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

[Adrian Johnson]

As Dr.Murdoch suggested, transformation of row 2 is important to make
sense in graphical depiction.
Thanks to all.


On Wed, Oct 12, 2016 at 4:25 PM, Adrian Johnson
<oriolebaltimore at gmail.com> wrote:
> 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.
>>> >>
>>> >
>>>
>>>
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.