more than one glyph in same track

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more than one glyph in same track

Alaguraj Veluchamy
Dear all,
How do i include 2 different types of glyphs to the same track.
For example an (1). xyplot with respect to the genome coordinate and (2). genes on another glyps with respect to the same genome coordinate.
Here i include two tracks. How to concatenate them in a single track in two separate graphs one next to the other.

[sRNA]
 feature       = sRNA
glyph         = xyplot
graph_type    = boxes
bicolor_pivot = zero
pos_color     = blue
neg_color     = red

[sRNA2]
feature       = sRNA_HL
glyph           = processed_transcript
bgcolor         = red
fgcolor         = red
height        = 6
label           = 0

Regards,
Alaguraj.V

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Re: more than one glyph in same track

Scott Cain
Hi Alaguraj,

Combining an xyplot glyph with other glyphs might be tricky depending
on the details.  In theory, you could provide callbacks for each of
the configuration parameters after feature, like this:

[newtrack]
feature = sRNA  sRNA_HL
glyph    = sub {
                 my $f = shift;
                 my $type = $f->type->method;
                 if ($type eq 'sRNA') {
                      return 'xyplot';
                 }
                 else {
                      return 'processed_transcript';
                 }
              }
bgcolor = sub {....}
...etc...

For a situation where a attribute wouldn't make sense, you could return undef.

Scott



On Thu, Jul 8, 2010 at 10:16 AM, Alaguraj Veluchamy
<[hidden email]> wrote:

> Dear all,
> How do i include 2 different types of glyphs to the same track.
> For example an (1). xyplot with respect to the genome coordinate and (2).
> genes on another glyps with respect to the same genome coordinate.
> Here i include two tracks. How to concatenate them in a single track in two
> separate graphs one next to the other.
>
> [sRNA]
>  feature       = sRNA
> glyph         = xyplot
> graph_type    = boxes
> bicolor_pivot = zero
> pos_color     = blue
> neg_color     = red
>
> [sRNA2]
> feature       = sRNA_HL
> glyph           = processed_transcript
> bgcolor         = red
> fgcolor         = red
> height        = 6
> label           = 0
>
> Regards,
> Alaguraj.V
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: more than one glyph in same track

Alaguraj Veluchamy
Hello Scott,
Thanks for your suggestion. I could able to manage two glyphys but the problem now is grouping the xyplot points and ungrouping the sRNA points.
The xyplot must be grouped into a single scale but the sRNA must not be in a single plane.
I tried group_on = display_name for xyplot alone and put an undef for sRNA. But its grouping the sRNA points too.

Other way i tried is to bring in subtracks. But current version doesnt support it.

Thanks and regards
Alaguraj.V

On Thu, Jul 8, 2010 at 4:42 PM, Scott Cain <[hidden email]> wrote:
Hi Alaguraj,

Combining an xyplot glyph with other glyphs might be tricky depending
on the details.  In theory, you could provide callbacks for each of
the configuration parameters after feature, like this:

[newtrack]
feature = sRNA  sRNA_HL
glyph    = sub {
                my $f = shift;
                my $type = $f->type->method;
                if ($type eq 'sRNA') {
                     return 'xyplot';
                }
                else {
                     return 'processed_transcript';
                }
             }
bgcolor = sub {....}
...etc...

For a situation where a attribute wouldn't make sense, you could return undef.

Scott



On Thu, Jul 8, 2010 at 10:16 AM, Alaguraj Veluchamy
<[hidden email]> wrote:
> Dear all,
> How do i include 2 different types of glyphs to the same track.
> For example an (1). xyplot with respect to the genome coordinate and (2).
> genes on another glyps with respect to the same genome coordinate.
> Here i include two tracks. How to concatenate them in a single track in two
> separate graphs one next to the other.
>
> [sRNA]
>  feature       = sRNA
> glyph         = xyplot
> graph_type    = boxes
> bicolor_pivot = zero
> pos_color     = blue
> neg_color     = red
>
> [sRNA2]
> feature       = sRNA_HL
> glyph           = processed_transcript
> bgcolor         = red
> fgcolor         = red
> height        = 6
> label           = 0
>
> Regards,
> Alaguraj.V
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: more than one glyph in same track

Lincoln Stein
This sounds like a complex display that would be better of with a custom glyph. Can you send a diagram of what you hope to display?

Lincoln

On Fri, Jul 9, 2010 at 2:41 AM, Alaguraj Veluchamy <[hidden email]> wrote:
Hello Scott,
Thanks for your suggestion. I could able to manage two glyphys but the problem now is grouping the xyplot points and ungrouping the sRNA points.
The xyplot must be grouped into a single scale but the sRNA must not be in a single plane.
I tried group_on = display_name for xyplot alone and put an undef for sRNA. But its grouping the sRNA points too.

Other way i tried is to bring in subtracks. But current version doesnt support it.

