RNA degradation plot

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Assa Yeroslaviz ★ 1.5k

@assa-yeroslaviz-1597

Last seen 21 days ago

Germany

Hi, I would like to know, if there is a possibility to plot the RNA Degradation with different line types. I tried it this way: deg <- AffyRNAdeg(affybatch) plotAffyRNAdeg(deg ,col = 1:length(ArrayIndex_norm)) legend(-1.5, 75, as.character(sampleNames(eset)), lty = 1:length(ArrayIndex_norm), col = 1:length(ArrayIndex_norm), cex = 0.6) But I'm getting only solid lines in my graph, but different types of lines in my legend. Is it possible to present several types of lines in my plot? THX Assa [[alternative HTML version deleted]]

graph graph • 1.2k views

ADD COMMENT • link updated 14.6 years ago by Benilton Carvalho ★ 4.3k • written 14.6 years ago by Assa Yeroslaviz ★ 1.5k

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Benilton Carvalho ★ 4.3k

@benilton-carvalho-1375

Last seen 4.7 years ago

Brazil/Campinas/UNICAMP

you need to pass 'lty' also to the plotAffyRNAdeg function (as you did with legend). b On Mon, Apr 12, 2010 at 12:49 PM, Assa Yeroslaviz <frymor at="" gmail.com=""> wrote: > Hi, > > I would like to know, if there is a possibility to plot the RNA Degradation > with different line types. > I tried it this way: > > deg <- AffyRNAdeg(affybatch) > plotAffyRNAdeg(deg ,col = 1:length(ArrayIndex_norm)) > legend(-1.5, 75, > ? ?as.character(sampleNames(eset)), > ? ?lty = 1:length(ArrayIndex_norm), > ? ?col = 1:length(ArrayIndex_norm), cex = 0.6) > > But I'm getting only solid lines in my graph, but different types of lines > in my legend. > > Is it possible to present several types of lines in my plot? > > THX > > Assa > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 14.6 years ago Benilton Carvalho ★ 4.3k

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nope that won't work: deg <- AffyRNAdeg(affybatch) plotAffyRNAdeg(deg, lty = 1:length(ArrayIndex_norm),col = 1:length(ArrayIndex_norm)) legend(-1.5, 75, as.character(sampleNames(eset)), lty = 1:length(ArrayIndex_norm), col = 1:length(ArrayIndex_norm), cex = 0.6) All of my lines are still solid. On Mon, Apr 12, 2010 at 14:01, Benilton Carvalho <beniltoncarvalho@gmail.com> wrote: > you need to pass 'lty' also to the plotAffyRNAdeg function (as you did > with legend). b > > On Mon, Apr 12, 2010 at 12:49 PM, Assa Yeroslaviz <frymor@gmail.com> > wrote: > > Hi, > > > > I would like to know, if there is a possibility to plot the RNA > Degradation > > with different line types. > > I tried it this way: > > > > deg <- AffyRNAdeg(affybatch) > > plotAffyRNAdeg(deg ,col = 1:length(ArrayIndex_norm)) > > legend(-1.5, 75, > > as.character(sampleNames(eset)), > > lty = 1:length(ArrayIndex_norm), > > col = 1:length(ArrayIndex_norm), cex = 0.6) > > > > But I'm getting only solid lines in my graph, but different types of > lines > > in my legend. > > > > Is it possible to present several types of lines in my plot? > > > > THX > > > > Assa > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]

