help with xy-plot data

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help with xy-plot data

Jayaraman, Pushkala

Hello,

Im back into Gbrowse and just started with displaying quantitative data on xyplots. Ive used the xy-plot glyph before to show density plots and that used to work fine.. but with quantitative data I seem to be runnig into problems..

 

Here is my gff3 file (as you may see, this is data form 5 samples each of them have a control score and a pain score. For the same position. I need to create subtracks for all 8 features. 5 sample types and also ‘pain’ and ‘control’ source. But it doesn’t seem to be accepting the different sample types although, it does show them in the box, it doesn’t filter them.

 

 

Chr1       CONTROL            methylation_score_1     31897    31898    0.9752066            +             .               ID=CTRL_0;Name=CTRL

Chr1       PAIN      methylation_score_1     31897    31898    0.9781421            +             .               ID=SNL_1;Name=SNL

Chr1       CONTROL            methylation_score_2     31897    31898    0.98540145          +             .               ID=CTRL_2;Name=CTRL

Chr1       PAIN      methylation_score_2     31897    31898    0.9862069            +             .               ID=SNL_3;Name=SNL

Chr1       CONTROL            methylation_score_3     31897    31898    0.9946524            +             .               ID=CTRL_4;Name=CTRL

Chr1       PAIN      methylation_score_3     31897    31898    0.97115386          +             .               ID=SNL_5;Name=SNL

Chr1       CONTROL            methylation_score_4     31897    31898    0.990566              +             .               ID=CTRL_6;Name=CTRL

Chr1       PAIN      methylation_score_4     31897    31898    0.9622642            +             .               ID=SNL_7;Name=SNL

Chr1       CONTROL            methylation_score_5     31897    31898    0.9723757            +             .               ID=CTRL_8;Name=CTRL

Chr1       PAIN      methylation_score_5     31897    31898    0.9896373            +             .               ID=SNL_9;Name=SNL

Chr1       CONTROL            methylation_score_1     31907    31908    0.9586777            +             .               ID=CTRL_10;Name=CTRL

Chr1       PAIN      methylation_score_1     31907    31908    0.9726776            +             .               ID=SNL_11;Name=SNL

Chr1       CONTROL            methylation_score_2     31907    31908    0.98540145          +             .               ID=CTRL_12;Name=CTRL

Chr1       PAIN      methylation_score_2     31907    31908    0.9724138            +             .               ID=SNL_13;Name=SNL

Chr1       CONTROL            methylation_score_3     31907    31908    0.96256685          +             .               ID=CTRL_14;Name=CTRL

Chr1       PAIN      methylation_score_3     31907    31908    0.93333334          +             .               ID=SNL_15;Name=SNL

Chr1       CONTROL            methylation_score_4     31907    31908    0.9433962            +             .               ID=CTRL_16;Name=CTRL

Chr1       PAIN      methylation_score_4     31907    31908    0.9496855            +             .               ID=SNL_17;Name=SNL

Chr1       CONTROL            methylation_score_5     31907    31908    0.98342544          +             .               ID=CTRL_18;Name=CTRL

Chr1       PAIN      methylation_score_5     31907    31908    0.95811516          +             .               ID=SNL_19;Name=SNL

 

 

Here is my conf file..

 

[LD5Chip]

feature        = methylation_score_1 methylation_score_2 methylation_score_3 methylation_score_4 methylation_score_5

glyph          = xyplot

graph_type     = points

fgcolor        = sub{

                                                                                my $feature = shift->source;

                                                                                return $feature eq "PAIN" ? "blue":"magenta";

                                                                }

bgcolor        = black

select         = source 'PAIN' 'CONTROL'

min_score    = 0

max_score    = 1

clip = 1

label = sub{

                                                my $feature = shift;

                                                my ($class)=$feature->load_id;

                                                return $class;

                                }

                               

scale          = right

group_on  = primary_tag

category       = Quantitative Data

key            = Methylation Studies

 

 

 

Hence if the source is PAIN or CONTROL selected, I do not see any glyphs on the track and can only see the 5 scales..

 

http://hastings.hmgc.mcw.edu:83/gbrowse2/i/rgd_904_test/abf91d4964cfdb46a90250e539d10768.png

 

 

 

What am I doing wrong??

