[BioC] RE : plotting probes along a chromosome

[Simon Noël]

Personally, I do use stripe.  It's not really hard to understand.

http://bioinfo.mikrobio.med.uni-giessen.de/wiki/index.php/Stripe

Simon Noël
CdeC
________________________________________
De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de J.Oosting at lumc.nl [J.Oosting at lumc.nl]
Date d'envoi : 16 juillet 2011 13:26
À : peter.shepard at gmail.com; bioconductor at stat.math.ethz.ch
Objet : Re: [BioC] plotting probes along a chromosome

A similar question with a number of possible solutions can be found on BioStar
http://biostar.stackexchange.com/questions/378/drawing-chromosome-ideogams-with-data/

Jan

________________________________________
Hello List,

I am trying to graph the position of probes ~50 nucleotides in length along
a chromosome and am looking for the best way to accomplish this. So far I
have tried the genomeGraphs package and can plot a chromosome and its bands
just fine. Next I attempt to plot assign the data coordinates using
>expres = new("GenericArray", intensity = intensity, probeStart =
exonProbePos, dp = DisplayPars(color="darkred", type="point"))
function. This accepts the values just fine. However, when I attempt to plot
it using ;

>
gdPlot(list(ideog,expres), minBase = minbase, maxBase =maxbase), I get the
following error:

Error in unit(x, default.units) : 'x' and 'units' must have length > 0

I am confused by this error because the input files that I give to "expres"

seem to match the ones given by the data provided by the package

I import the data:

"chr" "location" "strand" "expr"
"1" 4 180491934 -1 1.0
"2" 4 180491939 1 1.0
"3" 4 180491945 -1 1.0
"4" 4 180491963 1 1.0
"5" 4 180491993 -1 1.0
"6" 4 180491996 1 1.0
"7" 4 180491999 -1 1.0

using
>z<-read.table('p', header=TRUE)
the expres variable seems to accept a matrix of type "double"
which I build using
>expres_matrix<-as.matrix(z$expr)
and a list of "integers" wihich I give as z$location

when I do a class and typeof on these variables, they match the class/type
of the ones provided in the package but
when I run the plotting program, I get the error

I was initially trying this as a quick and dirty technique but am now stuck,
If anyone can suggest alternate/better methods, I am all ears.

Thanks

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