Re: [Gmod-gbrowse] wiggle questions

[Sheldon M. <she...@gm...>]

Hi Joan,

Assuming you are using local, rather than uploaded wiggle files.

> 1. On the WiggleTracks page->
> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
> In the first example image, the description is to the left of the
> wiggletrack
> while further down, it is under the track. How can I designate my
> preference?
> Mine are coming up underneath the track and I'd rather have it to the side.

The label_position in the first example is set to "left" and "top" in
the later example.

You control this in your config stanza
[WTRACK]
glyph = wiggle_density
label_position = left

For the description, it is usually on the bottom in a blue font.  If
you want to have description text on the left, you can use a callback
to add the desired text to the label, then use label_position = left

[WTRACK]
glyph = wiggle_density
label_position = left
label = sub {
    my $f = shift;
    my ($desc) = $f->attributes('Note');
    $desc ||= $f->source_tag;
    return $desc;
  }

However, take care that your description is not too long, or it will
be clipped on the left-hand side.  You also need to set a generous
image padding in your config (image_padding = xxx) so there is room
for your left-hand label.

NB: If you are uploading the data, rather than using it locally, you
can't use the "label=sub{...}" callback.  However, you can edit the
GFF (the GFF is what you get after you click 'Edit' after uploading a
WIG file) and add (or edit) a Name=Your+description+text; to each
line.  That way the label should grab the text by default.


> 2. Is there a limit to the number of features I put in a track.
> Right now, I have 70,000 SNPs each with 150 statistical tests associated
> with them.
> Is this going to crash?

Could you clarify?  You want 150 data points/snp?  Could you send a
sample of the data?

> I am trying to debug problems, sometimes the wiggle track is displayed as  a
> solid band,
> I wonder if that is a problem with size, or getting timed out  or something.
> Should they be cut up into smaller files representing regions of the
> chromosome?

It would be helpful to have your config info plus some sample data here

> 3. What do the color intensities represent?  Is the scale determined by max
> and min of each individual wig file?

Yes.  You can use autoscaling or fix the scale via the max_score and
min_score options

> Is default (no transformation) a linear scale?
Yes.

> If I want all tracks to have the same
> scale, how would I designate that.

use the same max_score and min_score for each track.


Sheldon

-- 
Sheldon J. McKay, PhD
Research Investigator
Cold Spring Harbor Laboratory
Office: 516-367-6998
Fax: 516 367-6851
Email: mc...@cs...
Skype: mckays630