How to plot NGS data?
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Bernd Jagla ▴ 30
@bernd-jagla-5120
Last seen 9.6 years ago
Hi, I have "a few" reference genomes from NGS resequencing experiments and annotation in GFF format that I would like to use in some of the plotting functions that are available (i.e. geneplotter, ChromHeatMap). Actually, I would to integrate these with expression results from correlated NGS RNA-seq experiments. My overall approach currently includes using BSGenome, GenenicFeature/FeatureDb, expressionSet and geneplotter/ChromHeatMap. I haven't figured out how to fill an expressionSet class with my counts and how to define regions / genes. Also, is this the class to use? There seem to be too many possible routes to go and I am feeling quite lost... I am now in the process of creating a BSGenome object using BSGenomeForge, which seems to be working. As all this seems to be quite complicated and I haven't found a complete guide on how to visualize NGS results I would like to verify this approach by someone and maybe get some pointers to help me on how to do visualization with RNA-seq experiments... Thanks a lot for your kind help and consideration. Bernd,
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@martin-morgan-1513
Last seen 5 days ago
United States
On 02/15/2012 06:14 AM, Bernd Jagla wrote: > > Hi, > > I have "a few" reference genomes from NGS resequencing experiments and > annotation in GFF format that I would like to use in some of the > plotting functions that are available (i.e. geneplotter, ChromHeatMap). > Actually, I would to integrate these with expression results from > correlated NGS RNA-seq experiments. Hi Bernd -- maybe good places to start are the ggbio vignette, available as a PDF on the page at http://bioconductor.org/packages/release/bioc/html/ggbio.html and the Gvis vignette (if you're willing to use the 'devel' version of R and Bioconductor) http://bioconductor.org/packages/2.10/bioc/html/Gviz.html Both might give you an idea of the possibilities. library(ShortRead); example(Snapshot) might also be a lighter-weight starting point. If you're able to say more precisely what you'd like, and where you're starting from (presumably BAM files, but maybe hints about organism, purpose of experiment, what you're hoping to get out of the visualization...), perhaps someone on the list will be able to provide some more explicit suggestions. Hope that provides some help. Martin > > My overall approach currently includes using BSGenome, > GenenicFeature/FeatureDb, expressionSet and geneplotter/ChromHeatMap. > > I haven't figured out how to fill an expressionSet class with my counts > and how to define regions / genes. Also, is this the class to use? There > seem to be too many possible routes to go and I am feeling quite lost... > > I am now in the process of creating a BSGenome object using > BSGenomeForge, which seems to be working. > > As all this seems to be quite complicated and I haven't found a complete > guide on how to visualize NGS results I would like to verify this > approach by someone and maybe get some pointers to help me on how to do > visualization with RNA-seq experiments... > > Thanks a lot for your kind help and consideration. > > Bernd, > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Hah! On Thu, Feb 16, 2012 at 1:11 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > http://bioconductor.org/packages/release/bioc/html/ggbio.html > > and the Gvis vignette (if you're willing to use the 'devel' version of R and > Bioconductor) > > ?http://bioconductor.org/packages/2.10/bioc/html/Gviz.html These packages are seriously cool! -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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seconding this, I did not know about Gviz, but with GRanges and rtracklayer it seems like an obvious choice. have been playing with ggbio lately as well, very cool but has some issues with ggplot2 dev (don't we all? Hadley...) thank you for the pointers, this is great. On Thu, Feb 16, 2012 at 2:47 AM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hah! > > On Thu, Feb 16, 2012 at 1:11 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > > > http://bioconductor.org/packages/release/bioc/html/ggbio.html > > > > and the Gvis vignette (if you're willing to use the 'devel' version of R > and > > Bioconductor) > > > > http://bioconductor.org/packages/2.10/bioc/html/Gviz.html > > These packages are seriously cool! > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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On Thu, Feb 16, 2012 at 10:10 AM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > seconding this, I did not know about Gviz, but with GRanges and rtracklayer > it seems like an obvious choice. > have been playing with ggbio lately as well, very cool but has some issues > with ggplot2 dev (don't we all? Hadley...) > Hi Tim, You are right, I have been working on the update based on ggplot2-dev and also with some API and functionality change in ggbio recently in git, should be released to bioc-dev after March 1st, I guess March 1st is Hadley's plan to release ggplot2 0.9. Sorry for the inconvenience so far... ggbio is designed in different way and serve different purpose, it's highly depend on and extend ggplot2 which make it general in the manner of grammar of graphics, also full of add-on features and it works most directly for core classes in bioconductor instead of bring a new constructor or class. I made lots of update(layout, geoms...) compared to the first release so far, probably need to rewrite or update the whole vignette again, please feel free to test ggbio again after March 1st on bioc-dev repos. btw: Gviz looks cool ~ I didn't know about it either, thanks a lot, Martin. thanks Tengfei > > thank you for the pointers, this is great. > > > On Thu, Feb 16, 2012 at 2:47 AM, Steve Lianoglou < > mailinglist.honeypot@gmail.com> wrote: > > > Hah! > > > > On Thu, Feb 16, 2012 at 1:11 AM, Martin Morgan <mtmorgan@fhcrc.org> > wrote: > > > > > http://bioconductor.org/packages/release/bioc/html/ggbio.html > > > > > > and the Gvis vignette (if you're willing to use the 'devel' version of > R > > and > > > Bioconductor) > > > > > > http://bioconductor.org/packages/2.10/bioc/html/Gviz.html > > > > These packages are seriously cool! > > > > -steve > > > > -- > > Steve Lianoglou > > Graduate Student: Computational Systems Biology > > | Memorial Sloan-Kettering Cancer Center > > | Weill Medical College of Cornell University > > Contact Info: http://cbio.mskcc.org/~lianos/contact > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper< > http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 [[alternative HTML version deleted]]
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Hi, I have to agree that after reading the vignette it seems all my question might have been answered... or are pretty close to being answered... THANKS A LOT for your continued support. Unfortunately I am having problems right now to use Gviz with my windows system... I am running into the following error message and don't know how to resolve this problem: > library(Gviz) Error : Klassen '"file", "connection"' sind nicht von 'namespace:IRanges' exportiert Fehler: Laden von Paket/Namensraum f?r ?Gviz? fehlgeschlagen Maybe someone can help me there??? Just for translation and what I understood: the classes file and connection are not defined in the namespace IRanges but are defined in base... I don't know how to unload base and if it is possible/useful to do so... or how to overwrite them... Thanks for looking into this... Best, Bernd > sessionInfo() R Under development (unstable) (2012-02-15 r58350) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] IRanges_1.13.24 BiocGenerics_0.1.4 loaded via a namespace (and not attached): [1] Biobase_2.15.3 biomaRt_2.11.1 Biostrings_2.23.6 [4] BSgenome_1.23.2 GenomicRanges_1.7.24 lattice_0.20-0 [7] RColorBrewer_1.0-5 RCurl_1.91-1.1 tools_2.15.0 [10] XML_3.9-4.1 zlibbioc_1.1.1 >
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Hi, On Thu, Feb 16, 2012 at 6:29 AM, Bernd Jagla <bernd at="" pasteur.fr=""> wrote: > Hi, > > I have to agree that after reading the vignette it seems all my question > might have been answered... or are pretty close to being answered... THANKS > A LOT for your continued support. > > Unfortunately I am having problems right now to use Gviz with my windows > system... I am running into the following error message and don't know how > to resolve this problem: > > >> library(Gviz) > Error : Klassen '"file", "connection"' sind nicht von 'namespace:IRanges' > exportiert > Fehler: Laden von Paket/Namensraum f?r ?Gviz? fehlgeschlagen > > Maybe someone can help me there??? > > Just for translation and what I understood: