heat map glyph

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heat map glyph

Jeff Nie
Hi,  
I am trying to display 50 gene level RNA-SEQ expression value (percentile) with subtrack and heat map glyph. I chose track space as compact, but one subtrack always show in two or three lines instead of one line. Any idea why? 
data is loaded to mysql db. The related config file look like this:
########
feature  = RNA-Seq
glyph    = heat_map
start_color = white
end_color   = black
min_score   = 0
max_score   = 100
category = RNA-Seq
bump = 1
key         = RNA-Seq Percentiled Gene Expression
subtrack select = Sample source
subtrack table  =  control 1;
                   control 2;
                   case1;
                   case2;
                   ......

Thanks,
Jeff 


Inline image 1






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Re: heat map glyph

Timothy Parnell
Hi Jeff,

The heat_map glyph was originally intended for continuous data along the chromosome, such as from a wig or bigWig file; for example, your RNASeq coverage derived from your Bam alignments.

Perusing the options of glyphs, perhaps you may want to consider using “graded_segments”, which is like the segments glyph (think genes) but automatically colors the segments based on the score. (You could also achieve a similar effect using the segments glyph and employ a callback to set the bgcolor based on the score).

As for the subtrack table, the space may be confusing things. If you do have spaces in your source tag (generally a bad idea), enclose the value in quotes, like “control 1”. Also, for the select, you want to use valid SeqFeature methods; look at the POD documentation for the Bio::SeqFeatureI module for a list of methods. In your case, use “source_tag” rather than “source”.

I think that should fix your problems.

Tim


On Oct 19, 2014, at 9:21 PM, Jeff Nie <[hidden email]<mailto:[hidden email]>> wrote:

Hi,
I am trying to display 50 gene level RNA-SEQ expression value (percentile) with subtrack and heat map glyph. I chose track space as compact, but one subtrack always show in two or three lines instead of one line. Any idea why?
data is loaded to mysql db. The related config file look like this:
########
feature  = RNA-Seq
glyph    = heat_map
start_color = white
end_color   = black
min_score   = 0
max_score   = 100
category = RNA-Seq
bump = 1
key         = RNA-Seq Percentiled Gene Expression
subtrack select = Sample source
subtrack table  =  control 1;
                   control 2;
                   case1;
                   case2;
                   ......

Thanks,
Jeff


<Screen Shot 2014-10-19 at 10.05.40 PM.png>





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Re: heat map glyph

Jeff Nie
Hi Tim,
I made all changes as you suggested, but still can't compact the track into one line. Why the compact drew displays the image into 3 lines instead of 1. 
Thank you for the help.
Jeff 

Inline image 1




On Mon, Oct 20, 2014 at 10:44 AM, Timothy Parnell <[hidden email]> wrote:
Hi Jeff,

The heat_map glyph was originally intended for continuous data along the chromosome, such as from a wig or bigWig file; for example, your RNASeq coverage derived from your Bam alignments.

Perusing the options of glyphs, perhaps you may want to consider using “graded_segments”, which is like the segments glyph (think genes) but automatically colors the segments based on the score. (You could also achieve a similar effect using the segments glyph and employ a callback to set the bgcolor based on the score).

As for the subtrack table, the space may be confusing things. If you do have spaces in your source tag (generally a bad idea), enclose the value in quotes, like “control 1”. Also, for the select, you want to use valid SeqFeature methods; look at the POD documentation for the Bio::SeqFeatureI module for a list of methods. In your case, use “source_tag” rather than “source”.

I think that should fix your problems.

Tim


On Oct 19, 2014, at 9:21 PM, Jeff Nie <[hidden email]<mailto:[hidden email]>> wrote:

Hi,
I am trying to display 50 gene level RNA-SEQ expression value (percentile) with subtrack and heat map glyph. I chose track space as compact, but one subtrack always show in two or three lines instead of one line. Any idea why?
data is loaded to mysql db. The related config file look like this:
########
feature  = RNA-Seq
glyph    = heat_map
start_color = white
end_color   = black
min_score   = 0
max_score   = 100
category = RNA-Seq
bump = 1
key         = RNA-Seq Percentiled Gene Expression
subtrack select = Sample source
subtrack table  =  control 1;
                   control 2;
                   case1;
                   case2;
                   ......

Thanks,
Jeff


<Screen Shot 2014-10-19 at 10.05.40 PM.png>





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Re: heat map glyph

Timothy Parnell
Hi Jeff,

The image looks normal to me.

Are you referring to the subtrack? If so, each subtrack is drawn separately. It is technically possible to draw them on top of each with transparency, but that only looks good with wiggle tracks.

