[Gmod-ajax] SNPcoverage histogram scale

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[Gmod-ajax] SNPcoverage histogram scale

Chathura Gunasekara
hi all,

Is it possible to Change the SNP coverage histogram scale. As shown in the figure the top histogram scale is 0 - 400 and the bottom histogram scale is 0-100. Is it possible to have same scale for both histograms ? 

That way it seems the change is more easily visible.



Inline image 2

Thank you.

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Chathura

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Re: SNPcoverage histogram scale

Colin
You can set the max_score attribute on the track if you know what the max_score will be. For example, set max_score=100 on both tracks.

-Colin

On Mon, Jan 30, 2017 at 12:17 PM, Chathura Gunasekara <[hidden email]> wrote:
hi all,

Is it possible to Change the SNP coverage histogram scale. As shown in the figure the top histogram scale is 0 - 400 and the bottom histogram scale is 0-100. Is it possible to have same scale for both histograms ? 

That way it seems the change is more easily visible.



Inline image 2

Thank you.

--
Chathura

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Re: SNPcoverage histogram scale

Colin
Additionally, you might consider https://github.com/elsiklab/multibigwig, which plots multiple bigwigs on a single track, thereby putting them both on the same scale automatically :)

-Colin

On Mon, Jan 30, 2017 at 3:35 PM, Colin <[hidden email]> wrote:
You can set the max_score attribute on the track if you know what the max_score will be. For example, set max_score=100 on both tracks.

-Colin

On Mon, Jan 30, 2017 at 12:17 PM, Chathura Gunasekara <[hidden email]> wrote:
hi all,

Is it possible to Change the SNP coverage histogram scale. As shown in the figure the top histogram scale is 0 - 400 and the bottom histogram scale is 0-100. Is it possible to have same scale for both histograms ? 

That way it seems the change is more easily visible.



Inline image 2

Thank you.

--
Chathura

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Re: SNPcoverage histogram scale

Colin
In reply to this post by Colin
You could do this via tracks.conf too, you just add a line that says max_score=1200, but trackList.json and tracks.conf can both co-exist, and can represent the same types of information. More info here http://gmod.org/wiki/JBrowse_Configuration_Guide#Configuration_Loading.2C_Files.2C_and_Formats




-Colin

On Mon, Jan 30, 2017 at 3:48 PM, Chathura Gunasekara <[hidden email]> wrote:
Thanks Colin, 
It worked by add thing this code to the json file. 

so this can be set only through trackList.json file as ,
{
         "storeClass"  :  "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "./S156157/S156157.sorted.bam",
         "label"       : "STTM_sorted.bam_coverage",
         "type"        : "JBrowse/View/Track/FeatureCoverage",
         "min_score"   : 0,
         "max_score"   : 1200,
         "key"         : "STTM_SNP_Coverage"
      }


right ?
not in the tracks.conf. file ?



On Mon, Jan 30, 2017 at 3:35 PM, Colin <[hidden email]> wrote:
You can set the max_score attribute on the track if you know what the max_score will be. For example, set max_score=100 on both tracks.

-Colin

On Mon, Jan 30, 2017 at 12:17 PM, Chathura Gunasekara <[hidden email]> wrote:
hi all,

Is it possible to Change the SNP coverage histogram scale. As shown in the figure the top histogram scale is 0 - 400 and the bottom histogram scale is 0-100. Is it possible to have same scale for both histograms ? 

That way it seems the change is more easily visible.



Inline image 2

Thank you.

--
Chathura

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Chathura


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