the classes file and connection > are not defined in the namespace IRanges but are defined in base... I don't > know how to unload base and if it is possible/useful to do so... or how to > overwrite them... Hmmm ... actually, these classes should be currently exported from BiocGenerics, but at one point they were defined in IRanges (before BiocGenerics was born). If I understand the German correctly (fat chance), it seems you have an older version of *some* package that is trying to import these classes from IRanges when it should really be grabbing them from BiocGenerics -- the strange thing is that I have slightly older versions of the same packages you are showing (still on R-devel/bioc2.10 though) and the install works for me. Did you install Gviz via biocLite? Maybe you can try updating your installed packages and try again, like so? The following commands will update all packages on your system w/o asking you to confirm [y/n] each one: library(BiocInstaller) biocLite(character(), ask=FALSE) HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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I have run into this issue yesterday with another package. There is an as yet unidentified problem with installability of current images of some packages in the devel branch. It has been pointed out that the windows binary for rtracklayer (see http://bioconductor.org/packages/2.10/bioc/html/rtracklayer.html ) is of much earlier vintage than that for other platforms, as it has not been passing check on windows for some time. This could lead to the sort of behavior seen here. I will be looking at the port to windows later today, and will share relevant news. On Thu, Feb 16, 2012 at 6:45 AM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > On Thu, Feb 16, 2012 at 6:29 AM, Bernd Jagla <bernd@pasteur.fr> wrote: > > Hi, > > > > I have to agree that after reading the vignette it seems all my question > > might have been answered... or are pretty close to being answered... > THANKS > > A LOT for your continued support. > > > > Unfortunately I am having problems right now to use Gviz with my windows > > system... I am running into the following error message and don't know > how > > to resolve this problem: > > > > > >> library(Gviz) > > Error : Klassen '"file", "connection"' sind nicht von 'namespace:IRanges' > > exportiert > > Fehler: Laden von Paket/Namensraum für ‘Gviz’ fehlgeschlagen > > > > Maybe someone can help me there??? > > > > Just for translation and what I understood: the classes file and > connection > > are not defined in the namespace IRanges but are defined in base... I > don't > > know how to unload base and if it is possible/useful to do so... or how > to > > overwrite them... > > Hmmm ... actually, these classes should be currently exported from > BiocGenerics, but at one point they were defined in IRanges (before > BiocGenerics was born). > > If I understand the German correctly (fat chance), it seems you have > an older version of *some* package that is trying to import these > classes from IRanges when it should really be grabbing them from > BiocGenerics -- the strange thing is that I have slightly older > versions of the same packages you are showing (still on > R-devel/bioc2.10 though) and the install works for me. > > Did you install Gviz via biocLite? > > Maybe you can try updating your installed packages and try again, like so? > > The following commands will update all packages on your system w/o > asking you to confirm [y/n] each one: > > library(BiocInstaller) > biocLite(character(), ask=FALSE) > > HTH, > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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I was able to get Gviz installed on an old windows system under R-devel. The trick was to install current rtracklayer from source -- the binary is still not building owing to an error in an example. You need the windows toolset to do this; see the R Installation and Administration manual if necessary. > sessionInfo() R Under development (unstable) (2012-02-16 r58364) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Gviz_0.1.12 rtracklayer_1.15.7 GenomicRanges_1.7.25 [4] IRanges_1.13.24 BiocGenerics_0.1.4 RCurl_1.91-1.1 [7] bitops_1.0-4.1 BiocInstaller_1.3.7 loaded via a namespace (and not attached): [1] AnnotationDbi_1.17.21 Biobase_2.15.3 biomaRt_2.11.1 [4] Biostrings_2.23.6 BSgenome_1.23.2 DBI_0.2-5 [7] lattice_0.20-0 RColorBrewer_1.0-5 Rsamtools_1.7.33 [10] RSQLite_0.11.1 tools_2.15.0 XML_3.9-4.1 [13] zlibbioc_1.1.1 On Thu, Feb 16, 2012 at 6:56 AM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > I have run into this issue yesterday with another package. There is an as > yet unidentified problem with installability of current images of some > packages in the devel branch. It has been pointed out that the windows > binary for rtracklayer > > (see http://bioconductor.org/packages/2.10/bioc/html/rtracklayer.html ) > > is of much earlier vintage than that for other platforms, as it has not > been passing check on windows for some time. This could lead to the sort > of behavior seen here. I will be looking at the port to windows later > today, and will share relevant news. > > > On Thu, Feb 16, 2012 at 6:45 AM, Steve Lianoglou < > mailinglist.honeypot@gmail.com> wrote: > >> Hi, >> >> On Thu, Feb 16, 2012 at 6:29 AM, Bernd Jagla <bernd@pasteur.fr> wrote: >> > Hi, >> > >> > I have to agree that after reading the vignette it seems all my question >> > might have been answered... or are pretty close to being answered... >> THANKS >> > A LOT for your continued support. >> > >> > Unfortunately I am having problems right now to use Gviz with my windows >> > system... I am running into the following error message and don't know >> how >> > to resolve this problem: >> > >> > >> >> library(Gviz) >> > Error : Klassen '"file", "connection"' sind nicht von >> 'namespace:IRanges' >> > exportiert >> > Fehler: Laden von Paket/Namensraum für ‘Gviz’ fehlgeschlagen >> > >> > Maybe someone can help me there??? >> > >> > Just for translation and what I understood: the classes file and >> connection >> > are not defined in the namespace IRanges but are defined in base... I >> don't >> > know how to unload base and if it is possible/useful to do so... or how >> to >> > overwrite them... >> >> Hmmm ... actually, these classes should be currently exported from >> BiocGenerics, but at one point they were defined in IRanges (before >> BiocGenerics was born). >> >> If I understand the German correctly (fat chance), it seems you have >> an older version of *some* package that is trying to import these >> classes from IRanges when it should really be grabbing them from >> BiocGenerics -- the strange thing is that I have slightly older >> versions of the same packages you are showing (still on >> R-devel/bioc2.10 though) and the install works for me. >> >> Did you install Gviz via biocLite? >> >> Maybe you can try updating your installed packages and try again, like so? >> >> The following commands will update all packages on your system w/o >> asking you to confirm [y/n] each one: >> >> library(BiocInstaller) >> biocLite(character(), ask=FALSE) >> >> HTH, >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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rtracklayer should be building on Windows by tomorrow. Sorry about the trouble. Michael On Thu, Feb 16, 2012 at 6:10 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > I was able to get Gviz installed on an old windows system under R-devel. > The trick was to install current rtracklayer from source -- the binary is > still not building owing to an error in an example. You need the windows > toolset to do this; see the R Installation and Administration manual if > necessary. > > > sessionInfo() > R Under development (unstable) (2012-02-16 r58364) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Gviz_0.1.12 rtracklayer_1.15.7 GenomicRanges_1.7.25 > [4] IRanges_1.13.24 BiocGenerics_0.1.4 RCurl_1.91-1.1 > [7] bitops_1.0-4.1 BiocInstaller_1.3.7 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.17.21 Biobase_2.15.3 biomaRt_2.11.1 > [4] Biostrings_2.23.6 BSgenome_1.23.2 DBI_0.2-5 > [7] lattice_0.20-0 RColorBrewer_1.0-5 Rsamtools_1.7.33 > [10] RSQLite_0.11.1 tools_2.15.0 XML_3.9-4.1 > [13] zlibbioc_1.1.1 > > > On Thu, Feb 16, 2012 at 6:56 AM, Vincent Carey > <stvjc@channing.harvard.edu>wrote: > > > I have run into this issue yesterday with another package. There is an > as > > yet unidentified problem with installability of current images of some > > packages in the devel branch. It has been pointed out that the windows > > binary for rtracklayer > > > > (see http://bioconductor.org/packages/2.10/bioc/html/rtracklayer.html ) > > > > is of much earlier vintage than that for other platforms, as