[BioC] Gviz: axes related parameters

Tue Feb 25 15:03:39 CET 2014

Hi Maxim,

I am not sure I understand why you claim there is no horizontal axis on 
these plots. The GenomeAxisTrack shows the only 'x-axis' information 
that is relevant to these data, and there is one right there in the 
plot!

What more information could possibly be conveyed to your boss or 
potential manuscript readers by repeating the same information six 
times in the DataTrack?

Best,

Jim

On Tuesday, February 25, 2014 8:35:46 AM, Maxim wrote:
> 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 at 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 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
>>>>
>>>
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>>>
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>>
>>
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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