 

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


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Re: [Gmod-gbrowse] help with xy-plot data

Timothy Parnell
Hi Pushkala,

I used to use xyplot glyph to make multiple graphs a lot with Bio::DB::GFF and GBrowse 1.x , but not so much experience with SeqFeature::Store and GBrowse 2.x.

Have you tried looking at this wiki page?? http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2

It looks like it's something you may want to try, and I think it may supersede the select option in the conf stanza.

Tim

--

Timothy J Parnell, PhD.
Research Associate
Howard Hughes Medical Institute
Department of Oncology
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT 84112



On 8/26/10 3:34 PM, "Jayaraman, Pushkala" <[hidden email]> wrote:

Hello,
Im back into Gbrowse and just started with displaying quantitative data on xyplots. Ive used the xy-plot glyph before to show density plots and that used to work fine.. but with quantitative data I seem to be runnig into problems..

Here is my gff3 file (as you may see, this is data form 5 samples each of them have a control score and a pain score. For the same position. I need to create subtracks for all 8 features. 5 sample types and also 'pain' and 'control' source. But it doesn't seem to be accepting the different sample types although, it does show them in the box, it doesn't filter them.


Chr1       CONTROL            methylation_score_1     31897    31898    0.9752066            +             .               ID=CTRL_0;Name=CTRL
Chr1       PAIN      methylation_score_1     31897    31898    0.9781421            +             .               ID=SNL_1;Name=SNL
Chr1       CONTROL            methylation_score_2     31897    31898    0.98540145          +             .               ID=CTRL_2;Name=CTRL
Chr1       PAIN      methylation_score_2     31897    31898    0.9862069            +             .               ID=SNL_3;Name=SNL
Chr1       CONTROL            methylation_score_3     31897    31898    0.9946524            +             .               ID=CTRL_4;Name=CTRL
Chr1       PAIN      methylation_score_3     31897    31898    0.97115386          +             .               ID=SNL_5;Name=SNL
Chr1       CONTROL            methylation_score_4     31897    31898    0.990566              +             .               ID=CTRL_6;Name=CTRL
Chr1       PAIN      methylation_score_4     31897    31898    0.9622642            +             .               ID=SNL_7;Name=SNL
Chr1       CONTROL            methylation_score_5     31897    31898    0.9723757            +             .               ID=CTRL_8;Name=CTRL
Chr1       PAIN      methylation_score_5     31897    31898    0.9896373            +             .               ID=SNL_9;Name=SNL
Chr1       CONTROL            methylation_score_1     31907    31908    0.9586777            +             .               ID=CTRL_10;Name=CTRL
Chr1       PAIN      methylation_score_1     31907    31908    0.9726776            +             .               ID=SNL_11;Name=SNL
Chr1       CONTROL            methylation_score_2     31907    31908    0.98540145          +             .               ID=CTRL_12;Name=CTRL
Chr1       PAIN      methylation_score_2     31907    31908    0.9724138            +             .               ID=SNL_13;Name=SNL
Chr1       CONTROL            methylation_score_3     31907    31908    0.96256685          +             .               ID=CTRL_14;Name=CTRL
Chr1       PAIN      methylation_score_3     31907    31908    0.93333334          +             .               ID=SNL_15;Name=SNL
Chr1       CONTROL            methylation_score_4     31907    31908    0.9433962            +             .               ID=CTRL_16;Name=CTRL
Chr1       PAIN      methylation_score_4     31907    31908    0.9496855            +             .               ID=SNL_17;Name=SNL
Chr1       CONTROL            methylation_score_5     31907    31908    0.98342544          +             .               ID=CTRL_18;Name=CTRL
Chr1       PAIN      methylation_score_5     31907    31908    0.95811516          +             .               ID=SNL_19;Name=SNL


Here is my conf file..

[LD5Chip]
feature        = methylation_score_1 methylation_score_2 methylation_score_3 methylation_score_4 methylation_score_5
glyph         = xyplot
graph_type     = points
fgcolor        = sub{
                                                                                my $feature = shift->source;
                                                                                return $feature eq "PAIN" ? "blue":"magenta";
                                                                }
bgcolor        = black
select         = source 'PAIN' 'CONTROL'
min_score    = 0
max_score    = 1
clip = 1
label = sub{
                                                my $feature = shift;
                                                my ($class)=$feature->load_id;
                                                return $class;
                                }

scale         = right
group_on  = primary_tag
category       = Quantitative Data
key           = Methylation Studies



Hence if the source is PAIN or CONTROL selected, I do not see any glyphs on the track and can only see the 5 scales..

[cid:3365684086_44938705]



What am I doing wrong??


Thanks,
Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu <http://www.rgd.mcw.edu>



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http://p.sf.net/sfu/intel-atom-d2d
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Re: [Gmod-gbrowse] help with xy-plot data

Jayaraman, Pushkala

Hi Tim,

Yeah, I did take a look at it.. Thought I could advance to that (the select table is really cool.. seems like a new set of features introduced after 2.08) once I get the basic configuration for this track working :)

I ended up asking the forum in my first step..Haha!

 

Would you or anyone else in the forum, by any chance happen to have a sample track configuration for any quantitative data using Bio::DB::GFF? I could try and use something similar if SeqFeatureStore doesn’t show results..but Im sure Im the one doing something wrong somewhere.  

 

I basically need to show 2 distinct points(for each sample.. there are 5 samples) for the same position. Is there any glyph I could use to compare 2 scores at the same position?

 

 

I was thinking on the lines of this:

For position 26793 there are 5 samples each with their own histogram. The histogram shows 2 scores(on the same box plot), one(blackened one) with control score and the transparent one with pain.

Is there a glyph of such sort?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Timothy Parnell [mailto:[hidden email]]
Sent: Thursday, August 26, 2010 5:15 PM
To: Jayaraman, Pushkala; [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] help with xy-plot data

 

Hi Pushkala,

 

I used to use xyplot glyph to make multiple graphs a lot with Bio::DB::GFF and GBrowse 1.x , but not so much experience with SeqFeature::Store and GBrowse 2.x.

 

Have you tried looking at this wiki page?? http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2

 

It looks like it's something you may want to try, and I think it may supersede the select option in the conf stanza.

 

Tim

 

--

 

Timothy J Parnell, PhD.

Research Associate

Howard Hughes Medical Institute

Department of Oncology

Huntsman Cancer Institute

University of Utah

Salt Lake City, UT 84112

 

 

 

On 8/26/10 3:34 PM, "Jayaraman, Pushkala" <[hidden email]> wrote:

 

Hello,

Im back into Gbrowse and just started with displaying quantitative data on xyplots. Ive used the xy-plot glyph before to show density plots and that used to work fine.. but with quantitative data I seem to be runnig into problems..

 

Here is my gff3 file (as you may see, this is data form 5 samples each of them have a control score and a pain score. For the same position. I need to create subtracks for all 8 features. 5 sample types and also 'pain' and 'control' source. But it doesn't seem to be accepting the different sample types although, it does show them in the box, it doesn't filter them.

 

 

Chr1       CONTROL            methylation_score_1     31897    31898    0.9752066            +             .               ID=CTRL_0;Name=CTRL

Chr1       PAIN      methylation_score_1     31897    31898    0.9781421            +             .               ID=SNL_1;Name=SNL

Chr1       CONTROL            methylation_score_2     31897    31898    0.98540145          +             .               ID=CTRL_2;Name=CTRL

Chr1       PAIN      methylation_score_2     31897    31898    0.9862069            +             .               ID=SNL_3;Name=SNL

Chr1       CONTROL            methylation_score_3     31897    31898    0.9946524            +             .               ID=CTRL_4;Name=CTRL

Chr1       PAIN      methylation_score_3     31897    31898    0.97115386          +             .               ID=SNL_5;Name=SNL

Chr1       CONTROL            methylation_score_4     31897    31898    0.990566              +             .               ID=CTRL_6;Name=CTRL

Chr1       PAIN      methylation_score_4     31897    31898    0.9622642            +             .               ID=SNL_7;Name=SNL

Chr1       CONTROL            methylation_score_5     31897    31898    0.9723757            +             .               ID=CTRL_8;Name=CTRL

Chr1       PAIN      methylation_score_5     31897    31898    0.9896373            +             .               ID=SNL_9;Name=SNL