it has not > > been passing check on windows for some time. This could lead to the sort > > of behavior seen here. I will be looking at the port to windows later > > today, and will share relevant news. > > > > > > On Thu, Feb 16, 2012 at 6:45 AM, Steve Lianoglou < > > mailinglist.honeypot@gmail.com> wrote: > > > >> Hi, > >> > >> On Thu, Feb 16, 2012 at 6:29 AM, Bernd Jagla <bernd@pasteur.fr> wrote: > >> > Hi, > >> > > >> > I have to agree that after reading the vignette it seems all my > question > >> > might have been answered... or are pretty close to being answered... > >> THANKS > >> > A LOT for your continued support. > >> > > >> > Unfortunately I am having problems right now to use Gviz with my > windows > >> > system... I am running into the following error message and don't know > >> how > >> > to resolve this problem: > >> > > >> > > >> >> library(Gviz) > >> > Error : Klassen '"file", "connection"' sind nicht von > >> 'namespace:IRanges' > >> > exportiert > >> > Fehler: Laden von Paket/Namensraum für ‘Gviz’ fehlgeschlagen > >> > > >> > Maybe someone can help me there??? > >> > > >> > Just for translation and what I understood: the classes file and > >> connection > >> > are not defined in the namespace IRanges but are defined in base... I > >> don't > >> > know how to unload base and if it is possible/useful to do so... or > how > >> to > >> > overwrite them... > >> > >> Hmmm ... actually, these classes should be currently exported from > >> BiocGenerics, but at one point they were defined in IRanges (before > >> BiocGenerics was born). > >> > >> If I understand the German correctly (fat chance), it seems you have > >> an older version of *some* package that is trying to import these > >> classes from IRanges when it should really be grabbing them from > >> BiocGenerics -- the strange thing is that I have slightly older > >> versions of the same packages you are showing (still on > >> R-devel/bioc2.10 though) and the install works for me. > >> > >> Did you install Gviz via biocLite? > >> > >> Maybe you can try updating your installed packages and try again, like > so? > >> > >> The following commands will update all packages on your system w/o > >> asking you to confirm [y/n] each one: > >> > >> library(BiocInstaller) > >> biocLite(character(), ask=FALSE) > >> > >> HTH, > >> -steve > >> > >> -- > >> Steve Lianoglou > >> Graduate Student: Computational Systems Biology > >> | Memorial Sloan-Kettering Cancer Center > >> | Weill Medical College of Cornell University > >> Contact Info: http://cbio.mskcc.org/~lianos/contact > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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The library is loading now... Thanks a lot for your kind help. Bernd On 17.02.2012 05:22, Michael Lawrence wrote: > rtracklayer should be building on Windows by tomorrow. Sorry about the > trouble. > > Michael > > On Thu, Feb 16, 2012 at 6:10 PM, Vincent Carey > <stvjc@channing.harvard.edu>wrote: > >> I was able to get Gviz installed on an old windows system under R-devel. >> The trick was to install current rtracklayer from source -- the binary is >> still not building owing to an error in an example. You need the windows >> toolset to do this; see the R Installation and Administration manual if >> necessary. >> >>> sessionInfo() >> R Under development (unstable) (2012-02-16 r58364) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Gviz_0.1.12 rtracklayer_1.15.7 GenomicRanges_1.7.25 >> [4] IRanges_1.13.24 BiocGenerics_0.1.4 RCurl_1.91-1.1 >> [7] bitops_1.0-4.1 BiocInstaller_1.3.7 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.17.21 Biobase_2.15.3 biomaRt_2.11.1 >> [4] Biostrings_2.23.6 BSgenome_1.23.2 DBI_0.2-5 >> [7] lattice_0.20-0 RColorBrewer_1.0-5 Rsamtools_1.7.33 >> [10] RSQLite_0.11.1 tools_2.15.0 XML_3.9-4.1 >> [13] zlibbioc_1.1.1 >> >> >> On Thu, Feb 16, 2012 at 6:56 AM, Vincent Carey >> <stvjc@channing.harvard.edu>wrote: >> >>> I have run into this issue yesterday with another package. There is an >> as >>> yet unidentified problem with installability of current images of some >>> packages in the devel branch. It has been pointed out that the windows >>> binary for rtracklayer >>> >>> (see http://bioconductor.org/packages/2.10/bioc/html/rtracklayer.html ) >>> >>> is of much earlier vintage than that for other platforms, as it has not >>> been passing check on windows for some time. This