Question: How to plot microRNA chromosome location
0
gravatar for Michael Lawrence
10.9 years ago by
Michael Lawrence620 wrote:
On Tue, Oct 28, 2008 at 2:59 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Mon, Oct 27, 2008 at 9:13 PM, Steve Lianoglou > <mailinglist.honeypot@gmail.com> wrote: > > Hi, > > > > On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote: > > > >> Hi all, > >> > >> > >> > >> I have check some useful packages to plot gene chromosome information > like > >> gene plotter, ideogram and GenomeGraphs. > >> > >> However, I don't know how to plot microRNA (miRNA) chromosome location. > >> > >> I would like to see the distribution of some miRNAs in the genome. > >> > >> > >> > >> I have known the miRNA chromosome info. > >> > >> miRNA name chromosome start end > >> > >> hsa-miR-130b 22 20337592 > >> 20337673 > >> > >> hsa-miR-33a 22 40626894 > >> 40626962 > >> > >> hsa-miR-15b 3 161605069 > >> 161605166 > >> > >> . > >> > >> > >> > >> Is there any packages that I provide the location and plotting it out? > > > > You could create a custom track and upload it to the UCSC genome browser. > > > Sorry for late reply here. In fact, there is an example in the rtracklayer vignette that does pretty much exactly this, except with miRNA target sites. Let me know if you need any more guidance. Thanks, Michael > > It looks like you got your info about 90% the way to GFF format: > > > > http://genome.ucsc.edu/FAQ/FAQformat#format3 > > > > You could tweak your info a bit, then write.table your way to a file you > can > > upload as a UCSC custom track. > > See the rtracklayer package for help here. > > > Is that good enough, or were you looking for something more? And if so, > > what? There's the GenomeGraphs library, which is pretty slick, but I'm > not > > sure if that's really what you're after: > > > > http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html > > _______________________________________________ > 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 COMMENTlink modified 10.9 years ago by Camper Chih-Wei Liu40 • written 10.9 years ago by Michael Lawrence620
Answer: How to plot microRNA chromosome location
0
gravatar for Camper Chih-Wei Liu
10.9 years ago by
Camper Chih-Wei Liu40 wrote:
I have tried GenomeGraphs package to plot chromosome miRNA maps. I got the results. However, there still two questions I want to ask. 1. Is there any package be able to plot chromosomes at one time. (Actually, I can do them all one by one and combine them manually.) 2. Is GenomeGraphs package be able to draw mouse chromosome maps or any other species? Thank you for answering. -camper ================================================== Camper Chih-Wei Liu National Cheng Kung University, Tainan, Taiwan Department of Computer Science and Information Engineering Intelligent Information Retrieval Lab: IIR Lab camper at cad.csie.ncku.edu.tw -----Original Message----- From: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com] Sent: Tuesday, October 28, 2008 9:14 AM To: Camper (Chih-Wei Liu) Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] How to plot microRNA chromosome location Hi, On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote: > Hi all, > > > > I have check some useful packages to plot gene chromosome > information like > gene plotter, ideogram and GenomeGraphs. > > However, I don't know how to plot microRNA (miRNA) chromosome > location. > > I would like to see the distribution of some miRNAs in the genome. > > > > I have known the miRNA chromosome info. > > miRNA name chromosome start end > > hsa-miR-130b 22 20337592 > 20337673 > > hsa-miR-33a 22 40626894 > 40626962 > > hsa-miR-15b 3 161605069 > 161605166 > > . > > > > Is there any packages that I provide the location and plotting it out? You could create a custom track and upload it to the UCSC genome browser. It looks like you got your info about 90% the way to GFF format: http://genome.ucsc.edu/FAQ/FAQformat#format3 You could tweak your info a bit, then write.table your way to a file you can upload as a UCSC custom track. Is that good enough, or were you looking for something more? And if so, what? There's the GenomeGraphs library, which is pretty slick, but I'm not sure if that's really what you're after: http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html Hope that helps, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Cornell Medical College of Cornell University http://cbio.mskcc.org/~lianos
ADD COMMENTlink written 10.9 years ago by Camper Chih-Wei Liu40
On Thu, 2008-11-06 at 01:36 +0800, Camper (Chih-Wei Liu) wrote: > I have tried GenomeGraphs package to plot chromosome miRNA maps. > I got the results. > > However, there still two questions I want to ask. > 1. Is there any package be able to plot chromosomes at one time. > (Actually, I can do them all one by one and combine them manually.) I assume that you mean all chromosomes on one figure. It does not seem currently possible at the moment (as gdPlot calls "grid.newpage()" in all cases). I had code to plot karyotypes-sort of plots somewhere, let me see if I can find it back and send it. > 2. Is GenomeGraphs package be able to draw mouse chromosome maps or any > other species? The man page for makeIdeogram() / Ideogram-class state that only human chromosomes are supported. Having that extended to