[BioC] GViz - successes and a few hopes

[Cook, Malcolm]

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?