questions about subtrack labels

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questions about subtrack labels

HAIMING WANG-2
Hi,

We're using subtracks to handle RNASeq data (bigwig files and medata). I have the following three questions about subtrack labels: 

1) there are extra numbers on subtrack labels, such as 1, 2, 3. (refer to attached Fig. 1). I'm not sure where they come from?

2) currently subtrack labels have the same background color as the main track, sometimes it's hard to read. Can we change the label background color in the conf file?

There is one RNASeq track with 50 subtracks: 

3) subtrack labels will be missing if I turn on more than 15 subtracks (refer to attached Fig 2). 

We're using GBrowse v2.48. I wonder if anyone experiences similar issues, also It would be very helpful if anyone can point me out which module handles subtrack labels (bgcolor)?

Thanks,
-Haiming

p.s. gbrowse conf and metadata

################ gbrowse conf #################

[tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = sub { { -index => '/path/metadata' } }

[tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRCCoverage]
feature = Coverage
database = tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC
glyph    = wiggle_xyplot
no_grid  = 1  
height   = 40 
key          = T.g. mRNAseq Transcriptomes of 25 strains during murine macrophage infection Coverage (Hassan et al.)
bgcolor      = sub { GBrowse::Display::rnaseqColorFromBigWig(shift) }
scale        = both
autoscale    = local
link         = javascript:void(0)
title        = sub{}
category     = Transcript Expression Evidence: B. RNA-seq : T.g. : mRNA-seq
group_label  = 1  
group_label_position = top
citation     = sub {  $CFG->citationFromDatabaseName( 'tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC' ) }


################### metadata file #########################

[B41/RUM_NU.bw]
:selected    = 0 
display_name = B41 (non-unique)
sample       = B41 
alignment    = non-unique
type         = Coverage

[B41/RUM_Unique.bw]
:selected    = 1 
display_name = B41 (unique)
sample       = B41 
alignment    = unique
type         = Coverage

[B73/RUM_NU.bw]
:selected    = 0 
display_name = B73 (non-unique)
sample       = B73 
alignment    = non-unique
type         = Coverage

[B73/RUM_Unique.bw]
:selected    = 1 
display_name = B73 (unique)
sample       = B73 
alignment    = unique
type         = Coverage





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subtrack1.tiff (163K) Download Attachment
subtrack2.tiff (133K) Download Attachment
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Re: questions about subtrack labels

Timothy Parnell
Hi Haiming,

You appear to be using a different subtrack method than with what I am familiar (the subtrack select and table method), but I think I can still answer your questions.

1. I think you are specifying labels twice. I'm guessing you have labels = 1 in the track defaults, plus you have group_label = 1 in the track stanza. Remove one or the other. One is clearly using the display_name object method, I don't know where the numbered labels are coming from. Perhaps some sort of enumeration from parsing the metadata file? I just use the label = 1 option in my confs, since both label = 0 and group_label = 1 leads to extra empty space where the main label would go.

2. I don't believe the subtrack label background color is specifiable. It uses the bgcolor option, which, with the wiggle_xyplot glyph, is also going to be the same color as the data. Since you are using bigWig files, you could try switching to the wiggle_whiskers glyph, which does not use the bgcolor option for data, allowing you to customize it for the label background. If you want to take a look at the code, I believe it inherits the draw_label() function from Bio::Graphics::Glyph::xyplot. It shouldn't be too difficult to add a new option.

3. Yes, I have noticed this behavior too. I do not know where the limit is coming from, or why it is even present, or how to fix it. Consequently, I simply try to avoid loading too many subtracks at a time!

Hope that helps,
Tim
________________________________
From: Haiming Wang [[hidden email]]
Sent: Wednesday, September 25, 2013 1:08 PM
To: [hidden email]
Cc: [hidden email]; [hidden email]
Subject: [Gmod-gbrowse] questions about subtrack labels

Hi,

We're using subtracks to handle RNASeq data (bigwig files and medata). I have the following three questions about subtrack labels:

1) there are extra numbers on subtrack labels, such as 1, 2, 3. (refer to attached Fig. 1). I'm not sure where they come from?

2) currently subtrack labels have the same background color as the main track, sometimes it's hard to read. Can we change the label background color in the conf file?

There is one RNASeq track with 50 subtracks:

3) subtrack labels will be missing if I turn on more than 15 subtracks (refer to attached Fig 2).

