Question: Gene density plot with points underneath
0
12.6 years ago by
Daniel Brewer1.9k
Daniel Brewer1.9k 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 -- ************************************************************** 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. This e-mail message is confidential and for use by the addre...{{dropped}}
cancer • 548 views
modified 12.6 years ago by Marcus Davy680 • written 12.6 years ago by Daniel Brewer1.9k
Answer: Gene density plot with points underneath
0
12.6 years ago by
Marcus Davy680
Marcus Davy680 wrote:
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 ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}