[BioC] GViz - successes and a few hopes
Cook, Malcolm
MEC at stowers.org
Tue Aug 13 15:57:47 CEST 2013
Florian,
Thanks for the detailed reply.
After a bit more wrangling with both GViz and ggbio I ultimately found that ggbio was able to meet all my needs.
Again, I found your design and documentation clear and consistent. It was a pleasure to learn your package and I am likely to use it again.
Best,
Malcolm
>Hi Malcolm,
>good to hear that Gviz is useful for you. See below for more.
>
>On 8/4/13 10:53 AM, "Cook, Malcolm" <MEC at stowers.org> wrote:
>
>>Florian,
>>
>>I am trying to employ GViz in preparation of figures to accompany a
>>manuscript in which we characterize the effect a protein knock-down has
>>on a particular histone modification profile across selected genes.
>>
>>I find your vignette very well written and helpful in my aims.
>>
>>Is it possible to plot multiple bigwigs on a single track, with distinct
>>colors and alpha blending. I am successfully using the streaming import
>>on bigwig files to load histone occupancy profiles on demand. Great!
>
>Currently there isn't. What is happening behind the scenes for a bigwig
>file is that the necessary data for the requested genomic region is
>extracted and the results are turned into a DataTrack object. From this
>point on, the generic DataTrack plotting method takes over. While
>DataTrack objects do support multiple samples as well as the use of alpha
>blending, the problem really is that bigwig files can only contain data
>for a single sample. This is the only reason why we have this one file <->
>one track limitation.
>
>>
>>I would like to be able to overplot two of these bigwigs on a single
>>track, with distinct colors and alpha blending. is there a backdoor way
>>of accomplishing this?
>
>Of course you could skip the automatic part that streams the bigwig data
>directly into a DataTrack and rebuild this part according to you own
>needs. All it takes is wrapper function that takes in the plotting
>coordinates and maybe a list of bigwig files that you want to merge. This
>function would than dynamically extract the data from the file, build a
>single DataTrack object containing multiple samples and finally plot this
>object using plotTracks. Obviously this would involve a bit of work but it
>shouldn't be too bad. One thing to keep in mind is that a multi sample
>DataTrack can only define a single set of coordinates, which may not be
>the case in your different bigwig files. So you may need to do a bit of
>interpolation, or take the union of all coordinates from all bigwig files.
>
>
>>
>>You documentation says that passing add=TRUE to plotTracks is needed to
>>add the plot to existing canvas without re-initializing. I am writing
>>multiple .png files in an apply, and find that without add=TRUE the
>>chromosome that I am passing i successive calls is not being respected.
>>So, in my hands, add=TRUE is required even though there is no issue of
>>reinitializing or not.
>
>I am afraid I can't follow you on this one. Maybe a short reproducible
>code example would help. I assume that you are calling plotTracks in each
>iteration of your apply function, together with the opening and closing of
>a fresh png device. In this case it should't really matter whether you use
>add=true or add=false. The only purpose of this parameter is to skip
>calling the grid equivalent of plot.new() before starting the actual
>plotting operation. This should have no effect at all on the selected
>chromosome. maybe an example will prove me wrong :-)
>
>>
>>It appears that shape = 'smallArrow' is not respected by GeneRegionTrack
>>and rect is used regardless.
>
>I can't reproduce this on my end. As a matter of fact, the default shape
>for this class is smallArrow, and I see this respected for instance when
>running the examples from the class' man page. Maybe the strand
>information of your object is all '*'? In this cases there will be no
>directional informations, alas, no arrows. Or did you set the stacking to
>'dense'? This may also cause the directional information to be lost when
>several elements have to be merged. Again, a reproducible example would
>help.
>
>>
>>Finally, are there any ways to annotate tracks further with text, shaded
>>boxes, horizontal/vertical lines?
>
>You can do horizontal lines using the 'baseline' parameter, at least for
>DataTrack objects. All other annotations are currently not supported, but
>very high up on my to do list.
>
>>
>>Thanks for a very clear vignette with lots of great examples.
>>
>>~ malcolm_cook at stowers.org / Shilatifard Lab / Compuational Biology
>>
>>
>>PS Is there a preferred way for hearing issues like this, or is email to
>>bioc list the best for you?
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