other organisms would be a matter of letting one specify cytobands and chromosomes for arbitray organisms (easier written here than done, there were several way of specify cytobands/centromere/telomere regions last time I looked) L. > Thank you for answering. > > -camper > > ================================================== > Camper Chih-Wei Liu > National Cheng Kung University, Tainan, Taiwan > Department of Computer Science and Information Engineering > Intelligent Information Retrieval Lab: IIR Lab > camper at cad.csie.ncku.edu.tw > > -----Original Message----- > From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] > Sent: Tuesday, October 28, 2008 9:14 AM > To: Camper (Chih-Wei Liu) > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] How to plot microRNA chromosome location > > Hi, > > On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote: > > > Hi all, > > > > > > > > I have check some useful packages to plot gene chromosome > > information like > > gene plotter, ideogram and GenomeGraphs. > > > > However, I don't know how to plot microRNA (miRNA) chromosome > > location. > > > > I would like to see the distribution of some miRNAs in the genome. > > > > > > > > I have known the miRNA chromosome info. > > > > miRNA name chromosome start end > > > > hsa-miR-130b 22 20337592 > > 20337673 > > > > hsa-miR-33a 22 40626894 > > 40626962 > > > > hsa-miR-15b 3 161605069 > > 161605166 > > > > . > > > > > > > > Is there any packages that I provide the location and plotting it out? > > You could create a custom track and upload it to the UCSC genome > browser. > > It looks like you got your info about 90% the way to GFF format: > > http://genome.ucsc.edu/FAQ/FAQformat#format3 > > You could tweak your info a bit, then write.table your way to a file > you can upload as a UCSC custom track. > > Is that good enough, or were you looking for something more? And if > so, what? There's the GenomeGraphs library, which is pretty slick, but > I'm not sure if that's really what you're after: > > http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html > > Hope that helps, > > -steve > > -- > Steve Lianoglou > Graduate Student: Physiology, Biophysics and Systems Biology > Weill Cornell Medical College of Cornell University > > http://cbio.mskcc.org/~lianos > > _______________________________________________ > 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 REPLYlink written 10.9 years ago by laurent140
Answer: How to plot microRNA chromosome location
0
gravatar for Camper Chih-Wei Liu
10.9 years ago by
Camper Chih-Wei Liu40 wrote:
Thank you very much. This package is very useful too. However, if I want to plot all miRNAs in one chromosome, it doesn't work. -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Michael Lawrence Sent: Saturday, November 01, 2008 9:27 AM To: Sean Davis Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] How to plot microRNA chromosome location On Tue, Oct 28, 2008 at 2:59 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Mon, Oct 27, 2008 at 9:13 PM, Steve Lianoglou > <mailinglist.honeypot at="" gmail.com=""> wrote: > > Hi, > > > > On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote: > > > >> Hi all, > >> > >> > >> > >> I have check some useful packages to plot gene chromosome information > like > >> gene plotter, ideogram and GenomeGraphs. > >> > >> However, I don't know how to plot microRNA (miRNA) chromosome location. > >> > >> I would like to see the distribution of some miRNAs in the genome. > >> > >> > >> > >> I have known the miRNA chromosome info. > >> > >> miRNA name chromosome start end > >> > >> hsa-miR-130b 22 20337592 > >> 20337673 > >> > >> hsa-miR-33a 22 40626894 > >> 40626962 > >> > >> hsa-miR-15b 3 161605069 > >> 161605166 > >> > >> . > >> > >> > >> > >> Is there any packages that I provide the location and plotting it out? > > > > You could create a custom track and upload it to the UCSC genome browser. > > > Sorry for late reply here. In fact, there is an example in the rtracklayer vignette that does pretty much exactly this, except with miRNA target sites. Let me know if you need any more guidance. Thanks, Michael > > It looks like you got your info about 90% the way to GFF format: > > > > http://genome.ucsc.edu/FAQ/FAQformat#format3 > > > > You could tweak your info a bit, then write.table your way to a file you > can > > upload as a UCSC custom track. > > See the rtracklayer package for help here. > > > Is that good enough, or were you looking for something more? And if so, > > what? There's the GenomeGraphs library, which is pretty slick, but I'm > not > > sure if that's really what you're after: > > > > http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html > > _______________________________________________ > 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 > [[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 COMMENTlink written 10.9 years ago by Camper Chih-Wei Liu40