Chr1       CONTROL            methylation_score_1     31907    31908    0.9586777            +             .               ID=CTRL_10;Name=CTRL

Chr1       PAIN      methylation_score_1     31907    31908    0.9726776            +             .               ID=SNL_11;Name=SNL

Chr1       CONTROL            methylation_score_2     31907    31908    0.98540145          +             .               ID=CTRL_12;Name=CTRL

Chr1       PAIN      methylation_score_2     31907    31908    0.9724138            +             .               ID=SNL_13;Name=SNL

Chr1       CONTROL            methylation_score_3     31907    31908    0.96256685          +             .               ID=CTRL_14;Name=CTRL

Chr1       PAIN      methylation_score_3     31907    31908    0.93333334          +             .               ID=SNL_15;Name=SNL

Chr1       CONTROL            methylation_score_4     31907    31908    0.9433962            +             .               ID=CTRL_16;Name=CTRL

Chr1       PAIN      methylation_score_4     31907    31908    0.9496855            +             .               ID=SNL_17;Name=SNL

Chr1       CONTROL            methylation_score_5     31907    31908    0.98342544          +             .               ID=CTRL_18;Name=CTRL

Chr1       PAIN      methylation_score_5     31907    31908    0.95811516          +             .               ID=SNL_19;Name=SNL

 

 

Here is my conf file..

 

[LD5Chip]

feature        = methylation_score_1 methylation_score_2 methylation_score_3 methylation_score_4 methylation_score_5

glyph         = xyplot

graph_type     = points

fgcolor        = sub{

                                                                                my $feature = shift->source;

                                                                                return $feature eq "PAIN" ? "blue":"magenta";

                                                                }

bgcolor        = black

select         = source 'PAIN' 'CONTROL'

min_score    = 0

max_score    = 1

clip = 1

label = sub{

                                                my $feature = shift;

                                                my ($class)=$feature->load_id;

                                                return $class;

                                }

 

scale         = right

group_on  = primary_tag

category       = Quantitative Data

key           = Methylation Studies

 

 

 

Hence if the source is PAIN or CONTROL selected, I do not see any glyphs on the track and can only see the 5 scales..

 

[cid:3365684086_44938705]

 

 

 

What am I doing wrong??

 

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>

 

 


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Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
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Re: [Gmod-gbrowse] help with xy-plot data

Ram Podicheti
In reply to this post by Jayaraman, Pushkala
Pushkala,
Can you try removing the min_score and max_score and see how it goes?

Ram


Jayaraman, Pushkala wrote:

