chromosome ordering in cPlot()/cColor()
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Axel Klenk ★ 1.0k
@axel-klenk-3224
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UPF, Barcelona, Spain
Dear Biocore Team, I'm using cPlot()/cColor() from package annotate to produce chromosome plots and am very impressed how easily this can be achieved. However, unfortunately, the chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11, etc. from bottom to top and I would like to reorder them to 1, 2, 3, ... from top to bottom but cannot find an easy way to do so... am I missing something here? I managed to get what I want by hacking buildChromLocation() but that's ugly and I don't want to maintain a modified function if not necessary. Would it be possible to add a replace method for the chromInfo slot to allow e.g. z <- buildChromLocation("hgug41112a") library("gtools") # for mixedsort() info <- chromInfo(z) chromInfo(z) <- info[rev(mixedsort(names(info)))] or maybe you can think of a better solution? Thanks in advance, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com
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@martin-morgan-1513
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Hi Axel -- Axel.Klenk at Actelion.Com writes: > Dear Biocore Team, > > I'm using cPlot()/cColor() from package annotate to produce chromosome > plots and > am very impressed how easily this can be achieved. However, unfortunately, > the > chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11, etc. > from bottom > to top and I would like to reorder them to 1, 2, 3, ... from top to bottom > but cannot find an > easy way to do so... am I missing something here? > > I managed to get what I want by hacking buildChromLocation() but that's > ugly and I don't > want to maintain a modified function if not necessary. > > Would it be possible to add a replace method for the chromInfo slot to > allow e.g. > > z <- buildChromLocation("hgug41112a") > library("gtools") # for mixedsort() > info <- chromInfo(z) > chromInfo(z) <- info[rev(mixedsort(names(info)))] > > or maybe you can think of a better solution? As a work-around, you might try example(cPlot) # get object z idx <- c("1", "5", "10", "X") zz <- initialize(z, chromLocs=chromLocs(z)[idx], chromInfo(z)[idx]) cPlot(zz) I'm not sure whether there are other consequences of this sort of change, and if there are it would be good if you would let me know before a more permanent solution is implemented. Martin > Thanks in advance, > > - axel > > > Axel Klenk > Research Informatician > Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / > Switzerland > > > > The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. > It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. > The content of this email is not legally binding unless confirmed by letter. > Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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@martin-morgan-1513
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Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > Hi Axel -- > > Axel.Klenk at Actelion.Com writes: > >> Dear Biocore Team, >> >> I'm using cPlot()/cColor() from package annotate to produce chromosome >> plots and >> am very impressed how easily this can be achieved. However, unfortunately, >> the >> chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11, etc. >> from bottom >> to top and I would like to reorder them to 1, 2, 3, ... from top to bottom >> but cannot find an >> easy way to do so... am I missing something here? >> >> I managed to get what I want by hacking buildChromLocation() but that's >> ugly and I don't >> want to maintain a modified function if not necessary. >> >> Would it be possible to add a replace method for the chromInfo slot to >> allow e.g. >> >> z <- buildChromLocation("hgug41112a") >> library("gtools") # for mixedsort() >> info <- chromInfo(z) >> chromInfo(z) <- info[rev(mixedsort(names(info)))] >> >> or maybe you can think of a better solution? > > As a work-around, you might try > > example(cPlot) # get object z > idx <- c("1", "5", "10", "X") > zz <- initialize(z, chromLocs=chromLocs(z)[idx], chromInfo(z)[idx]) oops, that should be zz <- initialize(z, chromLocs=chromLocs(z)[idx], chromInfo=chromInfo(z)[idx]) > cPlot(zz) > > I'm not sure whether there are other consequences of this sort of > change, and if there are it would be good if you would let me know > before a more permanent solution is implemented. > > Martin > >> Thanks in advance, >> >> - axel >> >> >> Axel Klenk >> Research Informatician >> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / >> Switzerland >> >> >> >> The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. >> It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. >> The content of this email is not legally binding unless confirmed by letter. >> Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com >> >> _______________________________________________ >> 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Hi Martin, thanks a lot for your help. I have tested your workaround on my data set and it produces the desired result -- thanks for pointing me to initialize()... I have not (yet :-)) observed any unwanted consequences of this change but unfortunately have stumbled over two more issues for which I have to ask for your assistance: > library("geneplotter") > example(cPlot) cPlot> ## A bit of a hack to not have a package dependency on hgu95av2 cPlot> ## but need to fiddle w/ the warn level to not fail the example anyways. cPlot> cPlot> curWarn <- options(warn=0) cPlot> on.exit(options(warn=curWarn), add=TRUE) Error in options(warn = curWarn) : invalid value for 'warn' > Clearly, the example code should read on.exit(options(curWarn), add=TRUE) or am I mistaken? I admit I am two minor R releases behind (see sessionInfo() below) but for me example(cPlot) does work neither on WinXP nor on RHEL4 64bit. But to get object 'z' I can run: > example(cColor) [...] > objects() [1] "curWarn" "probes" "probes2" "z" > p <- probes2[2:4] > mget(p, probesToChrom(z)) $`41807_at` [1] "9" $`931_at` [1] "13" $`39032_at` [1] "13" > cPlot(z, glen = 0.3) > cColor(p, c("red", "black", "black"), z, glen = 0.6) > Given that p contains probe names that are mapped to chr 9, 13, and 13 I had expected a red bar on chr 9 and two black bars on chr 13 -- however, I see a red bar on chr 9 and a black and a red bar on chr 13... maybe my expectation is just wrong? (This is of course a hopefully reproducible toy example -- I first observed this behaviour when mapping fold changes to chromosomes and a region known to be all down came out pretty multicoloured.) This is obviously without applying any workaround on chromosome order etc. and the results is the same when chromosomes are reordered. Can you reproduce/confirm this? library("geneplotter") example(cPlot) example(cColor) objects() p <- probes2[2:4] mget(p, probesToChrom(z)) cPlot(z, glen = 0.3) cColor(p, c("red", "black", "black"), z, glen = 0.6) Could you please let me know if this is the expected result or not ? Thanks in advance, - axel > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=German_Switzerland.1252;LC_CTYPE=German_Switzerland.1252;LC _MONETARY=German_Switzerland.1252;LC_NUMERIC=C;LC_TIME=German_Switzerl and.1252 attached base packages: [1] datasets stats graphics grDevices utils methods base other attached packages: [1] hgu95av2.db_2.2.12 RSQLite_0.7-1 DBI_0.2-4 fortunes_1.3-6 [5] limma_2.18.0 sfsmisc_1.0-7 geneplotter_1.22.0 lattice_0.17-25 [9] annotate_1.22.0 AnnotationDbi_1.6.0 Biobase_2.4.1 MASS_7.2-47 [13] RODBC_1.2-5 gmodels_2.15.0 loaded via a namespace (and not attached): [1] gdata_2.4.2 grid_2.9.0 gtools_2.6.1 RColorBrewer_1.0-2 [5] xtable_1.5-5 Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland Martin Morgan <mtmorgan at="" fhcrc.o="" rg=""> To Sent by: Axel.Klenk at actelion.com bioconductor-boun cc ces at stat.math.eth bioconductor at stat.math.ethz.ch z.ch Subject Re: [BioC] chromosome ordering in cPlot()/cColor() 25.08.2009 18:44 Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > Hi Axel -- > > Axel.Klenk at Actelion.Com writes: > >> Dear Biocore Team, >> >> I'm using cPlot()/cColor() from package annotate to produce chromosome >> plots and >> am very impressed how easily this can be achieved. However, unfortunately, >> the >> chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11, etc. >> from bottom >> to top and I would like to reorder them to 1, 2, 3, ... from top to bottom >> but cannot find an >> easy way to do so... am I missing something here? >> >> I managed to get what I want by hacking buildChromLocation() but that's >> ugly and I don't >> want to maintain a modified function if not necessary. >> >> Would it be possible to add a replace method for the chromInfo slot to >> allow e.g. >> >> z <- buildChromLocation("hgug41112a") >> library("gtools") # for mixedsort() >> info <- chromInfo(z) >> chromInfo(z) <- info[rev(mixedsort(names(info)))] >> >> or maybe you can think of a better solution? > > As a work-around, you might try > > example(cPlot) # get object z > idx <- c("1", "5", "10", "X") > zz <- initialize(z, chromLocs=chromLocs(z)[idx], chromInfo(z)[idx]) oops, that should be zz <- initialize(z, chromLocs=chromLocs(z)[idx], chromInfo=chromInfo(z)[idx]) > cPlot(zz) > > I'm not sure whether there are other consequences of this sort of > change, and if there are it would be good if you would let me know > before a more permanent solution is implemented. > > Martin > >> Thanks in advance, >> >> - axel >> >> >> Axel Klenk >> Research Informatician >> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / >> Switzerland >> >> >> >> The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. >> It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. >> The content of this email is not legally binding unless confirmed by letter. >> Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com >> >> _______________________________________________ >> 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ 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 The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com
