[BioC] Gviz: axes related parameters

[Dan Du]

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 at gene.com>:
> 
> > Hi,
> >
> > On Mon, Feb 24, 2014 at 7:03 AM, Maxim <deeepersound at 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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