>
> Hello,
>
> Im back into Gbrowse and just started with displaying quantitative
> data on xyplots. Ive used the xy-plot glyph before to show density
> plots and that used to work fine.. but with quantitative data I seem
> to be runnig into problems..
>
> Here is my gff3 file (as you may see, this is data form 5 samples each
> of them have a control score and a pain score. For the same position.
> I need to create subtracks for all 8 features. 5 sample types and also
> ‘pain’ and ‘control’ source. But it doesn’t seem to be accepting the
> different sample types although, it does show them in the box, it
> doesn’t filter them.
>
> Chr1 CONTROL methylation_score_1 31897 31898 0.9752066 + .
> ID=CTRL_0;Name=CTRL
>
> Chr1 PAIN methylation_score_1 31897 31898 0.9781421 + . ID=SNL_1;Name=SNL
>
> Chr1 CONTROL methylation_score_2 31897 31898 0.98540145 + .
> ID=CTRL_2;Name=CTRL
>
> Chr1 PAIN methylation_score_2 31897 31898 0.9862069 + . ID=SNL_3;Name=SNL
>
> Chr1 CONTROL methylation_score_3 31897 31898 0.9946524 + .
> ID=CTRL_4;Name=CTRL
>
> Chr1 PAIN methylation_score_3 31897 31898 0.97115386 + . ID=SNL_5;Name=SNL
>
> Chr1 CONTROL methylation_score_4 31897 31898 0.990566 + .
> ID=CTRL_6;Name=CTRL
>
> Chr1 PAIN methylation_score_4 31897 31898 0.9622642 + . ID=SNL_7;Name=SNL
>
> Chr1 CONTROL methylation_score_5 31897 31898 0.9723757 + .
> ID=CTRL_8;Name=CTRL
>
> Chr1 PAIN methylation_score_5 31897 31898 0.9896373 + . ID=SNL_9;Name=SNL
>
> Chr1 CONTROL methylation_score_1 31907 31908 0.9586777 + .
> ID=CTRL_10;Name=CTRL
>
> Chr1 PAIN methylation_score_1 31907 31908 0.9726776 + . ID=SNL_11;Name=SNL
>
> Chr1 CONTROL methylation_score_2 31907 31908 0.98540145 + .
> ID=CTRL_12;Name=CTRL
>
> Chr1 PAIN methylation_score_2 31907 31908 0.9724138 + . ID=SNL_13;Name=SNL
>
> Chr1 CONTROL methylation_score_3 31907 31908 0.96256685 + .
> ID=CTRL_14;Name=CTRL
>
> Chr1 PAIN methylation_score_3 31907 31908 0.93333334 + .
> ID=SNL_15;Name=SNL
>
> Chr1 CONTROL methylation_score_4 31907 31908 0.9433962 + .
> ID=CTRL_16;Name=CTRL
>
> Chr1 PAIN methylation_score_4 31907 31908 0.9496855 + . ID=SNL_17;Name=SNL
>
> Chr1 CONTROL methylation_score_5 31907 31908 0.98342544 + .
> ID=CTRL_18;Name=CTRL
>
> Chr1 PAIN methylation_score_5 31907 31908 0.95811516 + .
> ID=SNL_19;Name=SNL
>
> Here is my conf file..
>
> [LD5Chip]
>
> feature = methylation_score_1 methylation_score_2 methylation_score_3
> methylation_score_4 methylation_score_5
>
> glyph = xyplot
>
> graph_type = points
>
> fgcolor = sub{
>
> my $feature = shift->source;
>
> return $feature eq "PAIN" ? "blue":"magenta";
>
> }
>
> bgcolor = black
>
> select = source 'PAIN' 'CONTROL'
>
> min_score = 0
>
> max_score = 1
>
> clip = 1
>
> label = sub{
>
> my $feature = shift;
>
> my ($class)=$feature->load_id;
>
> return $class;
>
> }
>
> scale = right
>
> group_on = primary_tag
>
> category = Quantitative Data
>
> key = Methylation Studies
>
> Hence if the source is PAIN or CONTROL selected, I do not see any
> glyphs on the track and can only see the 5 scales..
>
> http://hastings.hmgc.mcw.edu:83/gbrowse2/i/rgd_904_test/abf91d4964cfdb46a90250e539d10768.png
>
> What am I doing wrong??
>
> Thanks,
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email] <mailto:[hidden email]>
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
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> speed time-to-market. Join now, and jumpstart your future.
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Re: [Gmod-gbrowse] help with xy-plot data

Jayaraman, Pushkala

Hi Ram,

I managed to get it to this far: wherein, for every position, each colour is one sample.

1.  can we increase the detailed numbering on the scale but keep it consistent? i.e instead of 0/0.5/1 we can have increments of 0.1 consistently throughout the entire track?

2.  When I click on the feature to get to the Gbrowse Details page, I get this:

CTRL Details

Requested feature not found in database.

Is this because there are too many features on the page?

 

I tried to read the xy glyph on cpan and didn’t find anything for it.

 

Before removal of the min_score and max_score, this is what I get:

http://hastings.hmgc.mcw.edu:83/gbrowse2/i/rgd_904_test/49d90d729fd615374b31998338449b72.png

 

After removal of the min_score and max_score, this is what I get:

http://hastings.hmgc.mcw.edu:83/gbrowse2/i/rgd_904_test/78ee4fe515d749e764816f1b3e9f0516.png

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Thursday, September 02, 2010 9:11 AM
To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] help with xy-plot data

 

Pushkala,

Can you try removing the min_score and max_score and see how it goes?

 

Ram

 

 

Jayaraman, Pushkala wrote:

> 

> Hello,

> 

> Im back into Gbrowse and just started with displaying quantitative

> data on xyplots. Ive used the xy-plot glyph before to show density

> plots and that used to work fine.. but with quantitative data I seem

> to be runnig into problems..