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Hi Axel -- Axel.Klenk at Actelion.Com wrote: > Hi Martin, > > thanks a lot for your help. I have tested your workaround on my data set > and it produces the desired result -- thanks for pointing me to > initialize()... initialize() is a low-level function, so think of this as a 'hack'. > I have not (yet :-)) observed any unwanted consequences of this change > but unfortunately have stumbled over two more issues for which I have to > ask for your assistance: > >> library("geneplotter") >> example(cPlot) > > cPlot> ## A bit of a hack to not have a package dependency on hgu95av2 > cPlot> ## but need to fiddle w/ the warn level to not fail the example > anyways. > cPlot> > cPlot> curWarn <- options(warn=0) > > cPlot> on.exit(options(warn=curWarn), add=TRUE) > Error in options(warn = curWarn) : invalid value for 'warn' > > Clearly, the example code should read > on.exit(options(curWarn), add=TRUE) > or am I mistaken? I admit I am two minor R releases behind (see > sessionInfo() > below) but for me example(cPlot) does work neither on WinXP nor on RHEL4 > 64bit. > But to get object 'z' I can run: yes I came across that yesterday and fixed it in the 'devel' version of this package; should have warned you, sorry. > >> example(cColor) > [...] > >> objects() > [1] "curWarn" "probes" "probes2" "z" > >> p <- probes2[2:4] > >> mget(p, probesToChrom(z)) > $`41807_at` > [1] "9" > > $`931_at` > [1] "13" > > $`39032_at` > [1] "13" > >> cPlot(z, glen = 0.3) >> cColor(p, c("red", "black", "black"), z, glen = 0.6) >> > > Given that p contains probe names that are mapped to chr 9, 13, and 13 I > had > expected a red bar on chr 9 and two black bars on chr 13 -- however, I see > a > red bar on chr 9 and a black and a red bar on chr 13... maybe my > expectation > is just wrong? I think plotting in multiple colors is meant to be supported by multiple calls to cColor, first with probes to be colored "red", then with probes to be collored "black". The development version has been updated to support multiple color specifications. Martin > (This is of course a hopefully reproducible toy example -- I first observed > this > behaviour when mapping fold changes to chromosomes and a region known > to be all down came out pretty multicoloured.) > > This is obviously without applying any workaround on chromosome order etc. > and the results is the same when chromosomes are reordered. > > Can you reproduce/confirm this? > > library("geneplotter") > example(cPlot) > example(cColor) > objects() > p <- probes2[2:4] > mget(p, probesToChrom(z)) > cPlot(z, glen = 0.3) > cColor(p, c("red", "black", "black"), z, glen = 0.6) > > Could you please let me know if this is the expected result or not ? > > Thanks in advance, > > - axel > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=German_Switzerland.1252;LC_CTYPE=German_Switzerland.1252; LC_MONETARY=German_Switzerland.1252;LC_NUMERIC=C;LC_TIME=German_Switze rland.1252 > > attached base packages: > [1] datasets stats graphics grDevices utils methods base > > other attached packages: > [1] hgu95av2.db_2.2.12 RSQLite_0.7-1 DBI_0.2-4 > fortunes_1.3-6 > [5] limma_2.18.0 sfsmisc_1.0-7 geneplotter_1.22.0 > lattice_0.17-25 > [9] annotate_1.22.0 AnnotationDbi_1.6.0 Biobase_2.4.1 > MASS_7.2-47 > [13] RODBC_1.2-5 gmodels_2.15.0 > > loaded via a namespace (and not attached): > [1] gdata_2.4.2 grid_2.9.0 gtools_2.6.1 > RColorBrewer_1.0-2 > [5] xtable_1.5-5 > > > Axel Klenk > Research Informatician > Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / > Switzerland > > > > > Martin Morgan > <mtmorgan at="" fhcrc.o=""> rg> To > Sent by: Axel.Klenk at actelion.com > bioconductor-boun cc > ces at stat.math.eth bioconductor at stat.math.ethz.ch > z.ch Subject > Re: [BioC] chromosome ordering in > cPlot()/cColor() > 25.08.2009 18:44 > > > > > > > > > > Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > >> Hi Axel -- >> >> Axel.Klenk at Actelion.Com writes: >> >>> Dear Biocore Team, >>> >>> I'm using cPlot()/cColor() from package annotate to produce chromosome >>> plots and >>> am very impressed how easily this can be achieved. However, > unfortunately, >>> the >>> chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11, > etc. >>> from bottom >>> to top and I would like to reorder them to 1, 2, 3, ... from top to > bottom >>> but cannot find an >>> easy way to do so... am I missing something here? >>> >>> I managed to get what I want by