could lead to the sort >>> of behavior seen here. I will be looking at the port to windows later >>> today, and will share relevant news. >>> >>> >>> On Thu, Feb 16, 2012 at 6:45 AM, Steve Lianoglou< >>> mailinglist.honeypot@gmail.com> wrote: >>> >>>> Hi, >>>> >>>> On Thu, Feb 16, 2012 at 6:29 AM, Bernd Jagla<bernd@pasteur.fr> wrote: >>>>> Hi, >>>>> >>>>> I have to agree that after reading the vignette it seems all my >> question >>>>> might have been answered... or are pretty close to being answered... >>>> THANKS >>>>> A LOT for your continued support. >>>>> >>>>> Unfortunately I am having problems right now to use Gviz with my >> windows >>>>> system... I am running into the following error message and don't know >>>> how >>>>> to resolve this problem: >>>>> >>>>> >>>>>> library(Gviz) >>>>> Error : Klassen '"file", "connection"' sind nicht von >>>> 'namespace:IRanges' >>>>> exportiert >>>>> Fehler: Laden von Paket/Namensraum für 'Gviz' fehlgeschlagen >>>>> >>>>> Maybe someone can help me there??? >>>>> >>>>> Just for translation and what I understood: the classes file and >>>> connection >>>>> are not defined in the namespace IRanges but are defined in base... I >>>> don't >>>>> know how to unload base and if it is possible/useful to do so... or >> how >>>> to >>>>> overwrite them... >>>> Hmmm ... actually, these classes should be currently exported from >>>> BiocGenerics, but at one point they were defined in IRanges (before >>>> BiocGenerics was born). >>>> >>>> If I understand the German correctly (fat chance), it seems you have >>>> an older version of *some* package that is trying to import these >>>> classes from IRanges when it should really be grabbing them from >>>> BiocGenerics -- the strange thing is that I have slightly older >>>> versions of the same packages you are showing (still on >>>> R-devel/bioc2.10 though) and the install works for me. >>>> >>>> Did you install Gviz via biocLite? >>>> >>>> Maybe you can try updating your installed packages and try again, like >> so? >>>> The following commands will update all packages on your system w/o >>>> asking you to confirm [y/n] each one: >>>> >>>> library(BiocInstaller) >>>> biocLite(character(), ask=FALSE) >>>> >>>> HTH, >>>> -steve >>>> >>>> -- >>>> Steve Lianoglou >>>> Graduate Student: Computational Systems Biology >>>> | Memorial Sloan-Kettering Cancer Center >>>> | Weill Medical College of Cornell University >>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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Just to chime in here: High up on my list of future developments is some sort of file-based track class, where all the genomic regions reside on disc in an indexed file, like BAM, bigWig or tabix. The actual ranges are only realized within R in the plotting method, so no need to fill the memory with unnecessary clatter. With the available infrastructure in Rsamtools this should be an easy extension, I just need to find some time to hack in the code. I guess some sort of NGS-specific visualization would be the next thing on the list. There is an experimental AlignedReadsTrack class, but right now that's really just a huge collection of bugs :-( Cheers, Florian Florian Hahne Novartis Institute For Biomedical Research Translational Sciences / Preclinical Safety / PCS Informatics Expert Data Integration and Modeling Bioinformatics CHBS, WKL-135.2.26 Novartis Institute For Biomedical Research, Werk Klybeck Klybeckstrasse 141 CH-4057 Basel Switzerland Phone: +41 61 6967127 Email : florian.hahne at novartis.com On 2/16/12 7:11 AM, "Martin Morgan" <mtmorgan at="" fhcrc.org=""> wrote: >On 02/15/2012 06:14 AM, Bernd Jagla wrote: >> >> Hi, >> >> I have "a few" reference genomes from NGS resequencing experiments and >> annotation in GFF format that I would like to use in some of the >> plotting functions that are available (i.e. geneplotter, ChromHeatMap). >> Actually, I would to integrate these with expression results from >> correlated NGS RNA-seq experiments. > >Hi Bernd -- maybe good places to start are the ggbio vignette, available >as a PDF on the page at > >http://bioconductor.org/packages/release/bioc/html/ggbio.html > >and the Gvis vignette (if you're willing to use the 'devel' version of R >and Bioconductor) > > http://bioconductor.org/packages/2.10/bioc/html/Gviz.html > >Both might give you an idea of the possibilities. library(ShortRead); >example(Snapshot) might