> 

> Here is my gff3 file (as you may see, this is data form 5 samples each

> of them have a control score and a pain score. For the same position.

> I need to create subtracks for all 8 features. 5 sample types and also

> ‘pain’ and ‘control’ source. But it doesn’t seem to be accepting the

> different sample types although, it does show them in the box, it

> doesn’t filter them.

> 

> Chr1 CONTROL methylation_score_1 31897 31898 0.9752066 + .

> ID=CTRL_0;Name=CTRL

> 

> Chr1 PAIN methylation_score_1 31897 31898 0.9781421 + . ID=SNL_1;Name=SNL

> 

> Chr1 CONTROL methylation_score_2 31897 31898 0.98540145 + .

> ID=CTRL_2;Name=CTRL

> 

> Chr1 PAIN methylation_score_2 31897 31898 0.9862069 + . ID=SNL_3;Name=SNL

> 

> Chr1 CONTROL methylation_score_3 31897 31898 0.9946524 + .

> ID=CTRL_4;Name=CTRL

> 

> Chr1 PAIN methylation_score_3 31897 31898 0.97115386 + . ID=SNL_5;Name=SNL

> 

> Chr1 CONTROL methylation_score_4 31897 31898 0.990566 + .

> ID=CTRL_6;Name=CTRL

> 

> Chr1 PAIN methylation_score_4 31897 31898 0.9622642 + . ID=SNL_7;Name=SNL

> 

> Chr1 CONTROL methylation_score_5 31897 31898 0.9723757 + .

> ID=CTRL_8;Name=CTRL

> 

> Chr1 PAIN methylation_score_5 31897 31898 0.9896373 + . ID=SNL_9;Name=SNL

> 

> Chr1 CONTROL methylation_score_1 31907 31908 0.9586777 + .

> ID=CTRL_10;Name=CTRL

> 

> Chr1 PAIN methylation_score_1 31907 31908 0.9726776 + . ID=SNL_11;Name=SNL

> 

> Chr1 CONTROL methylation_score_2 31907 31908 0.98540145 + .

> ID=CTRL_12;Name=CTRL

> 

> Chr1 PAIN methylation_score_2 31907 31908 0.9724138 + . ID=SNL_13;Name=SNL

> 

> Chr1 CONTROL methylation_score_3 31907 31908 0.96256685 + .

> ID=CTRL_14;Name=CTRL

> 

> Chr1 PAIN methylation_score_3 31907 31908 0.93333334 + .

> ID=SNL_15;Name=SNL

> 

> Chr1 CONTROL methylation_score_4 31907 31908 0.9433962 + .

> ID=CTRL_16;Name=CTRL

> 

> Chr1 PAIN methylation_score_4 31907 31908 0.9496855 + . ID=SNL_17;Name=SNL

> 

> Chr1 CONTROL methylation_score_5 31907 31908 0.98342544 + .

> ID=CTRL_18;Name=CTRL

> 

> Chr1 PAIN methylation_score_5 31907 31908 0.95811516 + .

> ID=SNL_19;Name=SNL

> 

> Here is my conf file..

> 

> [LD5Chip]

> 

> feature = methylation_score_1 methylation_score_2 methylation_score_3

> methylation_score_4 methylation_score_5

> 

> glyph = xyplot

> 

> graph_type = points

> 

> fgcolor = sub{

> 

> my $feature = shift->source;

> 

> return $feature eq "PAIN" ? "blue":"magenta";

> 

> }

> 

> bgcolor = black

> 

> select = source 'PAIN' 'CONTROL'

> 

> min_score = 0

> 

> max_score = 1

> 

> clip = 1

> 

> label = sub{

> 

> my $feature = shift;

> 

> my ($class)=$feature->load_id;

> 

> return $class;

> 

> }

> 

> scale = right

> 

> group_on = primary_tag

> 

> category = Quantitative Data

> 

> key = Methylation Studies

> 

> Hence if the source is PAIN or CONTROL selected, I do not see any

> glyphs on the track and can only see the 5 scales..

> 

> http://hastings.hmgc.mcw.edu:83/gbrowse2/i/rgd_904_test/abf91d4964cfdb46a90250e539d10768.png

> 

> What am I doing wrong??

