 -0.013055610
> jitter(rep(-1,5))
[1] NaN NaN NaN NaN NaN
>
This is caused by the last line inputting a negative number into runif
for
the maximum, and a positive number for the minimum and easily fixed
with
abs.
> runif(1,1,-1)
[1] NaN
Marcus
Version
_
platform powerpc-apple-darwin8.8.0
arch powerpc
os darwin8.8.0
system powerpc, darwin8.8.0
status
major 2
minor 4.1
year 2006
month 12
day 18
svn rev 40228
language R
version.string R version 2.4.1 (2006-12-18)
On 27/2/07 12:26 AM, "Daniel Brewer" <daniel.brewer at="" icr.ac.uk="">
wrote:
> Hi,
>
> Just a quick question. I have a dataset that has been divided into
> three groups. I would like to plot a density plot of the expression
> levels for a particular gene for each group. Also I would like to
plot
> the actual expression levels on a horizontal line under the density
> line. I think this is a reasonably standard thing to do. How would
I
> go about doing this? Is there a function that simplifies this?
>
> Many thanks
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