On Wed, Nov 5, 2008 at 12:53 PM, Camper (Chih-Wei Liu) < camper@cad.csie.ncku.edu.tw> wrote: > Thank you very much. > This package is very useful too. > However, if I want to plot all miRNAs in one chromosome, it doesn't work. > You might want to be a bit more specific here if you would like some suggestions. Sean > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Michael > Lawrence > Sent: Saturday, November 01, 2008 9:27 AM > To: Sean Davis > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] How to plot microRNA chromosome location > > On Tue, Oct 28, 2008 at 2:59 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Mon, Oct 27, 2008 at 9:13 PM, Steve Lianoglou > > <mailinglist.honeypot@gmail.com> wrote: > > > Hi, > > > > > > On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote: > > > > > >> Hi all, > > >> > > >> > > >> > > >> I have check some useful packages to plot gene chromosome information > > like > > >> gene plotter, ideogram and GenomeGraphs. > > >> > > >> However, I don't know how to plot microRNA (miRNA) chromosome > location. > > >> > > >> I would like to see the distribution of some miRNAs in the genome. > > >> > > >> > > >> > > >> I have known the miRNA chromosome info. > > >> > > >> miRNA name chromosome start end > > >> > > >> hsa-miR-130b 22 20337592 > > >> 20337673 > > >> > > >> hsa-miR-33a 22 40626894 > > >> 40626962 > > >> > > >> hsa-miR-15b 3 161605069 > > >> 161605166 > > >> > > >> . > > >> > > >> > > >> > > >> Is there any packages that I provide the location and plotting it out? > > > > > > You could create a custom track and upload it to the UCSC genome > browser. > > > > > > > > Sorry for late reply here. In fact, there is an example in the rtracklayer > vignette that does pretty much exactly this, except with miRNA target > sites. > > Let me know if you need any more guidance. > > Thanks, > Michael > > > > > It looks like you got your info about 90% the way to GFF format: > > > > > > http://genome.ucsc.edu/FAQ/FAQformat#format3 > > > > > > You could tweak your info a bit, then write.table your way to a file > you > > can > > > upload as a UCSC custom track. > > > > See the rtracklayer package for help here. > > > > > Is that good enough, or were you looking for something more? And if so, > > > what? There's the GenomeGraphs library, which is pretty slick, but I'm > > not > > > sure if that's really what you're after: > > > > > > http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html > > > > _______________________________________________ > > 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]] > > _______________________________________________ > 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 REPLYlink written 10.9 years ago by Sean Davis21k
On Wed, Nov 5, 2008 at 9:53 AM, Camper (Chih-Wei Liu) < camper@cad.csie.ncku.edu.tw> wrote: > Thank you very much. > This package is very useful too. > However, if I want to plot all miRNAs in one chromosome, it doesn't work. > The Genome Graphs tool at UCSC (not to be confused with the GenomeGraphs R package) may be what you need. http://genome.ucsc.edu/cgi-bin/hgGenome?org=human You can upload a track to the genome browser using rtracklayer, and then import it into that tool using their web interface. > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Michael > Lawrence > Sent: Saturday, November 01, 2008 9:27 AM > To: Sean Davis > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] How to plot microRNA chromosome location > > On Tue, Oct 28, 2008 at 2:59 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Mon, Oct 27, 2008 at 9:13 PM, Steve Lianoglou > > <mailinglist.honeypot@gmail.com> wrote: > > > Hi, > > > > > > On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote: > > > > > >> Hi all, > > >> > > >> > > >> > > >> I have check some useful packages to plot gene chromosome information > > like > > >> gene plotter, ideogram and GenomeGraphs. > > >> > > >> However, I don't know how to plot microRNA (miRNA) chromosome > location. > > >> > > >> I would like to see the distribution of some miRNAs in the genome. > > >> > > >> > > >> > > >> I have known the miRNA chromosome info. > > >> > > >> miRNA name chromosome start end > > >> > > >> hsa-miR-130b 22 20337592 > > >> 20337673 > > >> > > >> hsa-miR-33a 22 40626894 > > >> 40626962 > > >> > > >> hsa-miR-15b 3 161605069 > > >> 161605166 > > >> > > >> . > > >> > > >> > > >> > > >> Is there any packages that I provide the location and plotting it out? > > > > > > You could create a custom track and upload it to the UCSC genome > browser. > > > > > > > > Sorry for late reply here. In fact, there is an example in the rtracklayer > vignette that does pretty much exactly this, except with miRNA target > sites. > > Let me know if you need any more guidance. > > Thanks, > Michael > > > > > It looks like you got your info about 90% the way to GFF format: > > > > > > http://genome.ucsc.edu/FAQ/FAQformat#format3 > > > > > > You could tweak your info a bit, then write.table your way to a file > you > > can > > > upload as a UCSC custom track. > > > > See the rtracklayer package for help here. > > > > > Is that good enough, or were you looking for something more? And if so, > > > what? There's the GenomeGraphs library, which is pretty slick, but I'm > > not > > > sure if that's really what you're after: > > > > > > http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html > > > > _______________________________________________ > > 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]] > > _______________________________________________ > 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 REPLYlink written 10.9 years ago by Michael Lawrence620
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