hacking buildChromLocation() but that's >>> ugly and I don't >>> want to maintain a modified function if not necessary. >>> >>> Would it be possible to add a replace method for the chromInfo slot to >>> allow e.g. >>> >>> z <- buildChromLocation("hgug41112a") >>> library("gtools") # for mixedsort() >>> info <- chromInfo(z) >>> chromInfo(z) <- info[rev(mixedsort(names(info)))] >>> >>> or maybe you can think of a better solution? >> As a work-around, you might try >> >> example(cPlot) # get object z >> idx <- c("1", "5", "10", "X") >> zz <- initialize(z, chromLocs=chromLocs(z)[idx], chromInfo(z)[idx]) > > oops, that should be > > zz <- initialize(z, chromLocs=chromLocs(z)[idx], > chromInfo=chromInfo(z)[idx]) > >> cPlot(zz) >> >> I'm not sure whether there are other consequences of this sort of >> change, and if there are it would be good if you would let me know >> before a more permanent solution is implemented. >> >> Martin >> >>> Thanks in advance, >>> >>> - axel >>> >>> >>> Axel Klenk >>> Research Informatician >>> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / >>> Switzerland >>> >>> >>> >>> The information of this email and in any file transmitted with it is > strictly confidential and may be legally privileged. >>> It is intended solely for the addressee. If you are not the intended > recipient, any copying, distribution or any other use of this email is > prohibited and may be unlawful. In such case, you should please notify the > sender immediately and destroy this email. >>> The content of this email is not legally binding unless confirmed by > letter. >>> Any views expressed in this message are those of the individual sender, > except where the message states otherwise and the sender is authorised to > state them to be the views of the sender's company. For further information > about Actelion please see our website at http://www.actelion.com >>> _______________________________________________ >>> 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 > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > _______________________________________________ > 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 > > > > > The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. > It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. > The content of this email is not legally binding unless confirmed by letter. > Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com >
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Hi Martin, very good; all of my questions answered and I can move forward... thank you very much! - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland Martin Morgan <mtmorgan at="" fhcrc.o="" rg=""> To Axel.Klenk at Actelion.Com 26.08.2009 19:18 cc bioconductor at stat.math.ethz.ch Subject Re: [BioC] chromosome ordering in cPlot()/cColor() Hi Axel -- Axel.Klenk at Actelion.Com wrote: > Hi Martin, > > thanks a lot for your help. I have tested your workaround on my data set > and it produces the desired result -- thanks for pointing me to > initialize()... initialize() is a low-level function, so think of this as a 'hack'. > I have not (yet :-)) observed any unwanted consequences of this change > but unfortunately have stumbled over two more issues for which I have to > ask for your assistance: > >> library("geneplotter") >> example(cPlot) > > cPlot> ## A bit of a hack to not have a package dependency on hgu95av2 > cPlot> ## but need to fiddle w/ the warn level to not fail the example > anyways. > cPlot> > cPlot> curWarn <- options(warn=0) > > cPlot> on.exit(options(warn=curWarn), add=TRUE) > Error in options(warn = curWarn) : invalid value for 'warn' > > Clearly, the example code should read > on.exit(options(curWarn), add=TRUE) > or am I mistaken? I admit I am two minor R releases behind (see > sessionInfo() > below) but for me example(cPlot) does work neither on WinXP nor on RHEL4 > 64bit. > But to get object 'z' I can run: yes I came across that yesterday and fixed it in the 'devel' version of this package; should have warned you, sorry. > >> example(cColor) > [...] > >> objects() > [1] "curWarn" "probes" "probes2" "z" > >> p <- probes2[2:4] > >> mget(p, probesToChrom(z)) > $`41807_at` > [1] "9" > > $`931_at` > [1] "13" > > $`39032_at` > [1] "13" > >> cPlot(z, glen = 0.3) >> cColor(p, c("red", "black", "black"), z, glen = 0.6) >> > > Given that p contains probe names that are mapped to chr 9, 13, and 13 I > had > expected a red bar on chr 9 and two black bars on chr 13 -- however, I see > a > red bar on chr 9 and a black and a red bar on chr 13... maybe my > expectation > is just wrong? I think plotting in multiple colors is meant to be supported by multiple calls to cColor, first with probes to be colored "red", then with probes to be collored "black". The development version has been updated to support multiple color specifications. Martin > (This is of course