Hi Maxim, We consciously chose not to replicate x-axes for each track in a Gviz plot, and I do not think that your boss' argument is valid. Assuming that you have included a GenomeAxis track, the data are plotted along with a proper x-axis annotation. The whole purpose of this sort of visualisation is to make comparison across tracks as easy as possible. The scale of the x-axis is forced to be the same for all of the stacked tracks, and adding axis annotations would just create unnecessary visual clutter. If you need additional ammunition for a discussion with your boss you could refer him to the work of Edward Tufte or Bill Cleveland. If all he needs is a horizontal reference line you can archive that using the baseline display parameter. The following code would create something the looks pretty much like a standard xyplot, however without x-axis annotation. Please note that the innerMargin argument is only available in the current devel version. plotTracks(dtTrack, baseline=0, innerMargin=0, frame=T, col.baseline=1, col.axis=1, background.title=NA) Florian On 2/25/14 3:03 PM, "James W. MacDonald" <jmacdon at="" uw.edu=""> wrote: >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$end,showId = >> TRUE,geneSymbols=TRUE,name = "Gene Model",col.sampleNames="black" >> >>,background.title="white",col.axis="black",col.title="black",col=1,f ill=1 >> ,fontfamily="Helvetica") >> >> axisTrack <- GenomeAxisTrack() >> >> ### this happens in a loop >> >> myDataTrack[[i+2]]<-DataTrack(data = bDat[[i]][,2],start=bDat[[i]][,1 >> ],end=bDat[[i]][,1],chromosome=coords$chr,genome="hg19" >> ,name=myNames[c],ylim=c(mn,mx),type="polygon",fill >> .mountain=c(myCols[c],myCols[c]),col.mountain=myCols[c],col.sampleN ames= >> "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 >>>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor > >-- >James W. MacDonald, M.S. >Biostatistician >University of Washington >Environmental and Occupational Health Sciences >4225 Roosevelt Way NE, # 100 >Seattle WA 98105-6099 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor