Display a heat map like glyph for transcriptional profile data in wiggle format

[Tripti Grover]

Hi all,

I uploaded expression scores for my data using wiggle file (glyph : wiggle_density)  in variable step format using Mysql backend on mac os x, The expression scores  for my data range from 0 to 14. Currently the transcriptional profile is being displayed in a single color with lighter shade depicting less expression and darker one indicating more.

I have been trying to display the same data using a glyph, like the one we see in heat maps corresponding to an RGB scale  so that variation in expression level could be seen as a range of different colors instead of shades of just one color. How do i implement this with the same wiggle file in variable step format so that the same data could be implemented using a mysql backend??

Thanks in advance
--
Tripti Grover
Junior Research Fellow
Dept. of Plant Molecular Biology
University of Delhi South Campus
New Delhi-110021

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[Sheldon McKay-3]

Hi Tripti,

The full rainbow of colors is unfortunately not currently supported in
the wiggle_density glyph but you can do a two-color heat map using the
configuration options below.  How it works is that all values above or
below a pivot point (the mean value or zero), are plotted in your
choice of two different colors.

bicolor_pivot:
Where to pivot the two colors when drawing bicolor plots.  Options are
"mean" and "zero".  A numeric value can also be provided.

pos_color:
When drawing bicolor plots, the fill color to use for values that are
above the pivot point.

neg_color:
When drawing bicolor plots, the fill color to use for values that are
below the pivot point.


There is a heat_map glyph that uses the HSV color space that will let
you walk through the whole color spectrum.  However, the data would
have to be loaded as regular GFF (with the numerical value in the
sixth column).  If your data are really dense, this will not scale
well and it is best to stick with wiggle.

Sheldon


On Fri, Oct 16, 2009 at 1:24 PM, Tripti Grover <tripti.grover@...> wrote:

> Hi all,
>
> I uploaded expression scores for my data using wiggle file (glyph :
> wiggle_density)  in variable step format using Mysql backend on mac os x,
> The expression scores  for my data range from 0 to 14. Currently the
> transcriptional profile is being displayed in a single color with lighter
> shade depicting less expression and darker one indicating more.
>
> I have been trying to display the same data using a glyph, like the one we
> see in heat maps corresponding to an RGB scale  so that variation in
> expression level could be seen as a range of different colors instead of
> shades of just one color. How do i implement this with the same wiggle file
> in variable step format so that the same data could be implemented using a
> mysql backend??
>
> Thanks in advance
> --
> Tripti Grover
> Junior Research Fellow
> Dept. of Plant Molecular Biology
> University of Delhi South Campus
> New Delhi-110021
>
>
>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

Sent from Milford, CT, United States

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