a hopefully reproducible toy example -- I first observed > this > behaviour when mapping fold changes to chromosomes and a region known > to be all down came out pretty multicoloured.) > > This is obviously without applying any workaround on chromosome order etc. > and the results is the same when chromosomes are reordered. > > Can you reproduce/confirm this? > > library("geneplotter") > example(cPlot) > example(cColor) > objects() > p <- probes2[2:4] > mget(p, probesToChrom(z)) > cPlot(z, glen = 0.3) > cColor(p, c("red", "black", "black"), z, glen = 0.6) > > Could you please let me know if this is the expected result or not ? > > Thanks in advance, > > - axel > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=German_Switzerland.1252;LC_CTYPE=German_Switzerland.1252;LC _MONETARY=German_Switzerland.1252;LC_NUMERIC=C;LC_TIME=German_Switzerl and.1252 > > attached base packages: > [1] datasets stats graphics grDevices utils methods base > > other attached packages: > [1] hgu95av2.db_2.2.12 RSQLite_0.7-1 DBI_0.2-4 > fortunes_1.3-6 > [5] limma_2.18.0 sfsmisc_1.0-7 geneplotter_1.22.0 > lattice_0.17-25 > [9] annotate_1.22.0 AnnotationDbi_1.6.0 Biobase_2.4.1 > MASS_7.2-47 > [13] RODBC_1.2-5 gmodels_2.15.0 > > loaded via a namespace (and not attached): > [1] gdata_2.4.2 grid_2.9.0 gtools_2.6.1 > RColorBrewer_1.0-2 > [5] xtable_1.5-5 > > > Axel Klenk > Research Informatician > Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / > Switzerland > > > > > Martin Morgan > <mtmorgan at="" fhcrc.o=""> rg> To > Sent by: Axel.Klenk at actelion.com > bioconductor-boun cc > ces at stat.math.eth bioconductor at stat.math.ethz.ch > z.ch Subject > Re: [BioC] chromosome ordering in > cPlot()/cColor() > 25.08.2009 18:44 > > > > > > > > > > Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > >> Hi Axel -- >> >> Axel.Klenk at Actelion.Com writes: >> >>> Dear Biocore Team, >>> >>> I'm using cPlot()/cColor() from package annotate to produce chromosome >>> plots and >>> am very impressed how easily this can be achieved. However, > unfortunately, >>> the >>> chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11, > etc. >>> from bottom >>> to top and I would like to reorder them to 1, 2, 3, ... from top to > bottom >>> but cannot find an >>> easy way to do so... am I missing something here? >>> >>> I managed to get what I want by hacking buildChromLocation() but that's >>> ugly and I don't >>> want to maintain a modified function if not necessary. >>> >>> Would it be possible to add a replace method for the chromInfo slot to >>> allow e.g. >>> >>> z <- buildChromLocation("hgug41112a") >>> library("gtools") # for mixedsort() >>> info <- chromInfo(z) >>> chromInfo(z) <- info[rev(mixedsort(names(info)))] >>> >>> or maybe you can think of a better solution? >> As a work-around, you might try >> >> example(cPlot) # get object z >> idx <- c("1", "5", "10", "X") >> zz <- initialize(z, chromLocs=chromLocs(z)[idx], chromInfo(z)[idx]) > > oops, that should be > > zz <- initialize(z, chromLocs=chromLocs(z)[idx], > chromInfo=chromInfo(z)[idx]) > >> cPlot(zz) >> >> I'm not sure whether there are other consequences of this sort of >> change, and if there are it would be good if you would let me know >> before a more permanent solution is implemented. >> >> Martin >> >>> Thanks in advance, >>> >>> - axel >>> >>> >>> Axel Klenk >>> Research Informatician >>> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / >>> Switzerland >>> >>> >>> >>> The information of this email and in any file transmitted with it is > strictly confidential and may be legally privileged. >>> It is intended solely for the addressee. If you are not the intended > recipient, any copying, distribution or any other use of this email is > prohibited and may be unlawful. In such case, you should please notify the > sender immediately and destroy this email. >>> The content of this email is not legally binding unless confirmed by > letter. >>> Any views expressed in this message are those of the individual sender, > except where the message states otherwise and the sender is authorised to > state them to be the views of the sender's company. For further information > about Actelion please see our website at http://www.actelion.com >>> _______________________________________________ >>> 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 > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > _______________________________________________ > 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 > > > > > The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. > It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. > The content of this email is not legally binding unless confirmed by letter. > Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com > The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com
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