Or are you referring to the fact that the individual segments are drawn in three tiers to avoid overlap? If so, you’ll need to adjust your bump parameters. Your bump setting of 1 is normal collision control, which distributes overlapping segments vertically to prevent overlap. Change this to “bump = overlap” to get overlapping segments so they are drawn all in the same tier. There’s a few different options to try here, so you’ll need to experiment and see what you like the best. The relevant wiki is here
http://gmod.org/wiki/GBrowse_2.0_HOWTO#Glyph_and_Appearance_Options

Good luck,
Tim


On Oct 20, 2014, at 10:22 AM, Jeff Nie <[hidden email]<mailto:[hidden email]>> wrote:

Hi Tim,
I made all changes as you suggested, but still can't compact the track into one line. Why the compact drew displays the image into 3 lines instead of 1.
Thank you for the help.
Jeff

<Screen Shot 2014-10-20 at 11.12.49 AM.png>




On Mon, Oct 20, 2014 at 10:44 AM, Timothy Parnell <[hidden email]<mailto:[hidden email]>> wrote:
Hi Jeff,

The heat_map glyph was originally intended for continuous data along the chromosome, such as from a wig or bigWig file; for example, your RNASeq coverage derived from your Bam alignments.

Perusing the options of glyphs, perhaps you may want to consider using “graded_segments”, which is like the segments glyph (think genes) but automatically colors the segments based on the score. (You could also achieve a similar effect using the segments glyph and employ a callback to set the bgcolor based on the score).

As for the subtrack table, the space may be confusing things. If you do have spaces in your source tag (generally a bad idea), enclose the value in quotes, like “control 1”. Also, for the select, you want to use valid SeqFeature methods; look at the POD documentation for the Bio::SeqFeatureI module for a list of methods. In your case, use “source_tag” rather than “source”.

I think that should fix your problems.

Tim


On Oct 19, 2014, at 9:21 PM, Jeff Nie <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:

Hi,
I am trying to display 50 gene level RNA-SEQ expression value (percentile) with subtrack and heat map glyph. I chose track space as compact, but one subtrack always show in two or three lines instead of one line. Any idea why?
data is loaded to mysql db. The related config file look like this:
########
feature  = RNA-Seq
glyph    = heat_map
start_color = white
end_color   = black
min_score   = 0
max_score   = 100
category = RNA-Seq
bump = 1
key         = RNA-Seq Percentiled Gene Expression
subtrack select = Sample source
subtrack table  =  control 1;
                   control 2;
                   case1;
                   case2;
                   ......

Thanks,
Jeff


<Screen Shot 2014-10-19 at 10.05.40 PM.png>





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Re: heat map glyph

Jeff Nie
​Now, all work.
Thank you for the help.
J​

On Mon, Oct 20, 2014 at 10:31 PM, Timothy Parnell <[hidden email]> wrote:
Hi Jeff,

The image looks normal to me.

Are you referring to the subtrack? If so, each subtrack is drawn separately. It is technically possible to draw them on top of each with transparency, but that only looks good with wiggle tracks.

Or are you referring to the fact that the individual segments are drawn in three tiers to avoid overlap? If so, you’ll need to adjust your bump parameters. Your bump setting of 1 is normal collision control, which distributes overlapping segments vertically to prevent overlap. Change this to “bump = overlap” to get overlapping segments so they are drawn all in the same tier. There’s a few different options to try here, so you’ll need to experiment and see what you like the best. The relevant wiki is here
http://gmod.org/wiki/GBrowse_2.0_HOWTO#Glyph_and_Appearance_Options

Good luck,
Tim


On Oct 20, 2014, at 10:22 AM, Jeff Nie <[hidden email]<mailto:[hidden email]>> wrote:

Hi Tim,
I made all changes as you suggested, but still can't compact the track into one line. Why the compact drew displays the image into 3 lines instead of 1.
Thank you for the help.
Jeff

<Screen Shot 2014-10-20 at 11.12.49 AM.png>




On Mon, Oct 20, 2014 at 10:44 AM, Timothy Parnell <[hidden email]<mailto:[hidden email]>> wrote:
Hi Jeff,

The heat_map glyph was originally intended for continuous data along the chromosome, such as from a wig or bigWig file; for example, your RNASeq coverage derived from your Bam alignments.

Perusing the options of glyphs, perhaps you may want to consider using “graded_segments”, which is like the segments glyph (think genes) but automatically colors the segments based on the score. (You could also achieve a similar effect using the segments glyph and employ a callback to set the bgcolor based on the score).

As for the subtrack table, the space may be confusing things. If you do have spaces in your source tag (generally a bad idea), enclose the value in quotes, like “control 1”. Also, for the select, you want to use valid SeqFeature methods; look at the POD documentation for the Bio::SeqFeatureI module for a list of methods. In your case, use “source_tag” rather than “source”.

I think that should fix your problems.

Tim


On Oct 19, 2014, at 9:21 PM, Jeff Nie <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:

Hi,
I am trying to display 50 gene level RNA-SEQ expression value (percentile) with subtrack and heat map glyph. I chose track space as compact, but one subtrack always show in two or three lines instead of one line. Any idea why?
data is loaded to mysql db. The related config file look like this:
########
feature  = RNA-Seq
glyph    = heat_map
start_color = white
end_color   = black
min_score   = 0
max_score   = 100
category = RNA-Seq
bump = 1
key         = RNA-Seq Percentiled Gene Expression
subtrack select = Sample source
subtrack table  =  control 1;
                   control 2;
                   case1;
                   case2;
                   ......

Thanks,
Jeff


<Screen Shot 2014-10-19 at 10.05.40 PM.png>





------------------------------------------------------------------------------
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Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
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------------------------------------------------------------------------------
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Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
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