Set plot title in makeVennDiagram (ChIPpeakAnno)
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@antonio-miguel-de-jesus-domingues-5182
Last seen 10 months ago
Germany
Hi Bioconducters, I am comparing 2 list of ChIP peaks obtained with different peak callers and would like to change some of the graphical options of the plot created by makeVennDiagram. Crucially I would like to add a title to the plot. Is there any way to change the graphical options of makeVennDiagram? Cheers, António -- -- António Miguel de Jesus Domingues, PhD Neugebauer group Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Pfotenhauerstrasse 108 01307 Dresden Germany e-mail: domingue@mpi-cbg.de tel. +49 351 210 2481 The Unbearable Lightness of Molecular Biology [[alternative HTML version deleted]]
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 13 months ago
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Anotonio, Thanks for the great suggestion! Currently makeVennDiagram only supports limited plotting options, i.e., cex and count.col. I will add the title in my to do list. Best regards, Julie On 9/13/12 9:03 AM, "Ant?nio Miguel de Jesus Domingues" <amjdomingues at="" gmail.com=""> wrote: > Hi Bioconducters, > > I am comparing 2 list of ChIP peaks obtained with different peak callers > and would like to change some of the graphical options of the plot created > by makeVennDiagram. Crucially I would like to add a title to the plot. > > Is there any way to change the graphical options of makeVennDiagram? > > Cheers, > Ant?nio
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Hi Julie, Thanks! If it is not asking too much and how much work it takes, but adding colours to the background of the circles would also be nice for presentations and papers. Basically some possibilities along the lines of the R package VennDiagram (http://www.biomedcentral.com/1471-2105/12/35) Good package you've developed btw. António On 13 September 2012 15:35, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu>wrote: > Anotonio, > > Thanks for the great suggestion! Currently makeVennDiagram only supports > limited plotting options, i.e., cex and count.col. I will add the title in > my to do list. > > Best regards, > > Julie > > > On 9/13/12 9:03 AM, "António Miguel de Jesus Domingues" > <amjdomingues@gmail.com> wrote: > > > Hi Bioconducters, > > > > I am comparing 2 list of ChIP peaks obtained with different peak callers > > and would like to change some of the graphical options of the plot > created > > by makeVennDiagram. Crucially I would like to add a title to the plot. > > > > Is there any way to change the graphical options of makeVennDiagram? > > > > Cheers, > > António > > -- -- António Miguel de Jesus Domingues, PhD Neugebauer group Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Pfotenhauerstrasse 108 01307 Dresden Germany e-mail: domingue@mpi-cbg.de tel. +49 351 210 2481 The Unbearable Lightness of Molecular Biology [[alternative HTML version deleted]]
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Will do! Thanks for the positive feedback and great suggestion! Best regards, Julie On 9/13/12 9:41 AM, "António Miguel de Jesus Domingues" <amjdomingues@gmail.com> wrote: Hi Julie, Thanks! If it is not asking too much and how much work it takes, but adding colours to the background of the circles would also be nice for presentations and papers. Basically some possibilities along the lines of the R package VennDiagram (http://www.biomedcentral.com/1471-2105/12/35) Good package you've developed btw. António On 13 September 2012 15:35, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: Anotonio, Thanks for the great suggestion! Currently makeVennDiagram only supports limited plotting options, i.e., cex and count.col. I will add the title in my to do list. Best regards, Julie On 9/13/12 9:03 AM, "António Miguel de Jesus Domingues" <amjdomingues@gmail.com> wrote: > Hi Bioconducters, > > I am comparing 2 list of ChIP peaks obtained with different peak callers > and would like to change some of the graphical options of the plot created > by makeVennDiagram. Crucially I would like to add a title to the plot. > > Is there any way to change the graphical options of makeVennDiagram? > > Cheers, > António [[alternative HTML version deleted]]
