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

[David L Carlson]

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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