Now it's ok. So, alongChrom require the multi-colors selection... Thanks a lot ! Giulio >From: Wolfgang Huber <huber@ebi.ac.uk> >To: Giulio Di Giovanni <perimessaggini@hotmail.com> >CC: bioconductor@stat.math.ethz.ch >Subject: Re: [BioC] Geneplotter, alongChrom problem >Date: Tue, 22 Mar 2005 22:47:36 +0100 > >Hi Giulio, > >try > >alongChrom(eset, "Y", newChrom, xloc = "equispaced", > plotFormat = "image", scale = "zscale", colors = cm.colors(256)) > >It seems that the default value of the 'colors' parameter (namely, just the >single value "red"), is not good for the image plot format. > > Cheers, > Wolfgang > >Giulio Di Giovanni wrote: >>Hi to all, >> >>I have a problem using alongChrom in Geneplotter pkg, with the "image" >>plot. >>With this type of plot, all that I obtain is a single color filled image, >>instead the multicolor image. I didn't receive any error messages. >> >>I tried with different expression set and for different chromosomes, but >>with no differences. For example, the run from commonly known "An >>introduction to some graphics in Bioconductor" pdf document is: >> >> >>>library(annotate) >>>library(geneplotter) >>>library(hgu95av2) >>>data(eset) >>>newChrom <- buildChromLocation("hgu95av2") >>>newChrom >> >>Instance of a chromLocation class with the following fields: >> Organism: Homo sapiens >> Data source: hgu95av2 >> Number of chromosomes for this organism: 25 >> Chromosomes of this organism and their lengths in base pairs: >> 1 : 246127941 >> 2 : 243615958 >> 3 : 199344050 >> 4 : 191731959 >> 5 : 181034922 >> 6 : 170914576 >> 7 : 158545518 >> 8 : 146308819 >> 9 : 136372045 >> 10 : 135037215 >> 11 : 134482954 >> 12 : 132078379 >> 13 : 113042980 >> 14 : 105311216 >> 15 : 100256656 >> 16 : 90041932 >> 17 : 81860266 >> 18 : 76115139 >> 19 : 63811651 >> 20 : 63741868 >> 21 : 46976097 >> 22 : 49396972 >> X : 153692391 >> Y : 50286555 >> M : 16571 >> >>> >>>par(mfrow = c(2, 1)) >>>for (sc in c("max", "relative")) cPlot(newChrom, fg = "blue", >> >>+ scale = sc) >> >>> >>>cols <- c("red", "green", "blue") >>>cols <- cols[eset$cov3] # needs eset - expression set >>>par(mfrow = c(3, 2)) >>>alongChrom(eset, "1", newChrom, xloc = "equispaced", plotFormat = >>>"cumulative", >> >>+ col = cols, lwd = 2) >><environment: 027edb48=""> >> >>>alongChrom(eset, "1", newChrom, xloc = "physical", col = cols, >> >>+ lwd = 2) >><environment: 021b72b4=""> >> >>>alongChrom(eset, "1", newChrom, xloc = "equispaced", plotFormat = >>>"local", >> >>+ col = cols, lwd = 2) >> >>>alongChrom(eset, "1", newChrom, xloc = "equispaced", plotFormat = >>>"local", >> >>+ col = cols, type = "p", pch = 16) >> >>>alongChrom(eset, "1", newChrom, xlim = c(87511280, 127717880), >> >>+ xloc = "equispaced", plotFormat = "local", col = cols, type = "p", >>+ pch = 16) >> >>>alongChrom(eset, "Y", newChrom, xloc = "equispaced", plotFormat = >>>"image", scale="zscale") >>> >> >>All the plots are OK, but the last one as I said is a completly red >>image... >>I have the same result for all the datasets that I tried... >> >>Please, someone could suggest me what I'm doing wrong ? >> >>Thank you to all in advance, >> >>Giulio >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > >-- >Best regards > Wolfgang > >------------------------------------- >Wolfgang Huber >European Bioinformatics Institute >European Molecular Biology Laboratory >Cambridge CB10 1SD >England >Phone: +44 1223 494642 >Fax: +44 1223 494486 >Http: www.ebi.ac.uk/huber >-------------------------------------