Hi,

thanks for the information, the plot suggested by you is exactly what I
have right now!
Actually I like the plots that I was able to produce with Gviz a lot.

http://postimg.org/image/u9cs7014f/

The code was produced using a wrapper function, the relevant part producing
the DataTracks looks like:

x<-GeneRegionTrack(txdb,chromosome =
coords$chr,start=coords$start,end=coords$end,showId =
TRUE,geneSymbols=TRUE,name = "Gene Model",col.sampleNames="black"
,background.title="white",col.axis="black",col.title="black",col=1,fill=1
,fontfamily="Helvetica")

axisTrack <- GenomeAxisTrack()

### this happens in a loop

myDataTrack[[i+2]]<-DataTrack(data = bDat[[i]][,2],start=bDat[[i]][,1
],end=bDat[[i]][,1],chromosome=coords$chr,genome="hg19"
,name=myNames[c],ylim=c(mn,mx),type="polygon",fill
.mountain=c(myCols[c],myCols[c]),col.mountain=myCols[c],col.sampleNames=
"black",background.title="white",col.axis="black",col.title="black")


### then plot

myDataTrack[[1]]<-x

myDataTrack[[2]]<-axisTrack

plotTracks(myDataTrack,chromosome =
coords$chr,from=coords$start,to=coords$end)





Similar to my plots your plot has no real X-axis - I can live with that,
but my boss obviously thinks that quantitative data like this is best shown
in a classical x/y-plot (having a real x-axis, same color and style as
y-axis with both axes crossing). I will try to convince him that this is
not necessary.



Best

Maxim





2014-02-25 10:24 GMT+01:00 Dan Du <tooyoung@gmail.com>:

> Hi Maxim,
>
> Perhaps you should read the package vignette more carefully given that
> you had indeed read it, say the first subsection of Track classes maybe.
> Since you had never shown us what you had done with any Gviz related
> codes.
>
> And regarding the cross which you think is important, someone correct me
> if I am wrong, you will never get it with Gviz. Those stacking tracks
> are never mean to be overlapping.
>
> Here is my 2ct if color is all you / your boss want,
>
> data(twoGroups)
> dTrack <- DataTrack(twoGroups, name = "uniform", type='polygon',
> col.axis='red', background.title = "white")
> axisTrack <- GenomeAxisTrack(col='red', fontcolor="red")
> plotTracks(list(dTrack, axisTrack))
>
> HTH,
> Dan
>
>
> On Mon, 2014-02-24 at 20:30 +0100, Maxim wrote:
> > Hi,
> >
> > sorry, you're of course right, my question not phrased correctly. I
> didn't
> > mean "cut", rather cross, better intersect, i.e. a typical coordinate
> > system, where x and y intersect at coordinate (0,0), e.g.:
> >
> > http://en.wikipedia.org/wiki/File:Cartesian-coordinate-system.svg (of
> > course without negative x-values)
> >
> > In contrast to this, all my efforts to plot with Gviz resulted in plots
> > without any x-axis, so my actual question is:
> >
> > how to draw an x-axis in a gviz polygon, mountain or histogram plot? In
> the
> > documentation I couldn't find any parameter that allows setting x-axis
> > related parameters (e.g. color, where is the intersection with y-axis,
> > ticks ...), nor does the manual show an example that would suggest this
> is
> > possible. But perhaps I'm just looking for the wrong descriptions.
> >
> > Furthermore I aim at an axis, that indeed intersects the y-axis, e.g. a
> > plot like
> >
> > plot(1,frame.plot=T)
> >
> > does, whereas
> >
> > plot(1,frame.plot=F)
> >
> > does not. The latter aspect is not that important, having the x-axis (in
> > the same color as the y-axis) is most important!
> >
> > Thank you for your efforts!
> > Best
> > Maxim
> >
> >
> > 2014-02-24 18:28 GMT+01:00 Steve Lianoglou <lianoglou.steve@gene.com>:
> >
> > > Hi,
> > >
> > > On Mon, Feb 24, 2014 at 7:03 AM, Maxim <deeepersound@googlemail.com>
> > > wrote:
> > > > Hi,
> > > >
> > > > since very recently I'm using Gviz for plotting coverage vectors from
> > > > ChIP-seq data. I would like to stick to it as it draws gene models
> much
> > > > nicer than my previous attempts drawing them with my own plotting
> > > > functions. I wonder whether it is possible to have mountain/polygon
> or
> > > > histogram tracks with a continuous x-axis that indeed cuts the
> y-axis, at
> > > > best in the same color as the y-axis? This is because I personally
> like
> > > the
> > > > Gviz plots a lot but my boss expects me to produce typical plots
> with a
> > > > standard x/y coordinate system!
> > >
> > > Can you give a concrete example of what you mean? I'm having a hard
> > > time understanding what "cuts the y-axis" means.
> > >
> > > Perhaps you could provide  graphic of how gviz plots your data now,
> > > and another (perhaps using photoshop) of you you'd like it to look
> > > like.
> > >
> > > -steve
> > >
> > > --
> > > Steve Lianoglou
> > > Computational Biologist
> > > Genentech
> > >
> >
> >       [[alternative HTML version deleted]]
> >
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