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. >> >
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]]
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 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.