#10 negative numbers in the xyplot (expression) tracks

[albert vilella bertran]

Hi all,

I would like gbrowse to be able to render negative
numbers in the
xyplot (expression) tracks. AFAICS, the expression
tracks rely on
xyplot.pm module in Bio::Graphics. Right now,
expression plots are
only accepting positive scores, as this was initially
meant to be used
for expression analysis annotations.

Yet, there are a number of statistics of interest to be
plotted along
a genomic region that can take negative numbers. In
population
genomics, Tajima_D test of neutrality being an example.

As of today, there isn't, to my knowlegde, any way to
add a custom
annotation xyplot track that contains negative "scores"
and that is
properly rendered by gbrowse.

Here an example file:

--------------------------------------------------------------------------------
[expression]
glyph = xyplot
graph_type=boxes
fgcolor = black
bgcolor = blue
height=10
min_score=-3
max_score=3
label=1
key=Tajima_D

reference=CFTR
expression european_american 10000..12000
score=-0.02
expression european_american 12001..19999
score=0.001
expression european_american 20000..25000
score=-1
expression chinese 10000..12000 score=2
expression chinese 12001..19999 score=-0.5
expression chinese 20000..25000 score=3
--------------------------------------------------------------------------------

This file would be wrongly rendered right now in gbrowse:

http://wallace.bio.ub.es/screenshot1.png (124k)

Does anyone has any hint of what is needed to add this
feature?
Which source files should I be looking at?

Thanks in advance,

Albert.

[Nobody/Anonymous]

Logged In: NO

The xyplot glyph in bioperl CVS now includes
preliminary support for negative values.

[Lincoln Stein]

Logged In: YES
user_id=224205

The CVS versions of gbrowse and bioperl now support
negative numbers correctly.