AUTOSCALE GROUP in session metadata no longer implemented?

[tom carroll]

hi,

I have been setting auto scale groups in a session metadata txt file for users and using this to set up-front the auto scale groups for different sets of data in one session. 

I had added this feature to our Bioconductor package in the last release.

I have noticed this has stopped working and my auto scale groups in sample metadata file are no longer being used.

Could this be to do with the recent update?

Here is an example of session metadata file which was acting as hoped before update.

#sampleTable

Linking_id Antibody Tissue AUTOSCALE GROUP

CTCF_Ch12_1 CTCF Ch12 Group CTCF

CTCF_Ch12_2 CTCF Ch12 Group CTCF

CTCF_MEL_1 CTCF Mel Group CTCF

CTCF_MEL_2 CTCF Mel Group CTCF

Input_Ch12 IgGRabbit Ch12 Group IgGRabbit

Input_MEL IgGRabbit Mel Group IgGRabbit

Myc_Ch12_1 c-Myc Ch12 Group c-Myc

Myc_Ch12_2 c-Myc Ch12 Group c-Myc

Myc_MEL_1 c-Myc Mel Group c-Myc

Myc_MEL_2 c-Myc Mel Group c-Myc

#sampleMapping

#Bams

_Bam

#BigWigs

CTCF_Ch12_1_Bigwig CTCF_Ch12_1

CTCF_Ch12_2_Bigwig CTCF_Ch12_2

CTCF_MEL_1_Bigwig CTCF_MEL_1

CTCF_MEL_2_Bigwig CTCF_MEL_2

Input_Ch12_Bigwig Input_Ch12

Input_MEL_Bigwig Input_MEL

Myc_Ch12_1_Bigwig Myc_Ch12_1

Myc_Ch12_2_Bigwig Myc_Ch12_2

Myc_MEL_1_Bigwig Myc_MEL_1

Myc_MEL_2_Bigwig Myc_MEL_2

#Intervals

CTCF_Ch12_1_Interval CTCF_Ch12_1

CTCF_Ch12_2_Interval CTCF_Ch12_2

CTCF_MEL_1_Interval CTCF_MEL_1

CTCF_MEL_2_Interval CTCF_MEL_2

Myc_Ch12_1_Interval Myc_Ch12_1

Myc_Ch12_2_Interval Myc_Ch12_2

Myc_MEL_1_Interval Myc_MEL_1

Myc_MEL_2_Interval Myc_MEL_2

and an associated session XML 

<Global genome.value="hg19" groupTracksBy="Linking_id" nextAutoscaleGroup="2" locus="All" version="3">
  <Resources>
    <Resource name="SampleMetadata" path="SampleMetadata.txt" relativePath="TRUE"/>
    <Resource label="Input_Ch12_Bigwig" name="Input_Ch12_Bigwig" path="../GenomicFiles/Sorted_Input_Ch12Normalised.bw" relativePath="TRUE"/>
  </Resources>
  <Panel height="350" name="DataPanel" width="1115">
    <Track id="../GenomicFiles/Sorted_Input_Ch12Normalised.bw" name="Input_Ch12_Bigwig" autoScale="true" altColor="169,169,169" color="169,169,169" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" renderer="BAR_CHART" showDataRange="true" visible="true" sortable="true" normalize="false" windowFunction="mean">
      <DataRange baseline="0" drawBaseline="true" flipAxis="false" maximum="50" minimum="0" type="LINEAR"/>
    </Track>
  </Panel>
</Global>

Thank you for your help

tom

[tom carroll]

Just to add the link to related issue on Github.

https://github.com/igvteam/igv/issues/500

[James Robinson]

Could you open a new git issue for this?  It would help tremendously if you could include a self-contained test case in a zip file.  

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[tom carroll]

Thank you or reply. I'll make up a zip file example and post to a new git issue.

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[tom carroll]

I opened the git issue here. 

Thanks, tom

On Wednesday, January 17, 2018 at 6:33:31 PM UTC-5, Jim Robinson wrote:

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