[Gmod-gbrowse] 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


[image: Inline image 1]

[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 <***@gmail.com<mailto:***@gmail.com>> 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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[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

[image: Inline image 1]




On Mon, Oct 20, 2014 at 10:44 AM, Timothy Parnell <

Post by 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
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?
########
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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[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 <***@gmail.com<mailto:***@gmail.com>> 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 <***@hci.utah.edu<mailto:***@hci.utah.edu>> 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 <***@gmail.com<mailto:***@gmail.com><mailto:***@gmail.com<mailto:***@gmail.com>>> 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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[Jeff Nie]

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

On Mon, Oct 20, 2014 at 10:31 PM, Timothy Parnell <

Post by 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
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 <
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
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?
########
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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