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Antonio, Thanks to Jianhong, options from package VennDiagram are now available in ChIPpeakAnno:::makeVennDiagram (version 2.5.12). You can specify the title using main and background color using fill. For more options, please type ?venn.diagram. Here is an example by Jianhong, peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f")) peaks2 = RangedData(IRanges(start = c(967659, 2010898,2496700,3075866,3123260), end = c(967869, 2011108, 2496920, 3076166, 3123470), names = c("t1", "t2", "t3", "t4", "t5")), space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), feature=c("a","b","c","d","a")) makeVennDiagram(RangedDataList(peaks1,peaks2, peaks1, peaks2), NameOfPeaks=c("TF1", "TF2","TF3", "TF4"), totalTest=100,useFeature=TRUE, main="Venn Diagram", col = "transparent",fill = c("cornflowerblue", "green", "yellow", "darkorchid1"), alpha = 0.50,label.col = c("orange", "white", "darkorchid4", "white", "white", "white", "white", "white", "darkblue", "white", "white", "white", "white", "darkgreen", "white"), cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4")) Best regards, Julie On 9/13/12 9:41 AM, "Ant?nio Miguel de Jesus Domingues" <amjdomingues at="" gmail.com=""> wrote: Hi Julie, Thanks! If it is not asking too much and how much work it takes, but adding colours to the background of the circles would also be nice for presentations and papers. Basically some possibilities along the lines of the R package VennDiagram (http://www.biomedcentral.com/1471-2105/12/35) Good package you've developed btw. Ant?nio On 13 September 2012 15:35, Zhu, Lihua (Julie) <julie.zhu at="" umassmed.edu=""> wrote: Anotonio, Thanks for the great suggestion! Currently makeVennDiagram only supports limited plotting options, i.e., cex and count.col. I will add the title in my to do list. Best regards, Julie On 9/13/12 9:03 AM, "Ant?nio Miguel de Jesus Domingues" <amjdomingues at="" gmail.com=""> wrote: > Hi Bioconducters, > > I am comparing 2 list of ChIP peaks obtained with different peak callers > and would like to change some of the graphical options of the plot created > by makeVennDiagram. Crucially I would like to add a title to the plot. > > Is there any way to change the graphical options of makeVennDiagram? > > Cheers, > Ant?nio
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Hi Julie, thanks a lot! I am however struggling to install the v2.5.12. Is it available already? I was trying to go via: source("http://bioconductor.org/biocLite.R") biocLite("ChIPpeakAnno") library(ChIPpeakAnno) But that installs ChIPpeakAnno_2.4.0 (unrelated to the matter at hand but I have also been having mutiple problems installing packages from source since upgrading to R 2.15). > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ChIPpeakAnno_2.4.0 limma_3.12.3 [3] org.Hs.eg.db_2.7.1 GO.db_2.7.1 [5] RSQLite_0.11.2 DBI_0.2-5 [7] AnnotationDbi_1.18.3 BSgenome.Ecoli.NCBI.20080805_1.3.17 [9] BSgenome_1.24.0 GenomicRanges_1.8.13 [11] Biostrings_2.24.1 IRanges_1.14.4 [13] multtest_2.12.0 Biobase_2.16.0 [15] biomaRt_2.12.0 BiocGenerics_0.2.0 [17] gplots_2.11.0 MASS_7.3-21 [19] KernSmooth_2.23-8 caTools_1.13 [21] bitops_1.0-4.1 gdata_2.12.0 [23] gtools_2.7.0 loaded via a namespace (and not attached): [1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 ggplot2_0.9.2.1 [5] gtable_0.1.1 labeling_0.1 memoise_0.1 munsell_0.4 [9] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 [13] reshape2_1.2.1 scales_0.2.2 splines_2.15.1 stats4_2.15.1 [17] stringr_0.6.1 survival_2.36-14 XML_3.9-4 On 15 September 2012 05:03, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu>wrote: > Antonio, > > Thanks to Jianhong, options from package VennDiagram are now available in > ChIPpeakAnno:::makeVennDiagram (version 2.5.12). You can specify the title > using main and background color using fill. For more options, please type > ?venn.diagram. > > Here is an example by Jianhong, > > peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), > end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", > "Site3")), > space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f")) > peaks2 = RangedData(IRanges(start = c(967659, > 2010898,2496700,3075866,3123260), > end = c(967869, 2011108, 2496920, 3076166, 3123470), > names = c("t1", "t2", "t3", "t4", "t5")), > space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), > feature=c("a","b","c","d","a")) > makeVennDiagram(RangedDataList(peaks1,peaks2, peaks1, peaks2), > NameOfPeaks=c("TF1", "TF2","TF3", "TF4"), > totalTest=100,useFeature=TRUE, main="Venn Diagram", > col = "transparent",fill = c("cornflowerblue", "green", "yellow", > "darkorchid1"), > alpha = 0.50,label.col = c("orange", "white", "darkorchid4", "white", > "white", "white", "white", "white", "darkblue", "white", "white", "white", > "white", "darkgreen", "white"), cat.col = c("darkblue", "darkgreen", > "orange", "darkorchid4")) > > > Best regards, > > Julie > > > On 9/13/12 9:41 AM, "António Miguel de Jesus Domingues" < > amjdomingues@gmail.com> wrote: > > Hi Julie, > > Thanks! > > If it is not asking too much and how much work it takes, but adding > colours to the background of the circles would also be nice for > presentations and papers. Basically some possibilities along the lines of > the R package VennDiagram (http://www.biomedcentral.com/1471-2105/12/35) > > Good package you've developed btw. > > António > > On 13 September 2012 15:35, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> > wrote: > > Anotonio, > > Thanks for the great suggestion! Currently makeVennDiagram only supports > limited plotting options, i.e., cex and count.col. I will add the title in > my to do list. > > Best regards, > > Julie > > > On 9/13/12 9:03 AM, "António Miguel de Jesus Domingues" > <amjdomingues@gmail.com> wrote: > > > Hi Bioconducters, > > > > I am comparing 2 list of ChIP peaks obtained with different peak callers > > and would like to change some of the graphical options of the plot > created > > by makeVennDiagram. Crucially I would like to add a title to the plot. > > > > Is there any way to change the graphical options of makeVennDiagram? > > > > Cheers, > > António > > > > -- -- António Miguel de Jesus Domingues, PhD Neugebauer group Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Pfotenhauerstrasse 108 01307 Dresden Germany e-mail: domingue@mpi-cbg.de tel. +49 351 210 2481 The Unbearable Lightness of Molecular Biology [[alternative HTML version deleted]]
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Hi Antonio, See the help for useDevel(): library(BiocInstaller) ?useDevel Best, Jim On 9/18/2012 4:03 AM, Ant?nio Miguel de Jesus Domingues wrote: > Hi Julie, > > thanks a lot! I am however struggling to install the v2.5.12. Is it > available already? I was trying to go via: > source("http://bioconductor.org/biocLite.R") > biocLite("ChIPpeakAnno") > library(ChIPpeakAnno) > But that installs ChIPpeakAnno_2.4.0 (unrelated to the matter at hand but I > have also been having mutiple problems installing packages from source > since upgrading to R 2.15). > > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] ChIPpeakAnno_2.4.0 limma_3.12.3 > [3] org.Hs.eg.db_2.7.1 