FAQ

[BioC] Set plot title in makeVennDiagram (ChIPpeakAnno)

António Miguel de Jesus Domingues
Sep 13, 2012 at 1:03 pm
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: dom...@...de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology
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7 responses

  • Zhu, Lihua (Julie) at Sep 13, 2012 at 1:35 pm
    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"
    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
  • António Miguel de Jesus Domingues at Sep 13, 2012 at 1:41 pm
    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) 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"
    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: dom...@...de
    tel. +49 351 210 2481
    The Unbearable Lightness of Molecular Biology
  • Zhu, Lihua (Julie) at Sep 13, 2012 at 1:45 pm
    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" 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) 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"
    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
  • Zhu, Lihua (Julie) at Sep 15, 2012 at 3:03 am
    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"),
    totalTest0,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" 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) 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"
    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
  • António Miguel de Jesus Domingues at Sep 18, 2012 at 8:03 am
    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) 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" <
    amj...@...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) 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"
    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: dom...@...de
    tel. +49 351 210 2481
    The Unbearable Lightness of Molecular Biology
  • Zhu, Lihua (Julie) at Sep 18, 2012 at 1:36 pm
    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/ChIPpeakAnno/

    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" 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) 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" <amj...@...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) <jul...@...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"
    <amj...@...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
  • James W. MacDonald at Sep 18, 2012 at 1:57 pm
    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)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"),
    totalTest0,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)<jul...@...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"
    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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