[BioC] Set plot title in makeVennDiagram (ChIPpeakAnno)

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 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

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:

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 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).

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

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).

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 Antonio,


See the help for useDevel():


library(BiocInstaller)
?useDevel


Best,


Jim