also be a lighter-weight starting point. > >If you're able to say more precisely what you'd like, and where you're >starting from (presumably BAM files, but maybe hints about organism, >purpose of experiment, what you're hoping to get out of the >visualization...), perhaps someone on the list will be able to provide >some more explicit suggestions. > >Hope that provides some help. Martin > >> >> My overall approach currently includes using BSGenome, >> GenenicFeature/FeatureDb, expressionSet and geneplotter/ChromHeatMap. >> >> I haven't figured out how to fill an expressionSet class with my counts >> and how to define regions / genes. Also, is this the class to use? There >> seem to be too many possible routes to go and I am feeling quite lost... >> >> I am now in the process of creating a BSGenome object using >> BSGenomeForge, which seems to be working. >> >> As all this seems to be quite complicated and I haven't found a complete >> guide on how to visualize NGS results I would like to verify this >> approach by someone and maybe get some pointers to help me on how to do >> visualization with RNA-seq experiments... >> >> Thanks a lot for your kind help and consideration. >> >> Bernd, >> >> _______________________________________________ >> 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 > > >-- >Computational Biology >Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > >Location: M1-B861 >Telephone: 206 667-2793 > >_______________________________________________ >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
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Hi Florian, On Fri, Feb 17, 2012 at 11:00 AM, Hahne, Florian <florian.hahne at="" novartis.com=""> wrote: > Just to chime in here: > High up on my list of future developments is some sort of file-based track > class, where all the genomic regions reside on disc in an indexed file, > like BAM, bigWig or tabix. The actual ranges are only realized within R in > the plotting method, so no need to fill the memory with unnecessary > clatter. With the available infrastructure in Rsamtools this should be an > easy extension, I just need to find some time to hack in the code. I guess > some sort of NGS-specific visualization would be the next thing on the > list. There is an experimental AlignedReadsTrack class, but right now > that's really just a huge collection of bugs :-( I hacked a few "track-like" objects to use with GenomeGraphs some time ago in order to plot data from an rna-seq protocol we've been developing. The pictures look like this: http://cbio.mskcc.org/~lianos/files/bioconductor/DEPDC1.png "That's some bizarre RNA-seq data." you might say, but we only capture 3' ends of mRNAs in order to study alternative cleavage and polyadenylation. To do that, though, those lanes (above the genome axis) are probably something like the AlignedReadsTrack class you mention, which are built by working over a specified range of a BAM files, or by Rle(coverage) vectors. These coverage vectors are also smoothed using another package I'm whipping up which does (probably not very efficiently written) convolutions over Rle(coverage) vectors directly, which might be useful: https://github.com/lianos/biosignals/blob/master/R/convolve1d.R I'd also like to add "stranded" visualization ability, ie - plot (+) coverage north of 0 and (-) south, like you've already implemented by the looks of vignette. Lastly, the tails of the gene models you see below are pulling the models out of some local cache that was build by the info cached from local TranscriptDb objects ... this needs to be redone to use something like tabix or BAM stored gene model-like functionality (mine currently isn't particularly efficient at all). All this is to say that I have some things whipped together that might be useful in this realm and would be happy to help w/ this, too ... I'd totally love to switch to Gviz eventually when there is time to do so, and would happy to help if you haven't already done it. In that regard, if you actually *want* help with that, maybe you could ping (maybe on bioc-devel?) us when you think you might be ready to start tackling this part of Gviz? Anyway -- although I haven't used it, Gviz looks incredibly impressive, nice work! -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Hi Steve, Help is always appreciated. I will definitely let you know once my feeble