Thanks and regards
Alaguraj.V


On Thu, Jul 8, 2010 at 4:42 PM, Scott Cain <[hidden email]> wrote:
Hi Alaguraj,

Combining an xyplot glyph with other glyphs might be tricky depending
on the details.  In theory, you could provide callbacks for each of
the configuration parameters after feature, like this:

[newtrack]
feature = sRNA  sRNA_HL
glyph    = sub {
                my $f = shift;
                my $type = $f->type->method;
                if ($type eq 'sRNA') {
                     return 'xyplot';
                }
                else {
                     return 'processed_transcript';
                }
             }
bgcolor = sub {....}
...etc...

For a situation where a attribute wouldn't make sense, you could return undef.

Scott



On Thu, Jul 8, 2010 at 10:16 AM, Alaguraj Veluchamy
<[hidden email]> wrote:
> Dear all,
> How do i include 2 different types of glyphs to the same track.
> For example an (1). xyplot with respect to the genome coordinate and (2).
> genes on another glyps with respect to the same genome coordinate.
> Here i include two tracks. How to concatenate them in a single track in two
> separate graphs one next to the other.
>
> [sRNA]
>  feature       = sRNA
> glyph         = xyplot
> graph_type    = boxes
> bicolor_pivot = zero
> pos_color     = blue
> neg_color     = red
>
> [sRNA2]
> feature       = sRNA_HL
> glyph           = processed_transcript
> bgcolor         = red
> fgcolor         = red
> height        = 6
> label           = 0
>
> Regards,
> Alaguraj.V
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: more than one glyph in same track

Alaguraj Veluchamy
Hello Dr. Stein,
I would like to have a xyplot and the sRNA (there will be huge number of overlapping sRNA on both strands).
I want to show the bargraph of expression values (parameter) and their corresponding sRNA as gene/transcripts.
I have attached a picture of both information together (Fig1.png).
But i couldnt make a group_on for the graph (if i group the all the sRNA merge together as single molecule Fig2.png).

Is that possible to have a subtrack to show both information ?
My .conf file look like this:
# HL =highlight
# TOTAL_SCOREONSTRAND = srnahighlight


[Total sRNA modified]
feature = sRNA_HL sRNA_TOTAL_SCOREONSTRAND
glyph = sub{ my $feature = shift;return 'xyplot' if $feature->name eq 'srnatotal';return 'gene' if $feature->name eq 'srnahighlight';}
bgcolor    = sub{ my $feature = shift;return "red" if $feature->name eq 'srnatotal';return "blue" if $feature->name eq 'srnahighlight';}
height     = sub{ my $feature = shift;return 40 if $feature->name eq 'srnatotal';return 10 if $feature->name eq 'srnahighlight';}
group_on = sub{ my $feature = shift;return "display_name" if $feature->name eq 'srnatotal';return "undef" if $feature->name eq 'srnahighlight';}
fgcolor = black
label           = 0
show_border = 1
key = Total sRNA modified



Thanks and regards,
Alaguraj.V

On Fri, Jul 9, 2010 at 2:48 PM, Lincoln Stein <[hidden email]> wrote:
This sounds like a complex display that would be better of with a custom glyph. Can you send a diagram of what you hope to display?

Lincoln


On Fri, Jul 9, 2010 at 2:41 AM, Alaguraj Veluchamy <[hidden email]> wrote:
Hello Scott,
Thanks for your suggestion. I could able to manage two glyphys but the problem now is grouping the xyplot points and ungrouping the sRNA points.
The xyplot must be grouped into a single scale but the sRNA must not be in a single plane.
I tried group_on = display_name for xyplot alone and put an undef for sRNA. But its grouping the sRNA points too.

Other way i tried is to bring in subtracks. But current version doesnt support it.

Thanks and regards
Alaguraj.V


On Thu, Jul 8, 2010 at 4:42 PM, Scott Cain <[hidden email]> wrote:
Hi Alaguraj,

Combining an xyplot glyph with other glyphs might be tricky depending
on the details.  In theory, you could provide callbacks for each of
the configuration parameters after feature, like this:

[newtrack]
feature = sRNA  sRNA_HL
glyph    = sub {
                my $f = shift;
                my $type = $f->type->method;
                if ($type eq 'sRNA') {
                     return 'xyplot';
                }
                else {
                     return 'processed_transcript';
                }
             }
bgcolor = sub {....}
...etc...

For a situation where a attribute wouldn't make sense, you could return undef.

Scott



On Thu, Jul 8, 2010 at 10:16 AM, Alaguraj Veluchamy
<[hidden email]> wrote:
> Dear all,
> How do i include 2 different types of glyphs to the same track.
> For example an (1). xyplot with respect to the genome coordinate and (2).
> genes on another glyps with respect to the same genome coordinate.
> Here i include two tracks. How to concatenate them in a single track in two
> separate graphs one next to the other.
>
> [sRNA]
>  feature       = sRNA
> glyph         = xyplot
> graph_type    = boxes
> bicolor_pivot = zero
> pos_color     = blue
> neg_color     = red
>
> [sRNA2]
> feature       = sRNA_HL
> glyph           = processed_transcript
> bgcolor         = red
> fgcolor         = red
> height        = 6
> label           = 0
>
> Regards,
> Alaguraj.V
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>


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Fig1.png (13K) Download Attachment
Fig2.png (3K) Download Attachment