Geneplotter, alongChrom problem
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@giulio-di-giovanni-950
Last seen 7.7 years ago
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 Organism geneplotter Organism geneplotter • 879 views ADD COMMENT 0 Entering edit mode @wolfgang-huber-3550 Last seen 4 months ago EMBL European Molecular Biology Laboratâ€¦ 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
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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 >-------------------------------------