[BioC] GViz Annotation Track Stacking

Hahne, Florian florian.hahne at novartis.com
Tue May 20 09:07:19 CEST 2014


Hi Lance,
All of this should be happening in the .computeGroupRange function in
Gviz.R.
The following switch statement seems to do something reasonable for the
left or right justification, but ignores any extra space for above and
below. Should be trivial to fix:
 switch(as.character(just),
                       "left"={
                           if(!rev){
                               start(finalRanges) <- start(finalRanges) -
(spaceBefore + labelWidths + spaceAfter)
                           }else{
                               end(finalRanges) <- end(finalRanges) +
spaceAfter + labelWidths + spaceBefore
                           }
                           sb <- spaceBefore
                           sa <- spaceAfter
                       },
                       "right"={
                           if(!rev){
                               end(finalRanges) <-  end(finalRanges) +
spaceAfter + labelWidths + spaceBefore
                           }else{
                               start(finalRanges) <- start(finalRanges) -
(spaceBefore + labelWidths + spaceAfter)
                           }
                           sb <- spaceBefore
                           sa <- spaceAfter
                       },
                       "above"={
                           sa <- sb <- 0
                       },
                       "below"={
                           sa <- sb <- 0
                       },
                       stop(sprintf("Unknown label justification '%s'",
just)))





On 19/05/14 17:05, "Lance Parsons" <lparsons at princeton.edu> wrote:

>I've recently started using the option to put group labels below the
>features in Gviz 1.8.1 AnnotationTracks (just.group="below").  However,
>I have noticed that when the label is larger than the feature, the
>stacking algorithm does not move the features onto a separate line as it
>does when justification is to the left.  See the example photos:
>
>just.group="left": http://imgur.com/VfUN3G0
>
>just.group="below": http://imgur.com/zmRGtxD
>
>I have been putting the labels below since that often makes it clearer
>which feature is being labeled (at least in my cases with small
>features). I'd be willing to help work on a patch for this, but could
>use a little help finding the relevant code.  It'd be great to update
>the stacking code to account for label widths below the feature as well
>as to have an option to control the spacing when a label is to the left
>(or right) of a feature.
>
>-- 
>Lance Parsons - Scientific Programmer
>134 Carl C. Icahn Laboratory
>Lewis-Sigler Institute for Integrative Genomics
>Princeton University
>



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