> 

> Thanks,

> 

> Pushkala Jayaraman

> 

> Programmer/Analyst

> 

> Rat Genome Database

> 

> Human and Molecular Genetics Center

> 

> Medical College of Wisconsin

> 

> Email: [hidden email] <mailto:[hidden email]>

> 

> Work: 414-955-2229

> 

> www.rgd.mcw.edu <http://www.rgd.mcw.edu>

> 

> ------------------------------------------------------------------------

> 

> ------------------------------------------------------------------------------

> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program

> Be part of this innovative community and reach millions of netbook users

> worldwide. Take advantage of special opportunities to increase revenue and

> speed time-to-market. Join now, and jumpstart your future.

> http://p.sf.net/sfu/intel-atom-d2d

> ------------------------------------------------------------------------

> 

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


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Re: [Gmod-gbrowse] help with xy-plot data

Jayaraman, Pushkala
In reply to this post by Ram Podicheti

Ram, Thanks for helping me out with that pointer,

That was one of the things I was looking for. I played with it a little more and was pretty satisfied with the results that showed up there..

For the convenience of everyone in the  forum, I am putting in the track configuration that displays data from 5 samples for 2 values a test and a control value.  

 

 

 

[LD5Chip]

feature      = methylation_score_1 methylation_score_2 methylation_score_3 methylation_score_4 methylation_score_5

glyph        = xyplot

graph_type   = points

point_symbol  = filled_triangle

part_color = sub{

                          my $feature = shift;

                          #my ($source)=$feature->source;

                          #return $source eq 'PAIN' ? "blue":"magenta";

                          my ($sample)=$feature->primary_tag;

                          return 'red' if $sample eq "methylation_score_1";

                          return 'blue' if $sample eq "methylation_score_2";

                          return 'green' if $sample eq "methylation_score_3";

                          return 'orange' if $sample eq "methylation_score_4";

                          return 'black' if $sample eq "methylation_score_5";

            }

 

# point_symbol = sub{

                          # my $feature = shift;

                          # my ($source)=$feature->source;

                          # return $source eq 'PAIN' ? "filled_triangle":"filled_square";

                      # }                

select       = source 'PAIN' 'CONTROL'

label = sub{

                  my $feature = shift;

                  my ($name)=$feature->load_id;

                  return $name;

            }

scale         = both

height       = 500

#bicolor_pivot  =1

group_on    = source

#balloon hover = sub {bring_bubble(shift)}

#balloon sticky = 1

category      = Quantitative Data

key           = Methylation Studies-need to work on

 

[LD5Chip:5000]

hide = 1

 

 

 

this is how it appears in the screen: I was able to show the average scores that gbrowse xyplot methods compute without me forcing them to use the 0/1 limit. (attached herewith)

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

-----Original Message-----
From: Ram Podicheti [mailto:[hidden email]]
Sent: Thursday, September 02, 2010 9:11 AM
To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] help with xy-plot data

 

Pushkala,

Can you try removing the min_score and max_score and see how it goes?

 

Ram

 

 

Jayaraman, Pushkala wrote:

> 

> Hello,

> 

> Im back into Gbrowse and just started with displaying quantitative

> data on xyplots. Ive used the xy-plot glyph before to show density

> plots and that used to work fine.. but with quantitative data I seem

> to be runnig into problems..

> 

> Here is my gff3 file (as you may see, this is data form 5 samples each

> of them have a control score and a pain score. For the same position.

> I need to create subtracks for all 8 features. 5 sample types and also

> ‘pain’ and ‘control’ source. But it doesn’t seem to be accepting the

> different sample types although, it does show them in the box, it

> doesn’t filter them.

> 

> Chr1 CONTROL methylation_score_1 31897 31898 0.9752066 + .

> ID=CTRL_0;Name=CTRL

> 

> Chr1 PAIN methylation_score_1 31897 31898 0.9781421 + . ID=SNL_1;Name=SNL

> 

> Chr1 CONTROL methylation_score_2 31897 31898 0.98540145 + .

> ID=CTRL_2;Name=CTRL

> 

> Chr1 PAIN methylation_score_2 31897 31898 0.9862069 + . ID=SNL_3;Name=SNL

> 

> Chr1 CONTROL methylation_score_3 31897 31898 0.9946524 + .