We're using GBrowse v2.48. I wonder if anyone experiences similar issues, also It would be very helpful if anyone can point me out which module handles subtrack labels (bgcolor)?

Thanks,
-Haiming

p.s. gbrowse conf and metadata

################ gbrowse conf #################

[tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = sub { { -index => '/path/metadata' } }

[tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRCCoverage]
feature = Coverage
database = tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC
glyph    = wiggle_xyplot
no_grid  = 1
height   = 40
key          = T.g. mRNAseq Transcriptomes of 25 strains during murine macrophage infection Coverage (Hassan et al.)
bgcolor      = sub { GBrowse::Display::rnaseqColorFromBigWig(shift) }
scale        = both
autoscale    = local
link         = javascript:void(0)
title        = sub{}
category     = Transcript Expression Evidence: B. RNA-seq : T.g. : mRNA-seq
group_label  = 1
group_label_position = top
citation     = sub {  $CFG->citationFromDatabaseName( 'tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC' ) }


################### metadata file #########################

[B41/RUM_NU.bw]
:selected    = 0
display_name = B41 (non-unique)
sample       = B41
alignment    = non-unique
type         = Coverage

[B41/RUM_Unique.bw]
:selected    = 1
display_name = B41 (unique)
sample       = B41
alignment    = unique
type         = Coverage

[B73/RUM_NU.bw]
:selected    = 0
display_name = B73 (non-unique)
sample       = B73
alignment    = non-unique
type         = Coverage

[B73/RUM_Unique.bw]
:selected    = 1
display_name = B73 (unique)
sample       = B73
alignment    = unique
type         = Coverage





------------------------------------------------------------------------------
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Re: questions about subtrack labels

Haiming Wang
In reply to this post by HAIMING WANG-2
Hi Tim,

Thanks a lot for your answers and they're very helpful! You are right that labels are specified twice and set group_label = 0 does remove the extra numbers. In terms of label bgcolor, thanks for pointing out the difference between wiggle_whiskers and wiggle_xyplot. wiggle_whiskers allows me to customize label bgcolor. I think I'm going to test it and switch to wiggle_whiskers. Once again, thank you!

-Haiming


On Wed, Sep 25, 2013 at 6:07 PM, Timothy Parnell <[hidden email]> wrote:
Hi Haiming,

You appear to be using a different subtrack method than with what I am familiar (the subtrack select and table method), but I think I can still answer your questions.

1. I think you are specifying labels twice. I'm guessing you have labels = 1 in the track defaults, plus you have group_label = 1 in the track stanza. Remove one or the other. One is clearly using the display_name object method, I don't know where the numbered labels are coming from. Perhaps some sort of enumeration from parsing the metadata file? I just use the label = 1 option in my confs, since both label = 0 and group_label = 1 leads to extra empty space where the main label would go.

2. I don't believe the subtrack label background color is specifiable. It uses the bgcolor option, which, with the wiggle_xyplot glyph, is also going to be the same color as the data. Since you are using bigWig files, you could try switching to the wiggle_whiskers glyph, which does not use the bgcolor option for data, allowing you to customize it for the label background. If you want to take a look at the code, I believe it inherits the draw_label() function from Bio::Graphics::Glyph::xyplot. It shouldn't be too difficult to add a new option.

3. Yes, I have noticed this behavior too. I do not know where the limit is coming from, or why it is even present, or how to fix it. Consequently, I simply try to avoid loading too many subtracks at a time!

Hope that helps,
Tim
________________________________
From: Haiming Wang [[hidden email]]
Sent: Wednesday, September 25, 2013 1:08 PM
To: [hidden email]
Cc: [hidden email]; [hidden email]
Subject: [Gmod-gbrowse] questions about subtrack labels

Hi,

We're using subtracks to handle RNASeq data (bigwig files and medata). I have the following three questions about subtrack labels:

1) there are extra numbers on subtrack labels, such as 1, 2, 3. (refer to attached Fig. 1). I'm not sure where they come from?

2) currently subtrack labels have the same background color as the main track, sometimes it's hard to read. Can we change the label background color in the conf file?

There is one RNASeq track with 50 subtracks:

3) subtrack labels will be missing if I turn on more than 15 subtracks (refer to attached Fig 2).

We're using GBrowse v2.48. I wonder if anyone experiences similar issues, also It would be very helpful if anyone can point me out which module handles subtrack labels (bgcolor)?

