Question: plotting probes along a chromosome
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gravatar for Pete Shepard
7.9 years ago by
Pete Shepard240
Pete Shepard240 wrote:
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 [[alternative HTML version deleted]]
graph genomegraphs assign • 758 views
ADD COMMENTlink modified 7.9 years ago by Oosting, J. PATH550 • written 7.9 years ago by Pete Shepard240
Answer: plotting probes along a chromosome
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gravatar for Oosting, J. PATH
7.9 years ago by
Oosting, J. PATH550 wrote:
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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.9 years ago by Oosting, J. PATH550
Personally, I do use stripe. It's not really hard to understand. http://bioinfo.mikrobio.med.uni-giessen.de/wiki/index.php/Stripe Simon No?l 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 ? : 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.9 years ago by SimonNoƫl450
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