GO.db_2.7.1 > [5] RSQLite_0.11.2 DBI_0.2-5 > [7] AnnotationDbi_1.18.3 BSgenome.Ecoli.NCBI.20080805_1.3.17 > [9] BSgenome_1.24.0 GenomicRanges_1.8.13 > [11] Biostrings_2.24.1 IRanges_1.14.4 > [13] multtest_2.12.0 Biobase_2.16.0 > [15] biomaRt_2.12.0 BiocGenerics_0.2.0 > [17] gplots_2.11.0 MASS_7.3-21 > [19] KernSmooth_2.23-8 caTools_1.13 > [21] bitops_1.0-4.1 gdata_2.12.0 > [23] gtools_2.7.0 > > loaded via a namespace (and not attached): > [1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 > ggplot2_0.9.2.1 > [5] gtable_0.1.1 labeling_0.1 memoise_0.1 > munsell_0.4 > [9] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 > RCurl_1.91-1 > [13] reshape2_1.2.1 scales_0.2.2 splines_2.15.1 > stats4_2.15.1 > [17] stringr_0.6.1 survival_2.36-14 XML_3.9-4 > > On 15 September 2012 05:03, Zhu, Lihua (Julie)<julie.zhu at="" umassmed.edu="">wrote: > >> Antonio, >> >> Thanks to Jianhong, options from package VennDiagram are now available in >> ChIPpeakAnno:::makeVennDiagram (version 2.5.12). You can specify the title >> using main and background color using fill. For more options, please type >> ?venn.diagram. >> >> Here is an example by Jianhong, >> >> peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), >> end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", >> "Site3")), >> space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f")) >> peaks2 = RangedData(IRanges(start = c(967659, >> 2010898,2496700,3075866,3123260), >> end = c(967869, 2011108, 2496920, 3076166, 3123470), >> names = c("t1", "t2", "t3", "t4", "t5")), >> space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), >> feature=c("a","b","c","d","a")) >> makeVennDiagram(RangedDataList(peaks1,peaks2, peaks1, peaks2), >> NameOfPeaks=c("TF1", "TF2","TF3", "TF4"), >> totalTest=100,useFeature=TRUE, main="Venn Diagram", >> col = "transparent",fill = c("cornflowerblue", "green", "yellow", >> "darkorchid1"), >> alpha = 0.50,label.col = c("orange", "white", "darkorchid4", "white", >> "white", "white", "white", "white", "darkblue", "white", "white", "white", >> "white", "darkgreen", "white"), cat.col = c("darkblue", "darkgreen", >> "orange", "darkorchid4")) >> >> >> Best regards, >> >> Julie >> >> >> On 9/13/12 9:41 AM, "Ant?nio Miguel de Jesus Domingues"< >> amjdomingues at gmail.com> wrote: >> >> Hi Julie, >> >> Thanks! >> >> If it is not asking too much and how much work it takes, but adding >> colours to the background of the circles would also be nice for >> presentations and papers. Basically some possibilities along the lines of >> the R package VennDiagram (http://www.biomedcentral.com/1471-2105/12/35) >> >> Good package you've developed btw. >> >> Ant?nio >> >> On 13 September 2012 15:35, Zhu, Lihua (Julie)<julie.zhu at="" umassmed.edu=""> >> wrote: >> >> Anotonio, >> >> Thanks for the great suggestion! Currently makeVennDiagram only supports >> limited plotting options, i.e., cex and count.col. I will add the title in >> my to do list. >> >> Best regards, >> >> Julie >> >> >> On 9/13/12 9:03 AM, "Ant?nio Miguel de Jesus Domingues" >> <amjdomingues at="" gmail.com=""> wrote: >> >>> Hi Bioconducters, >>> >>> I am comparing 2 list of ChIP peaks obtained with different peak callers >>> and would like to change some of the graphical options of the plot >> created >>> by makeVennDiagram. Crucially I would like to add a title to the plot. >>> >>> Is there any way to change the graphical options of makeVennDiagram? >>> >>> Cheers, >>> Ant?nio >> >> >> > > > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Antonio, You could download the most recent version of ChIPpeakAnno from the repository using svn. svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAn no/ Alternatively, you could download ChIPpeakAnno_2.5.12.tar.gz at http://www.bioconductor.org/packages/2.11/bioc/html/ChIPpeakAnno.html Best