[BioC] Set plot title and background in makeVennDiagram (ChIPpeakAnno)

James W. MacDonald jmacdon at uw.edu
Tue Sep 18 15:57:58 CEST 2012


Hi Antonio,

See the help for useDevel():

library(BiocInstaller)
?useDevel

Best,

Jim



On 9/18/2012 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)<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, "António 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.
>>
>> António
>>
>> 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, "António 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,
>>> António
>>
>>
>>
>
>
>
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-- 
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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