Hi Wan Ting,
I have a vague memory that the code that does autoscaling for xyplot
changed at some point recently. However, I can't find any thread that
talks about this. Therefore, I'm throwing your query to the GBrowse
list, in the hopes that someone there has a better memory than I do.
I suspect that this change may have been deliberate. Scaling across a
large range of values is difficult. If you don't change the scale
from region to region, small values get lost. If you do change scale,
then users have to pay close attention to the scale bars on each page.
Dave C.
On Mon, Sep 14, 2009 at 3:10 AM, POH Wan Ting <
pohwat1@...> wrote:
> Hi,
>
>
>
> I have just installed GBrowse1.9971 and it seems that the density plots will
> not be rescaled according (attached: densitytrack.png). I tried using the
> same conf settings on another server with the old gbrowse and it turns out
> well (attached: old_density.png). And according to
> Bio::Graphics::Glyph::xyplot,
>
> -max_score Maximum value of the feature's "score" attribute
> [Default: Calculated]
>
>
>
>
>
> Conf file:
>
> aggregators = profilePosDensity{intensity:FME715_density_positive}
>
> [PosDensity]
>
> feature = profilePosDensity
>
> glyph = xyplot
>
> graph_type = boxes
>
> height = 50
>
> min_score = 0
>
> scale = both
>
> fgcolor = red
>
> bgcolor = red
>
> label = 0
>
> category = FME715
>
> citation =
>
> key = FME715 Positive Density
>
>
>
> gff file:
>
> chr1 FME715_density_positive intensity 1 3003353 0
> . . Density FME715_density_positive
>
> chr1 FME715_density_positive intensity 3003354 3003403 1
> . . Density FME715_density_positive
>
> chr1 FME715_density_positive intensity 3003404 3015750 0
> . . Density FME715_density_positive
>
> chr1 FME715_density_positive intensity 3015751 3015780 1
> . . Density FME715_density_positive
>
> chr1 FME715_density_positive intensity 3015781 3027621 0
> . . Density FME715_density_positive
>
> chr1 FME715_density_positive intensity 3027622 3027655 1
> . . Density FME715_density_positive
>
> chr1 FME715_density_positive intensity 3027656 3077266 0
> . . Density FME715_density_positive
>
> chr1 FME715_density_positive intensity 3077267 3077316 1
> . . Density FME715_density_positive
>
> chr1 FME715_density_positive intensity 3077317 3116697 0
> . . Density FME715_density_positive
>
> chr1 FME715_density_positive intensity 3116698 3116729 2
> . . Density FME715_density_positive
>
>
>
> Thank you. Your help is very much appreciated.
>
>
>
>
>
> Best Regards,
>
> Wan Ting
>
>
>
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