"hide empty subtracks" not working - bigwig metadata file

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

"hide empty subtracks" not working - bigwig metadata file

HAIMING WANG-2

Hi,


It appears that GBrowse does not even display subtrack headers when there is no data  to display, as shown by the blank spaces in the image attached, which should display eight subtracks instead of six. "hide empty subtracks" is set to false. The following is the related config. I wonder if anyone has any idea about this issue? Thanks!


[tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC:database]
db_adaptor    = Bio::DB::BigWigSetEuPath
db_args       = sub { { -index => '/path/tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC/metadata' } }

[tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRCCoverage]
feature = Coverage
database = tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC
glyph    = wiggle_xyplot
no_grid  = 1  
height   = 40
key          = Transcriptomes of Cat Enteroepithelial Stages (CZ-H3) ...
bgcolor      = sub { GBrowse::Display::rnaseqColorFromBigWig(shift) }
scale        = both
autoscale    = local
link         = javascript:void(0)
category     = Transcript Expression Evidence: B. RNA-seq: T gondii ME49 mRNA-seq: Logged
group_label  = 0  
group_label_position = top

hide empty subtracks = 0


-Haiming


------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

hide_empty_subtracks.tiff (167K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: "hide empty subtracks" not working - bigwig metadata file

Timothy Parnell
Hi Haiming,

I am guessing this is a side effect of having empty tracks. The space is almost certainly allotted prior to rendering the track, and no returned data from the database adaptor means no subtrack is rendered, which also means no subtrack title as it would be rendered with the xyplot data.

One possible workaround would be to munge the raw wig data and include 0s at all positions rather than no (null) data, so that the graph would have something (even if it’s just a bunch of 0s) to draw.

Unfortunately, I’m not familiar enough with the code to suggest a real fix.

Tim

On Dec 15, 2014, at 1:14 PM, Haiming Wang <[hidden email]<mailto:[hidden email]>> wrote:

Hi,

It appears that GBrowse does not even display subtrack headers when there is no data  to display, as shown by the blank spaces in the image attached, which should display eight subtracks instead of six. "hide empty subtracks" is set to false. The following is the related config. I wonder if anyone has any idea about this issue? Thanks!

[tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC:database]
db_adaptor    = Bio::DB::BigWigSetEuPath
db_args       = sub { { -index => '/path/tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC/metadata' } }

[tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRCCoverage]
feature = Coverage
database = tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC
glyph    = wiggle_xyplot
no_grid  = 1
height   = 40
key          = Transcriptomes of Cat Enteroepithelial Stages (CZ-H3) ...
bgcolor      = sub { GBrowse::Display::rnaseqColorFromBigWig(shift) }
scale        = both
autoscale    = local
link         = javascript:void(0)
category     = Transcript Expression Evidence: B. RNA-seq: T gondii ME49 mRNA-seq: Logged
group_label  = 0
group_label_position = top
hide empty subtracks = 0

-Haiming
<hide_empty_subtracks.tiff>------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: "hide empty subtracks" not working - bigwig metadata file

HAIMING WANG-2
Hi Tim,

Thanks a lot for your suggestion! I agree that include 0s at raw wig data should help in this case. I'm afraid that we might have removed 0s while converting raw scores into log scale. But, it would be ideal if wiggle_xyplot can always display a subtrack title even for empty region.

Best,
-Haiming

________________________________________
From: Timothy Parnell <[hidden email]>
Sent: Thursday, December 18, 2014 11:47 AM
To: Haiming Wang
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] "hide empty subtracks" not working - bigwig metadata        file

Hi Haiming,

I am guessing this is a side effect of having empty tracks. The space is almost certainly allotted prior to rendering the track, and no returned data from the database adaptor means no subtrack is rendered, which also means no subtrack title as it would be rendered with the xyplot data.

One possible workaround would be to munge the raw wig data and include 0s at all positions rather than no (null) data, so that the graph would have something (even if it’s just a bunch of 0s) to draw.

Unfortunately, I’m not familiar enough with the code to suggest a real fix.

Tim

On Dec 15, 2014, at 1:14 PM, Haiming Wang <[hidden email]<mailto:[hidden email]>> wrote:

Hi,

It appears that GBrowse does not even display subtrack headers when there is no data  to display, as shown by the blank spaces in the image attached, which should display eight subtracks instead of six. "hide empty subtracks" is set to false. The following is the related config. I wonder if anyone has any idea about this issue? Thanks!

[tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC:database]
db_adaptor    = Bio::DB::BigWigSetEuPath
db_args       = sub { { -index => '/path/tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC/metadata' } }

[tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRCCoverage]
feature = Coverage
database = tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC
glyph    = wiggle_xyplot
no_grid  = 1
height   = 40
key          = Transcriptomes of Cat Enteroepithelial Stages (CZ-H3) ...
bgcolor      = sub { GBrowse::Display::rnaseqColorFromBigWig(shift) }
scale        = both
autoscale    = local
link         = javascript:void(0)
category     = Transcript Expression Evidence: B. RNA-seq: T gondii ME49 mRNA-seq: Logged
group_label  = 0
group_label_position = top
hide empty subtracks = 0

-Haiming
<hide_empty_subtracks.tiff>------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse