wiggle_density and no neg_colors

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wiggle_density and no neg_colors

Sofia Robb-4
I am using wiggle_density glyph and I cannot get the neg_color to show up. They appear as white.

I have tried with and without including fg_color, it seems to make no difference. How can I get this to work?

wig:
Chr10 149387 149388 -100.0
Chr10 149466 149467 100.0
Chr10 149467 149468 90.0
Chr10 149532 149533 100.0
Chr10 149533 149534 90.9

[NB_CpG_Wig]
feature        = methylated_cytosine:CpG_NB
glyph          = wiggle_density
height         = 30
bicolor_pivot =  zero
fgcolor        = purple
pos_color        = purple
neg_color        = black
description    = 0
category       = Methylation
key            = NB:CpG Methylation Profile


Thanks,
Sofia

--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside


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Re: wiggle_density and no neg_colors

Timothy Parnell
Hi Sofia,

The wiggle_density glyph works best with continuous genomic data. Think Bam coverage or conservation scores, where every base has a score.

Your sample wig appears to be fairly sparse, representing only (I assume) CpG dinucleotides. All of those intervening bases will be no score, so will appear white. Have you zoomed in to individual data points? You should see a vertical line in the designated color at each scored interval.

Have you tried switching to a different glyph, like xyplot_glyph, and do you see the data points then? I think with this variable sparse data you would be better served with this glyph instead of wiggle_density.

Tim

On Dec 18, 2013, at 12:39 PM, Sofia Robb <[hidden email]> wrote:

> I am using wiggle_density glyph and I cannot get the neg_color to show up. They appear as white.
>
> I have tried with and without including fg_color, it seems to make no difference. How can I get this to work?
>
> wig:
> Chr10 149387 149388 -100.0
> Chr10 149466 149467 100.0
> Chr10 149467 149468 90.0
> Chr10 149532 149533 100.0
> Chr10 149533 149534 90.9
>
> [NB_CpG_Wig]
> feature        = methylated_cytosine:CpG_NB
> glyph          = wiggle_density
> height         = 30
> bicolor_pivot =  zero
> fgcolor        = purple
> pos_color        = purple
> neg_color        = black
> description    = 0
> category       = Methylation
> key            = NB:CpG Methylation Profile
>
>
> Thanks,
> Sofia
>
> --
> Sofia Robb, Ph.D
> Wessler and Stajich Laboratories
> University of California Riverside
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Re: wiggle_density and no neg_colors

Sofia Robb-4
Hi Tim,

Thanks for your reply.

Attached is a screen shot of my wiggle_density of CpG dinucleotides (just as you guessed).  As you can see, the positions without data have no box ( which is perfect!!), and the positions with data have a box (also perfect!! ). The boxes (with data) are either colored purple or white. I have carefully checked my data, and at the bps of the white boxes have a negative score in the wig files. (Chr2 1678361 1678362 -100.0)

I just feel as though I am missing something simple. Here is the sample of what I would like to do ( http://gmod.org/wiki/Glyphs_and_Glyph_Options#wiggle_density). It seems as though it should be sooo possible!

 I have tried the xyplot (i attached another image), the neg_color works, but does not look anywhere as nice as the density glyph, it looks so cluttered.

Thanks again,
Sofia


On Wed, Dec 18, 2013 at 4:02 PM, Timothy Parnell <[hidden email]> wrote:
Hi Sofia,

The wiggle_density glyph works best with continuous genomic data. Think Bam coverage or conservation scores, where every base has a score.

Your sample wig appears to be fairly sparse, representing only (I assume) CpG dinucleotides. All of those intervening bases will be no score, so will appear white. Have you zoomed in to individual data points? You should see a vertical line in the designated color at each scored interval.

Have you tried switching to a different glyph, like xyplot_glyph, and do you see the data points then? I think with this variable sparse data you would be better served with this glyph instead of wiggle_density.

Tim

On Dec 18, 2013, at 12:39 PM, Sofia Robb <[hidden email]> wrote:

> I am using wiggle_density glyph and I cannot get the neg_color to show up. They appear as white.
>
> I have tried with and without including fg_color, it seems to make no difference. How can I get this to work?
>
> wig:
> Chr10 149387  149388  -100.0
> Chr10 149466  149467  100.0
> Chr10 149467  149468  90.0
> Chr10 149532  149533  100.0
> Chr10 149533  149534  90.9
>
> [NB_CpG_Wig]
> feature        = methylated_cytosine:CpG_NB
> glyph          = wiggle_density
> height         = 30
> bicolor_pivot =  zero
> fgcolor        = purple
> pos_color        = purple
> neg_color        = black
> description    = 0
> category       = Methylation
> key            = NB:CpG Methylation Profile
>
>
> Thanks,
> Sofia
>
> --
> Sofia Robb, Ph.D
> Wessler and Stajich Laboratories
> University of California Riverside
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside


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Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
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