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
I have suspect that the most common answer to this will be 'don't', for all the reasons statisticians don't like mixing vertical scales on the same plot. See http://www.perceptualedge.com/articles/visual_business_intelligence/dual-scaled_axes.pdf for one article on that topic. But if you must, is there any reason you can't divide the first row by (say) 1000, barplot normally with axes=false, and then put an explicit axis up each side with something like axis(2, at=seq(0,3, 0.5), labels= seq(0,2500,500)) ) #first row axis, left column axis(4) S Ellison> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Adrian > Johnson > Sent: 12 October 2016 17:21 > To: r-help > Subject: [R] barplot beside=TRUE - values differ on scales > > 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.******************************************************************* This email and any attachments are confidential. Any use...{{dropped:8}}
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]]
On 12/10/2016 12:20 PM, Adrian Johnson 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.I would simply rescale one row and add a second axis. For example, if d holds your matrix: scale <- max(d[1,])/max(d[2,]) adjusted <- d adjusted[2,] <- scale*adjusted[2,] barplot(adjusted, beside = TRUE) ticks <- pretty(d[2,]) axis(side = 4, at = ticks*scale, labels = ticks) Duncan Murdoch
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. >> >
Thanks Duncan. I am sorry I cannot scale second row (d[2,]). I was looking for a way to plot d[2,] values next to d[1,] with a right side axis=4 on right side. -2,-1,0,1,2 thanks Adrian On Wed, Oct 12, 2016 at 12:42 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:> On 12/10/2016 12:20 PM, Adrian Johnson 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. > > > I would simply rescale one row and add a second axis. For example, if d > holds your matrix: > > scale <- max(d[1,])/max(d[2,]) > adjusted <- d > adjusted[2,] <- scale*adjusted[2,] > barplot(adjusted, beside = TRUE) > ticks <- pretty(d[2,]) > axis(side = 4, at = ticks*scale, labels = ticks) > > Duncan Murdoch > >
Hi Adrian, Perhaps what you want is this: ajdat<-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" ))) library(plotrix) twoord.plot(0.8:6.8,ajdat[2,],1.2:7.2,ajdat[1,], main="Gene expression by chromosome loss/gain", lylim=c(-2.2,10),lytickpos=-2:2, xtickpos=1:7,xticklab=colnames(ajdat), ylab="Chromosome loss/gain",rylab="GN", type="bar",lcol=2,rcol=3,halfwidth=0.2) Jim On Thu, Oct 13, 2016 at 3:20 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.