Hello all, I would like to recreate the plot shown here (from a useR 2009 presentation): http://www.agrocampus-ouest.fr/math/useR-2009/abstracts/pdf/Hocking.pdf I downloaded the code for that image, and discovered that it relies on external web services, and also having PERL installed on the computer. I believe this could be done "locally" using the "seqLogo" function/package (see http://www.bioconductor.org/packages/2.2/bioc/html/seqLogo.html), combined with the subplot function (from the "TeachingDemos" package). So my questions are: 1) Might there be other packages/functions that I are more fitting for the task of recreating this plot ? 2) Can someone give some pointers on how the subplot function could be used to create such an image ? (I am not sure how to create such a layout, especially when it needs to be dynamic to the number of cluster choosen) Thanks in advance for any help, Best, Tal ----------------Contact Details:------------------------------------------------------- Contact me: Tal.Galili@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) ---------------------------------------------------------------------------------------------- [[alternative HTML version deleted]]
Hello, Check for function "layout". With it you can create separate plotting regions one for each graph. And these regions can be customized depending on the size of the objects you want to plot. Regards, Carlos. On Fri, Jul 2, 2010 at 1:34 PM, Tal Galili <tal.galili@gmail.com> wrote:> Hello all, > > I would like to recreate the plot shown here (from a useR 2009 > presentation): > http://www.agrocampus-ouest.fr/math/useR-2009/abstracts/pdf/Hocking.pdf > > I downloaded the code for that image, and discovered that it relies on > external web services, and also having PERL installed on the computer. > > I believe this could be done "locally" using the "seqLogo" function/package > (see http://www.bioconductor.org/packages/2.2/bioc/html/seqLogo.html), > combined with the subplot function (from the "TeachingDemos" package). > > So my questions are: > 1) Might there be other packages/functions that I are more fitting for the > task of recreating this plot ? > 2) Can someone give some pointers on how the subplot function could be used > to create such an image ? (I am not sure how to create such a > layout, especially when it needs to be dynamic to the number of cluster > choosen) > > > Thanks in advance for any help, > Best, > Tal > > > > > > > > ----------------Contact > Details:------------------------------------------------------- > Contact me: Tal.Galili@gmail.com | 972-52-7275845 > Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | > www.r-statistics.com (English) > > ---------------------------------------------------------------------------------------------- > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Hi Carlos, I was debating with myself if that is the strategy to go (or the one using subplots). Following some thread on the subject from lately, I am a bit hesitant (but maybe "layout" *is* the better strategy). http://r.789695.n4.nabble.com/plot-focus-tt2272699.html I am hoping for some more input on the subject. (and thank you for replying) Best, Tal ----------------Contact Details:------------------------------------------------------- Contact me: Tal.Galili@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) ---------------------------------------------------------------------------------------------- On Fri, Jul 2, 2010 at 3:48 PM, Carlos Ortega <coforfe@gmail.com> wrote:> Hello, > > Check for function "layout". > With it you can create separate plotting regions one for each graph. And > these regions can be customized depending on the size of the objects you > want to plot. > > Regards, > Carlos. > > On Fri, Jul 2, 2010 at 1:34 PM, Tal Galili <tal.galili@gmail.com> wrote: > >> Hello all, >> >> I would like to recreate the plot shown here (from a useR 2009 >> presentation): >> http://www.agrocampus-ouest.fr/math/useR-2009/abstracts/pdf/Hocking.pdf >> >> I downloaded the code for that image, and discovered that it relies on >> external web services, and also having PERL installed on the computer. >> >> I believe this could be done "locally" using the "seqLogo" >> function/package >> (see http://www.bioconductor.org/packages/2.2/bioc/html/seqLogo.html), >> combined with the subplot function (from the "TeachingDemos" package). >> >> So my questions are: >> 1) Might there be other packages/functions that I are more fitting for the >> task of recreating this plot ? >> 2) Can someone give some pointers on how the subplot function could be >> used >> to create such an image ? (I am not sure how to create such a >> layout, especially when it needs to be dynamic to the number of cluster >> choosen) >> >> >> Thanks in advance for any help, >> Best, >> Tal >> >> >> >> >> >> >> >> ----------------Contact >> Details:------------------------------------------------------- >> Contact me: Tal.Galili@gmail.com | 972-52-7275845 >> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | >> www.r-statistics.com (English) >> >> ---------------------------------------------------------------------------------------------- >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > >[[alternative HTML version deleted]]
Hi, The 'aqp' package originally used the subplot function to add images to to a dendrogram plot. I have since changed to use base graphics primitives, as the results tend to scale better. I avoided the use of 'layout' because sometimes it is convenient to add further embellishments that transcend panels in the figure. Have a look at some of the code in this package, it is on R-Forge: http://aqp.r-forge.r-project.org/ Cheers, Dylan On Fri, Jul 2, 2010 at 4:34 AM, Tal Galili <tal.galili at gmail.com> wrote:> Hello all, > > I would like to recreate the plot shown here (from a useR 2009 > presentation): > http://www.agrocampus-ouest.fr/math/useR-2009/abstracts/pdf/Hocking.pdf > > I downloaded the code for that image, and discovered that it relies on > external web services, and also having PERL installed on the computer. > > I believe this could be done "locally" using the "seqLogo" function/package > (see http://www.bioconductor.org/packages/2.2/bioc/html/seqLogo.html), > combined with the subplot function (from the "TeachingDemos" package). > > So my questions are: > 1) Might there be other packages/functions that I are more fitting for the > task of recreating this plot ? > 2) Can someone give some pointers on how the subplot function could be used > to create such an image ? (I am not sure how to create such a > layout, especially when it needs to be dynamic to the number of cluster > choosen) > > > Thanks in advance for any help, > Best, > Tal > > > > > > > > ----------------Contact > Details:------------------------------------------------------- > Contact me: Tal.Galili at gmail.com | ?972-52-7275845 > Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | > www.r-statistics.com (English) > ---------------------------------------------------------------------------------------------- > > ? ? ? ?[[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >
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