ADD REPLY • link 14.6 years ago Assa Yeroslaviz ★ 1.5k

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hmmm... i see... let's wait a little bit then. b On Mon, Apr 12, 2010 at 1:16 PM, Assa Yeroslaviz <frymor at="" gmail.com=""> wrote: > nope that won't work: > > deg <- AffyRNAdeg(affybatch) > plotAffyRNAdeg(deg, lty = 1:length(ArrayIndex_norm),col = > 1:length(ArrayIndex_norm)) > legend(-1.5, 75, > ??? as.character(sampleNames(eset)), > ??? lty = 1:length(ArrayIndex_norm), > ??? col = 1:length(ArrayIndex_norm), cex = 0.6) > > All of my lines are still solid. > > On Mon, Apr 12, 2010 at 14:01, Benilton Carvalho > <beniltoncarvalho at="" gmail.com=""> wrote: >> >> you need to pass 'lty' also to the plotAffyRNAdeg function (as you did >> with legend). b >> >> On Mon, Apr 12, 2010 at 12:49 PM, Assa Yeroslaviz <frymor at="" gmail.com=""> >> wrote: >> > Hi, >> > >> > I would like to know, if there is a possibility to plot the RNA >> > Degradation >> > with different line types. >> > I tried it this way: >> > >> > deg <- AffyRNAdeg(affybatch) >> > plotAffyRNAdeg(deg ,col = 1:length(ArrayIndex_norm)) >> > legend(-1.5, 75, >> > ? ?as.character(sampleNames(eset)), >> > ? ?lty = 1:length(ArrayIndex_norm), >> > ? ?col = 1:length(ArrayIndex_norm), cex = 0.6) >> > >> > But I'm getting only solid lines in my graph, but different types of >> > lines >> > in my legend. >> > >> > Is it possible to present several types of lines in my plot? >> > >> > THX >> > >> > Assa >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > >

ADD REPLY • link 14.6 years ago Benilton Carvalho ★ 4.3k

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Hi, when looking at the "plotAffyRNAdeg" code, there is a 'for' loop at the end of the function. The 'col' argument is passed but the lty parameter is not. you can use fix(plotAffyRNAdeg) to temporarily modify the function. 1 - add a ltys = NULL argument to the main function (ie : plotAffyRNAdeg) 2 - add lty=ltys[i] in the call to lines *for (i in 1:dim(mns)[1]) lines(0:((dim(mns)[2] - 1)), mns[i, ], col = cols[i], lty=ltys[i])* then it will work. (I've just tested it) hope it helps. Tony On 12 April 2010 14:32, Benilton Carvalho <beniltoncarvalho@gmail.com>wrote: > hmmm... i see... let's wait a little bit then. b > > On Mon, Apr 12, 2010 at 1:16 PM, Assa Yeroslaviz <frymor@gmail.com> wrote: > > nope that won't work: > > > > deg <- AffyRNAdeg(affybatch) > > plotAffyRNAdeg(deg, lty = 1:length(ArrayIndex_norm),col = > > 1:length(ArrayIndex_norm)) > > legend(-1.5, 75, > > as.character(sampleNames(eset)), > > lty = 1:length(ArrayIndex_norm), > > col = 1:length(ArrayIndex_norm), cex = 0.6) > > > > All of my lines are still solid. > > > > On Mon, Apr 12, 2010 at 14:01, Benilton Carvalho > > <beniltoncarvalho@gmail.com> wrote: > >> > >> you need to pass 'lty' also to the plotAffyRNAdeg function (as you did > >> with legend). b > >> > >> On Mon, Apr 12, 2010 at 12:49 PM, Assa Yeroslaviz <frymor@gmail.com> > >> wrote: > >> > Hi, > >> > > >> > I would like to know, if there is a possibility to plot the RNA > >> > Degradation > >> > with different line types. > >> > I tried it this way: > >> > > >> > deg <- AffyRNAdeg(affybatch) > >> > plotAffyRNAdeg(deg ,col = 1:length(ArrayIndex_norm)) > >> > legend(-1.5, 75, > >> > as.character(sampleNames(eset)), > >> > lty = 1:length(ArrayIndex_norm), > >> > col = 1:length(ArrayIndex_norm), cex = 0.6) > >> > > >> > But I'm getting only solid lines in my graph, but different types of > >> > lines > >> > in my legend. > >> > > >> > Is it possible to present several types of lines in my plot? > >> > > >> > THX > >> > > >> > Assa > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > _______________________________________________ > >> > Bioconductor mailing list > >> > Bioconductor@stat.math.ethz.ch > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > Search the archives: > >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

ADD REPLY • link 14.6 years ago Anthony Ferrari ▴ 110

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