[Gmod-ajax] SNP coverage histogram color

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[Gmod-ajax] SNP coverage histogram color

Chathura Gunasekara

​Hello,
Is there a way to change the histogram color of the SNP coverage.
Inline image 1

​For example this gray color is not prominent when i try to use this kind of image for a publication.
If I want to change it to purple, can i do that ?
​Thank you​


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Re: SNP coverage histogram color

Ke Jiang
Isn't this the point of SNP coverage track type: to highlight SNPs with colors but fade others in grey coverage? If you'd like to make publication quality plots for coverage, I suggest you to use the "coverage" track or custom coverage track from BigWig files.

Ke

On Mon, Jan 16, 2017 at 11:01 PM, Chathura Gunasekara <[hidden email]> wrote:

​Hello,
Is there a way to change the histogram color of the SNP coverage.
Inline image 1

​For example this gray color is not prominent when i try to use this kind of image for a publication.
If I want to change it to purple, can i do that ?
​Thank you​


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Re: SNP coverage histogram color

Keiran Raine
In reply to this post by Chathura Gunasekara
Hi Chathura,

Not sure if this is exactly what you need, but take a look at the plugin proportialmultibw:




Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 4983
Office: H104

On 17 Jan 2017, at 04:01, Chathura Gunasekara <[hidden email]> wrote:


​Hello,
Is there a way to change the histogram color of the SNP coverage.
<Screen Shot 2017-01-16 at 10.01.40 PM.JPG>

​For example this gray color is not prominent when i try to use this kind of image for a publication.
If I want to change it to purple, can i do that ?
​Thank you​


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Re: SNP coverage histogram color

Colin
It is sort of a "hidden setting", but you can actually change colors on the SNPCoverage track using CSS

See css/sequence.css:

/* colors for bases must be specified as hex or rgb/hsl strings, no named colors such as 'red' */
.base_n {
    background-color: #C6C6C6;
}
.base_a {
    background-color: #00BF00;
}
.base_c {
    background-color: #4747ff;
}
.base_t {
    background-color: #f00;
}
.base_g {
    background-color: #d5bb04;
}
.base_reference {
    background-color: #a33;
}
.base_deletion {
    background-color: #999;
}

.sequence.nocolor .base {
    background-color: #ddd;
}


If you change those, it will be reflected in your SNPCoverage track. 

The .base_reference is the background grey of the SNPCoverage plot, and if you actually add to the list and make .base_skip you can make the intron grey change color.

-Colin

On Tue, Jan 17, 2017 at 9:11 AM, Keiran Raine <[hidden email]> wrote:
Hi Chathura,

Not sure if this is exactly what you need, but take a look at the plugin proportialmultibw:




Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:+44%201223%20834244" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 4983
Office: H104

On 17 Jan 2017, at 04:01, Chathura Gunasekara <[hidden email]> wrote:


​Hello,
Is there a way to change the histogram color of the SNP coverage.
<Screen Shot 2017-01-16 at 10.01.40 PM.JPG>

​For example this gray color is not prominent when i try to use this kind of image for a publication.
If I want to change it to purple, can i do that ?
​Thank you​


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Chathura
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Re: SNP coverage histogram color

Chathura Gunasekara
Thanks Colin,
This is exactly what I wanted. And Thanks to Keiran Too. I learned something new 

On Tue, Jan 17, 2017 at 9:38 AM, Colin <[hidden email]> wrote:
It is sort of a "hidden setting", but you can actually change colors on the SNPCoverage track using CSS

See css/sequence.css:

/* colors for bases must be specified as hex or rgb/hsl strings, no named colors such as 'red' */
.base_n {
    background-color: #C6C6C6;
}
.base_a {
    background-color: #00BF00;
}
.base_c {
    background-color: #4747ff;
}
.base_t {
    background-color: #f00;
}
.base_g {
    background-color: #d5bb04;
}
.base_reference {
    background-color: #a33;
}
.base_deletion {
    background-color: #999;
}

.sequence.nocolor .base {
    background-color: #ddd;
}


If you change those, it will be reflected in your SNPCoverage track. 

The .base_reference is the background grey of the SNPCoverage plot, and if you actually add to the list and make .base_skip you can make the intron grey change color.

-Colin

On Tue, Jan 17, 2017 at 9:11 AM, Keiran Raine <[hidden email]> wrote:
Hi Chathura,

Not sure if this is exactly what you need, but take a look at the plugin proportialmultibw:




Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:+44%201223%20834244" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 4983
Office: H104

On 17 Jan 2017, at 04:01, Chathura Gunasekara <[hidden email]> wrote:


​Hello,
Is there a way to change the histogram color of the SNP coverage.
<Screen Shot 2017-01-16 at 10.01.40 PM.JPG>

​For example this gray color is not prominent when i try to use this kind of image for a publication.
If I want to change it to purple, can i do that ?
​Thank you​


--
Chathura
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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