[BioC] GViz - successes and a few hopes

Cook, Malcolm MEC at stowers.org
Sun Aug 4 10:53:24 CEST 2013


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!

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?

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.

It appears that shape = 'smallArrow' is not respected by GeneRegionTrack and rect is used regardless.

Finally, are there any ways to annotate tracks further with text, shaded boxes, horizontal/vertical lines?

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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