Thanks,
-Haiming

p.s. gbrowse conf and metadata

################ gbrowse conf #################

[tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = sub { { -index => '/path/metadata' } }

[tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRCCoverage]
feature = Coverage
database = tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC
glyph    = wiggle_xyplot
no_grid  = 1
height   = 40
key          = T.g. mRNAseq Transcriptomes of 25 strains during murine macrophage infection Coverage (Hassan et al.)
bgcolor      = sub { GBrowse::Display::rnaseqColorFromBigWig(shift) }
scale        = both
autoscale    = local
link         = javascript:void(0)
title        = sub{}
category     = Transcript Expression Evidence: B. RNA-seq : T.g. : mRNA-seq
group_label  = 1
group_label_position = top
citation     = sub {  $CFG->citationFromDatabaseName( 'tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC' ) }


################### metadata file #########################

[B41/RUM_NU.bw]
:selected    = 0
display_name = B41 (non-unique)
sample       = B41
alignment    = non-unique
type         = Coverage

[B41/RUM_Unique.bw]
:selected    = 1
display_name = B41 (unique)
sample       = B41
alignment    = unique
type         = Coverage

[B73/RUM_NU.bw]
:selected    = 0
display_name = B73 (non-unique)
sample       = B73
alignment    = non-unique
type         = Coverage

[B73/RUM_Unique.bw]
:selected    = 1
display_name = B73 (unique)
sample       = B73
alignment    = unique
type         = Coverage








------------------------------------------------------------------------------
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Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk
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Re: questions about subtrack labels

HAIMING WANG-2
In reply to this post by HAIMING WANG-2
FYI: previous message got bounced back from the mailing list, sending it again.

Hi Tim,

Thanks a lot for your answers and they're very helpful! You are right that labels are specified twice and set group_label = 0 does remove the extra numbers. In terms of label bgcolor, thanks for pointing out the difference between wiggle_whiskers and wiggle_xyplot. wiggle_whiskers allows me to customize label bgcolor. I think I'm going to test it and switch to wiggle_whiskers. Once again, thank you!
-Haiming

On Sep 25, 2013, at 3:08 PM, Haiming Wang wrote:

Hi,

We're using subtracks to handle RNASeq data (bigwig files and medata). I have the following three questions about subtrack labels: 

1) there are extra numbers on subtrack labels, such as 1, 2, 3. (refer to attached Fig. 1). I'm not sure where they come from?

2) currently subtrack labels have the same background color as the main track, sometimes it's hard to read. Can we change the label background color in the conf file?

There is one RNASeq track with 50 subtracks: 

3) subtrack labels will be missing if I turn on more than 15 subtracks (refer to attached Fig 2). 

We're using GBrowse v2.48. I wonder if anyone experiences similar issues, also It would be very helpful if anyone can point me out which module handles subtrack labels (bgcolor)?

Thanks,
-Haiming

p.s. gbrowse conf and metadata

################ gbrowse conf #################

[tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = sub { { -index => '/path/metadata' } }

[tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRCCoverage]
feature = Coverage
database = tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC
glyph    = wiggle_xyplot
no_grid  = 1  
height   = 40 
key          = T.g. mRNAseq Transcriptomes of 25 strains during murine macrophage infection Coverage (Hassan et al.)
bgcolor      = sub { GBrowse::Display::rnaseqColorFromBigWig(shift) }
scale        = both
autoscale    = local
link         = javascript:void(0)
title        = sub{}
category     = Transcript Expression Evidence: B. RNA-seq : T.g. : mRNA-seq
group_label  = 1  
group_label_position = top
citation     = sub {  $CFG->citationFromDatabaseName( 'tgonME49_Saeij_Jeroen_25_strains_rnaSeq_RSRC' ) }


################### metadata file #########################

[B41/RUM_NU.bw]
:selected    = 0 
display_name = B41 (non-unique)
sample       = B41 
alignment    = non-unique
type         = Coverage

[B41/RUM_Unique.bw]
:selected    = 1 
display_name = B41 (unique)
sample       = B41 
alignment    = unique
type         = Coverage

[B73/RUM_NU.bw]
:selected    = 0 
display_name = B73 (non-unique)
sample       = B73 
alignment    = non-unique
type         = Coverage

[B73/RUM_Unique.bw]
:selected    = 1 
display_name = B73 (unique)
sample       = B73 
alignment    = unique
type         = Coverage




<subtrack1.tiff><subtrack2.tiff>------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk_______________________________________________
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------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk
_______________________________________________
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