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
>

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