attempts are mature enough for public consumption. The main thing to get right is to cleanly embed the file reference concept in the class hierarchy, so that all RangedTrack objects know how to deal with file-based information. The real work will probably be implementing all the readers for the different file types (bigBed, bigWig, BAM, etc), although most of this should be available from either the Rsamtools or rtracklayer packages. With a generic input structure in place one could go wild and even read coordinates and the associated data off a database without changing a line of code in the downstream plotting methods. Along these lines, having gene models stored in local TranscriptDb object isn't such a bad option (after all it's how gene information is available in Bioconductor these days), and there should be a clean way to directly plot from those. You see, there are plenty of opportunities to improve the package, and certainly enough work for all of us :-) Will give you a shout once the undergarments are ready, Florian Florian Hahne Novartis Institute For Biomedical Research Translational Sciences / Preclinical Safety / PCS Informatics Expert Data Integration and Modeling Bioinformatics CHBS, WKL-135.2.26 Novartis Institute For Biomedical Research, Werk Klybeck Klybeckstrasse 141 CH-4057 Basel Switzerland Phone: +41 61 6967127 Email : florian.hahne at novartis.com On 2/17/12 5:50 PM, "Steve Lianoglou" <mailinglist.honeypot at="" gmail.com=""> wrote: >Hi Florian, > >On Fri, Feb 17, 2012 at 11:00 AM, Hahne, Florian ><florian.hahne at="" novartis.com=""> wrote: >> Just to chime in here: >> High up on my list of future developments is some sort of file- based >>track >> class, where all the genomic regions reside on disc in an indexed file, >> like BAM, bigWig or tabix. The actual ranges are only realized within R >>in >> the plotting method, so no need to fill the memory with unnecessary >> clatter. With the available infrastructure in Rsamtools this should be >>an >> easy extension, I just need to find some time to hack in the code. I >>guess >> some sort of NGS-specific visualization would be the next thing on the >> list. There is an experimental AlignedReadsTrack class, but right now >> that's really just a huge collection of bugs :-( > >I hacked a few "track-like" objects to use with GenomeGraphs some time >ago in order to plot data from an rna-seq protocol we've been >developing. The pictures look like this: > >http://cbio.mskcc.org/~lianos/files/bioconductor/DEPDC1.png > >"That's some bizarre RNA-seq data." you might say, but we only capture >3' ends of mRNAs in order to study alternative cleavage and >polyadenylation. > >To do that, though, those lanes (above the genome axis) are probably >something like the AlignedReadsTrack class you mention, which are >built by working over a specified range of a BAM files, or by >Rle(coverage) vectors. > >These coverage vectors are also smoothed using another package I'm >whipping up which does (probably not very efficiently written) >convolutions over Rle(coverage) vectors directly, which might be >useful: > >https://github.com/lianos/biosignals/blob/master/R/convolve1d.R > >I'd also like to add "stranded" visualization ability, ie - plot (+) >coverage north of 0 and (-) south, like you've already implemented by >the looks of vignette. > >Lastly, the tails of the gene models you see below are pulling the >models out of some local cache that was build by the info cached from >local TranscriptDb objects ... this needs to be redone to use >something like tabix or BAM stored gene model-like functionality (mine >currently isn't particularly efficient at all). > >All this is to say that I have some things whipped together that might >be useful in this realm and would be happy to help w/ this, too ... >I'd totally love to switch to Gviz eventually when there is time to do >so, and would happy to help if you haven't already done it. > >In that regard, if you actually *want* help with that, maybe you could >ping (maybe on bioc-devel?) us when you think you might be ready to >start tackling this part of Gviz? > >Anyway -- although I haven't used it, Gviz looks incredibly >impressive, nice work! > >-steve > >-- >Steve Lianoglou >Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University >Contact Info: http://cbio.mskcc.org/~lianos/contact
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