[BioC] multiple pairs plot in a single window
James W. MacDonald
jmacdon at uw.edu
Tue Mar 19 15:52:54 CET 2013
Hi Natasha,
I see. Well, you can't use either split.screen() or par(mfrow()) and
pairs() at the same time, as the pairs() function itself internally uses
par(mfrow()) to create all the pairs plots. So what happens is you are
changing the graphics settings, then the pairs() function saves those
parameters, sets them the way it needs them, does the plot, and the
resets back to your settings before exiting.
Anyway, I am not entirely clear what you want. If you simply want a
single file with four pages in it, then you want to use a pdf output.
IIRC, none of the other graphics drivers support multiple pages. If you
really want them all on a single page, then you might need to write a
function of your own based in part on the code in pairs().
Best,
Jim
On 3/19/13 6:12 AM, Natasha Sahgal wrote:
> Hi Jim,
>
> Sorry, didn't realise.
>
> The pairs function from the graphics package. So if I do something like:
>
> png("Data4.png")
> pairs(d, upper.panel=panel.cor, labels=group, main="Data 4")
> dev.off()
>
> it works, and I generate 4 separate scatterplots for each dataset.
>
> However I want all 4 plots in a single figure/file, rather than having 4 separate files. (I.e. 1 row with 4 columns, or 2 rows with 2 columns each).
>
> Thus, I then tried,
>
> png("AllData.png")
> par(mfrow=c(1,4))
> pairs(a, upper.panel=panel.cor, labels=group, main="Data 1")
> pairs(b,upper.panel=panel.cor,labels=group,main="Data 2")
> pairs(c, upper.panel=panel.cor,labels=group,main="Data 3")
> pairs(d, upper.panel=panel.cor, labels=group, main="Data 4")
> dev.off()
>
> But this did not give me a single plot window with all 4 plots, rather just the last plot for Data 4. Then I found the split.screen function (graphics package), the code in my previous email, but that too gave just the final plot for data 4 (and this did look weird!)
>
>
> My Data is basically 4 datasets (e.g. array &/or RNA-Seq) each with 4 samples.
>
>
> Hope that makes sense.
>
> Many Thanks,
> Natasha
>
>
> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] scatterplot3d_0.3-33 Hmisc_3.10-1 survival_2.36-14
> [4] DESeq_1.10.1 lattice_0.20-10 locfit_1.5-8
> [7] Biobase_2.18.0 BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] annotate_1.36.0 AnnotationDbi_1.20.2 cluster_1.14.3
> [4] DBI_0.2-5 genefilter_1.40.0 geneplotter_1.36.0
> [7] grid_2.15.2 IRanges_1.16.4 parallel_2.15.2
> [10] RColorBrewer_1.0-5 RSQLite_0.11.2 stats4_2.15.2
> [13] tools_2.15.2 XML_3.95-0.1 xtable_1.7-0
>
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at uw.edu]
> Sent: 18 March 2013 20:44
> To: Natasha Sahgal
> Cc: Bioconductor mailing list
> Subject: Re: [BioC] multiple pairs plot in a single window
>
> Hi Natasha,
>
> The pairs() function from what package? By 'didn't work' what exactly do you mean? You are not giving us much to go on here.
>
> Best,
>
> Jim
>
>
> On 3/18/13 7:59 AM, Natasha Sahgal wrote:
>> Dear List,
>>
>> I have 4 datasets and am interested in generating a pairs plot for each.
>> However, I'm interested in all the 4 pairs plots to be in a single window.
>>
>> I tried mfrow but that didn't work, then I tried split.screen (code below) but that doesn't work either.
>>
>> # Window With 2 Rows, Top & Bottom Row In 2 Columns
>> #jpeg("multScatter.jpg",height=1000,width=1000)
>> split.screen(c(2,1)) # Makes Screen 1 and 2 split.screen(c(1,2),
>> screen=1) # Makes Screen 3 and 4 split.screen(c(1,2), screen=2) #
>> Makes Screen 5 and 6
>>
>> # Pairs plots on Screens 3, 4, 5 & 6
>> screen(3)
>> pairs(a, upper.panel=panel.cor, labels=group, main="Data 1")
>> screen(4)
>> pairs(b,upper.panel=panel.cor,labels=group,main="Data 2")
>> screen(5)
>> pairs(c, upper.panel=panel.cor,labels=group,main="Data 3")
>> screen(6)
>> pairs(d, upper.panel=panel.cor, labels=group, main="Data 4")
>> #dev.off()
>>
>> ###############
>>
>> # Window With 1 Rows and 4 columns
>> #jpeg("multScatter.jpg",height=1000,width=1000)
>> split.screen(c(1,4)) # Makes Screen 1 to 4
>> screen(1)
>> pairs(a, upper.panel=panel.cor, labels=group, main="Data 1")
>> screen(2)
>> pairs(b,upper.panel=panel.cor,labels=group,main="Data 2")
>> screen(3)
>> pairs(c, upper.panel=panel.cor,labels=group,main="Data 3")
>> screen(4)
>> pairs(d, upper.panel=panel.cor, labels=group, main="Data 4")
>> #dev.off()
>>
>> Any help or alternatives would be highly appreacited!
>>
>>
>> ManyThanks,
>> Natasha
>>
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