> ID=CTRL_4;Name=CTRL

> 

> Chr1 PAIN methylation_score_3 31897 31898 0.97115386 + . ID=SNL_5;Name=SNL

> 

> Chr1 CONTROL methylation_score_4 31897 31898 0.990566 + .

> ID=CTRL_6;Name=CTRL

> 

> Chr1 PAIN methylation_score_4 31897 31898 0.9622642 + . ID=SNL_7;Name=SNL

> 

> Chr1 CONTROL methylation_score_5 31897 31898 0.9723757 + .

> ID=CTRL_8;Name=CTRL

> 

> Chr1 PAIN methylation_score_5 31897 31898 0.9896373 + . ID=SNL_9;Name=SNL

> 

> Chr1 CONTROL methylation_score_1 31907 31908 0.9586777 + .

> ID=CTRL_10;Name=CTRL

> 

> Chr1 PAIN methylation_score_1 31907 31908 0.9726776 + . ID=SNL_11;Name=SNL

> 

> Chr1 CONTROL methylation_score_2 31907 31908 0.98540145 + .

> ID=CTRL_12;Name=CTRL

> 

> Chr1 PAIN methylation_score_2 31907 31908 0.9724138 + . ID=SNL_13;Name=SNL

> 

> Chr1 CONTROL methylation_score_3 31907 31908 0.96256685 + .

> ID=CTRL_14;Name=CTRL

> 

> Chr1 PAIN methylation_score_3 31907 31908 0.93333334 + .

> ID=SNL_15;Name=SNL

> 

> Chr1 CONTROL methylation_score_4 31907 31908 0.9433962 + .

> ID=CTRL_16;Name=CTRL

> 

> Chr1 PAIN methylation_score_4 31907 31908 0.9496855 + . ID=SNL_17;Name=SNL

> 

> Chr1 CONTROL methylation_score_5 31907 31908 0.98342544 + .

> ID=CTRL_18;Name=CTRL

> 

> Chr1 PAIN methylation_score_5 31907 31908 0.95811516 + .

> ID=SNL_19;Name=SNL

> 

> Here is my conf file..

> 

> [LD5Chip]

> 

> feature = methylation_score_1 methylation_score_2 methylation_score_3

> methylation_score_4 methylation_score_5

> 

> glyph = xyplot

> 

> graph_type = points

> 

> fgcolor = sub{

> 

> my $feature = shift->source;

> 

> return $feature eq "PAIN" ? "blue":"magenta";

> 

> }

> 

> bgcolor = black

> 

> select = source 'PAIN' 'CONTROL'

> 

> min_score = 0

> 

> max_score = 1

> 

> clip = 1

> 

> label = sub{

> 

> my $feature = shift;

> 

> my ($class)=$feature->load_id;

> 

> return $class;

> 

> }

> 

> scale = right

> 

> group_on = primary_tag

> 

> category = Quantitative Data

> 

> key = Methylation Studies

> 

> Hence if the source is PAIN or CONTROL selected, I do not see any

> glyphs on the track and can only see the 5 scales..

> 

> http://hastings.hmgc.mcw.edu:83/gbrowse2/i/rgd_904_test/abf91d4964cfdb46a90250e539d10768.png

> 

> What am I doing wrong??

> 

> Thanks,

> 

> Pushkala Jayaraman

> 

> Programmer/Analyst

> 

> Rat Genome Database

> 

> Human and Molecular Genetics Center

> 

> Medical College of Wisconsin

> 

> Email: [hidden email] <mailto:[hidden email]>

> 

> Work: 414-955-2229

> 

> www.rgd.mcw.edu <http://www.rgd.mcw.edu>

> 

> ------------------------------------------------------------------------

> 

> ------------------------------------------------------------------------------

> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program

> Be part of this innovative community and reach millions of netbook users

> worldwide. Take advantage of special opportunities to increase revenue and

> speed time-to-market. Join now, and jumpstart your future.

> http://p.sf.net/sfu/intel-atom-d2d

> ------------------------------------------------------------------------

> 

> _______________________________________________

> Gmod-gbrowse mailing list

> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

>  

 


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Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
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