[R] barplot beside=TRUE - values differ on scales

[Adrian Johnson]

Hello Dr. Carlson,
thanks for the tip. It is exactly what I am looking for.

I see the trick lies in
axis(4, c(-1000, -500, 0, 500, 1000), c(-2, -1, 0, 1, 2))

Would you please help understand why two different vectors of ranges
are defined and yet I see only vector with -2,-1,0,1,2 is visible.

Thanks a lot.
Adrian





On Wed, Oct 12, 2016 at 3:46 PM, David L Carlson <dcarlson at tamu.edu> wrote:
> Are you looking for something like this?
>
> Assuming your data is d:
>
>> d[2, ] <- d[2, ]*500
>> oldp <- par(mar=c(4.1, 4.1, 4.1, 4.1))
>> barplot(d, ylim=c(-1000, 3000), beside=TRUE, axes=FALSE)
>> axis(2, c(0, 1000, 2000, 3000))
>> axis(4, c(-1000, -500, 0, 500, 1000), c(-2, -1, 0, 1, 2))
>> mtext("GN", 2, 2)
>> mtext("CN", 4, 2, at=0)
>> par(oldp)
>
>
>
> -------------------------------------
> David L Carlson
> Department of Anthropology
> Texas A&M University
> College Station, TX 77840-4352
>
>
>
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Adams, Jean
> Sent: Wednesday, October 12, 2016 12:44 PM
> To: Adrian Johnson
> Cc: r-help
> Subject: Re: [R] barplot beside=TRUE - values differ on scales
>
> Adrian,
>
> Very interesting.
>
> What do you think of using colors to indicate the five possible loss/gain
> levels?
> For example:
>
> a <- structure(c(112L, 0L, 579L, 1L, 131L, 1L, 2234L, 2L, 2892L, 1L,
>   528L, 0L, 582L, 2L), .Dim = c(2L, 7L), .Dimnames = list(c("GN",
>   "CN"), c("DC5", "DC8", "DC14", "DC18", "DC19", "DC20", "DC23"
>   )))
>
> loss.gain <- c(-2, -1, 0, 1, 2)
> colorz <- c("blue", "lightblue", "gray", "orange", "red")
> barplot(a["GN", ], col=colorz[match(a["CN", ], loss.gain)])
>
> Jean
>
> On Wed, Oct 12, 2016 at 11:55 AM, Adrian Johnson <oriolebaltimore at gmail.com>
> wrote:
>
>> Hi Adams,
>> The story I am trying to show visually relationship between GN and CN
>> for every column. Each column represents a patient. In each patient, a
>> particular chromosome region (CN) is either lost (-2 or -1) or gained
>> (1 or 2). Typically if loss (one copy loss - as humans have pair of
>> chromosome) or homozygous (two copies loss) theoretically indicate
>> decrease in number of copies of gene located in that region of
>> chromosome. The number of copies of a gene located in that chromosomal
>> regions are indicated by GN.
>> through this barplot, I intend to show that in 7 cases (columns) if a
>> relationship exist by plotting GN and CN next to each other.  If I log
>> values in GN, I am loosing the minor differences between cases in GN.
>> hope I could convince/explain.
>> thanks
>> adrian
>>
>> On Wed, Oct 12, 2016 at 12:36 PM, Adams, Jean <jvadams at usgs.gov> wrote:
>> > Adrian,
>> >
>> > What story are you trying to tell?  Or what question are you trying to
>> > answer by visualizing these data?  How is a bar plot of these numbers
>> going
>> > to help?  I'm just wondering if perhaps a different visualization might
>> make
>> > more sense, for example, a scatter plot of GN vs. CN.
>> >
>> > m <- structure(c(112L, 0L, 579L, 1L, 131L, 1L, 2234L, 2L, 2892L, 1L,
>> >   528L, 0L, 582L, 2L), .Dim = c(2L, 7L), .Dimnames = list(c("GN",
>> >   "CN"), c("DC5", "DC8", "DC14", "DC18", "DC19", "DC20", "DC23"
>> >   )))
>> > plot(m["GN", ], m["CN", ])
>> >
>> > Jean
>> >
>> >
>> > On Wed, Oct 12, 2016 at 11:20 AM, Adrian Johnson <
>> oriolebaltimore at gmail.com>
>> > wrote:
>> >>
>> >> Dear group,
>> >> I have been struggling to barplot two different measurements from one
>> >> subject. These two measures differ in range.  I want to plot row 1
>> >> axis on left side and row 2 values on right side.
>> >>
>> >> For a given column I want to plot GN and CN next to each other.
>> >>
>> >> my dput code is below
>> >> :
>> >>
>> >> structure(c(112L, 0L, 579L, 1L, 131L, 1L, 2234L, 2L, 2892L, 1L,
>> >> 528L, 0L, 582L, 2L), .Dim = c(2L, 7L), .Dimnames = list(c("GN",
>> >> "CN"), c("DC5", "DC8", "DC14", "DC18", "DC19", "DC20", "DC23"
>> >> )))
>> >>
>> >>
>> >> As you can see:
>> >>    DC5 DC8 DC14 DC18 DC19 DC20 DC23
>> >> GN 112 579  131 2234 2892  528  582
>> >> CN   0   1    1    2    1    0    2
>> >>
>> >> GN values are range from 100 - 3000
>> >> while CN are always -2 or -1 or 0 or 1 or 2
>> >>
>> >> Also I cannot log GN values and plot because a difference in 100 units
>> >> also matters in my experiment.
>> >>
>> >> Any help would be greatly appreciated.
>> >>
>> >> Thanks
>> >> Adrian
>> >>
>> >> ______________________________________________
>> >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>> >> PLEASE do read the posting guide
>> >> http://www.R-project.org/posting-guide.html
>> >> and provide commented, minimal, self-contained, reproducible code.
>> >>
>> >
>>
>>
>
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>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> and provide commented, minimal, self-contained, reproducible code.