regards, Julie On 9/18/12 4:03 AM, "António Miguel de Jesus Domingues" <amjdomingues@gmail.com> wrote: Hi Julie, thanks a lot! I am however struggling to install the v2.5.12. Is it available already? I was trying to go via: source("http://bioconductor.org/biocLite.R") biocLite("ChIPpeakAnno") library(ChIPpeakAnno) But that installs ChIPpeakAnno_2.4.0 (unrelated to the matter at hand but I have also been having mutiple problems installing packages from source since upgrading to R 2.15). > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ChIPpeakAnno_2.4.0 limma_3.12.3 [3] org.Hs.eg.db_2.7.1 GO.db_2.7.1 [5] RSQLite_0.11.2 DBI_0.2-5 [7] AnnotationDbi_1.18.3 BSgenome.Ecoli.NCBI.20080805_1.3.17 [9] BSgenome_1.24.0 GenomicRanges_1.8.13 [11] Biostrings_2.24.1 IRanges_1.14.4 [13] multtest_2.12.0 Biobase_2.16.0 [15] biomaRt_2.12.0 BiocGenerics_0.2.0 [17] gplots_2.11.0 MASS_7.3-21 [19] KernSmooth_2.23-8 caTools_1.13 [21] bitops_1.0-4.1 gdata_2.12.0 [23] gtools_2.7.0 loaded via a namespace (and not attached): [1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 ggplot2_0.9.2.1 [5] gtable_0.1.1 labeling_0.1 memoise_0.1 munsell_0.4 [9] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 [13] reshape2_1.2.1 scales_0.2.2 splines_2.15.1 stats4_2.15.1 [17] stringr_0.6.1 survival_2.36-14 XML_3.9-4 On 15 September 2012 05:03, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: Antonio, Thanks to Jianhong, options from package VennDiagram are now available in ChIPpeakAnno:::makeVennDiagram (version 2.5.12). You can specify the title using main and background color using fill. For more options, please type ?venn.diagram. Here is an example by Jianhong, peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f")) peaks2 = RangedData(IRanges(start = c(967659, 2010898,2496700,3075866,3123260), end = c(967869, 2011108, 2496920, 3076166, 3123470), names = c("t1", "t2", "t3", "t4", "t5")), space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), feature=c("a","b","c","d","a")) makeVennDiagram(RangedDataList(peaks1,peaks2, peaks1, peaks2), NameOfPeaks=c("TF1", "TF2","TF3", "TF4"), totalTest=100,useFeature=TRUE, main="Venn Diagram", col = "transparent",fill = c("cornflowerblue", "green", "yellow", "darkorchid1"), alpha = 0.50,label.col = c("orange", "white", "darkorchid4", "white", "white", "white", "white", "white", "darkblue", "white", "white", "white", "white", "darkgreen", "white"), cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4")) Best regards, Julie On 9/13/12 9:41 AM, "António Miguel de Jesus Domingues" <amjdomingues@gmail.com <http:="" amjdomingues@gmail.com=""> > wrote: Hi Julie, Thanks! If it is not asking too much and how much work it takes, but adding colours to the background of the circles would also be nice for presentations and papers. Basically some possibilities along the lines of the R package VennDiagram (http://www.biomedcentral.com/1471-2105/12/35) Good package you've developed btw. António On 13 September 2012 15:35, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu <http:="" julie.zhu@umassmed.edu=""> > wrote: Anotonio, Thanks for the great suggestion! Currently makeVennDiagram only supports limited plotting options, i.e., cex and count.col. I will add the title in my to do list. Best regards, Julie On 9/13/12 9:03 AM, "António Miguel de Jesus Domingues" <amjdomingues@gmail.com <http:="" amjdomingues@gmail.com=""> > wrote: > Hi Bioconducters, > > I am comparing 2 list of ChIP peaks obtained with different peak callers > and would like to change some of the graphical options of the plot created > by makeVennDiagram. Crucially I would like to add a title to the plot. > > Is there any way to change the graphical options of makeVennDiagram? > > Cheers, > António [[alternative HTML version deleted]]
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