Visualising genomics Data using tracktables

 

Overview

  • Requirements for high-throughput visualisation.
  • Integration with IGV.
  • Tracktables toolset and examples.

More Sample - More time

  • Most analysis contains some visualisation of data in a browser.
    • Multiplexed samples
    • More Groups, More Samples
  • rtracklayer and sraDB provide some excellent functionality.

...but

  • Want to combine sample metadata and have tight control of how data is displayed.
  • Integration into a report.

Requirements

Pipeline Related

  • Automated presentation of data.
  • Data  annotated and with metadata.
  • Portable.
  • Easy integration with other efforts in reproducible research.
  • Flexible to where data is maintained.

Interactive Use.

  • Ease in casting Bioconductor objects into use in IGV.
  • Speed up iterations in reviewing results.

Integrated Genome Viewer

  • Accepts some commands via ports.
    • New, echo, load file , goto location
  • Complex customisation requires XML.
  • Sample metadata requires separate formatted text file.
  • For large number of samples these requirements can be very time consuming to arrange manually.
  • Portable
    • Local as opposed to server
  • Highly customisable.
  • Handles many data  types.

Building an IGV XML

fileSheet  
   
    SampleName bigwig                              interval                       bam
[1,] "EBF"      "/PATH_TO_FILE//EBF_Example.bw"     "/PATH_TO_FILE//EBF_Peaks.bed" NA 
[2,] "H3K4me3"  "/PATH_TO_FILE//H3K4me3_Example.bw" NA                             NA 
[3,] "H3K9ac"   "/PATH_TO_FILE//H3K9ac_Example.bw"  NA                             NA 
[4,] "RNAPol2"  "/PATH_TO_FILE//RNAPol2_Example.bw" NA                             NA 

 MakeIGVSessionXML(fileSheet,igvdirectory=getwd(),"Example","mm9")
[1] "/Users/Ziwei/why/Example.xml"



<Global genome.value="mm9" groupTracksBy="Linking_id" locus="All" version="3">
  <Resources>
    <Resource name="SampleMetadata" path="SampleMetadata.txt" relativePath="TRUE"/>
    <Resource label="EBF_Interval" name="EBF_Interval" path="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/EBF_Peaks.bed" relativePath="TRUE"/>
    <Resource label="EBF_Bigwig" name="EBF_Bigwig" path="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/EBF_Example.bw" relativePath="TRUE"/>
    <Resource label="H3K4me3_Bigwig" name="H3K4me3_Bigwig" path="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/H3K4me3_Example.bw" relativePath="TRUE"/>
    <Resource label="H3K9ac_Bigwig" name="H3K9ac_Bigwig" path="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/H3K9ac_Example.bw" relativePath="TRUE"/>
    <Resource label="RNAPol2_Bigwig" name="RNAPol2_Bigwig" path="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/RNAPol2_Example.bw" relativePath="TRUE"/>
  </Resources>
  <Panel height="350" name="DataPanel" width="1115">
    <Track id="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/EBF_Peaks.bed" name="EBF_Interval" altColor="169,169,169" color="169,169,169" displayMode="character" featureVisibilityWindow="-1" fontSize="10" height="40" renderer="BASIC_FEATURE" showDataRange="true" sortable="true" visible="true" windowFunction="count" autoScale="true" normalize="false"/>
    <Track id="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/EBF_Example.bw" name="EBF_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>
    <Track id="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/H3K4me3_Example.bw" name="H3K4me3_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>
    <Track id="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/H3K9ac_Example.bw" name="H3K9ac_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>
    <Track id="../../../Library/Frameworks/R.framework/Versions/3.2/Resources/library/tracktables/extdata/RNAPol2_Example.bw" name="RNAPol2_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>

Example IGV XML

Building the HTML table

> SampleSheet
     SampleName Antibody  Species
[1,] "EBF"      "EBF"     "ProB" 
[2,] "H3K4me3"  "H3K4me3" "ProB" 
[3,] "H3K9ac"   "H3K9ac"  "ProB" 
[4,] "RNAPol2"  "RNAPol2" "ProB" 
HTMLreport <- maketracktable(fileSheet=FileSheet,SampleSheet=SampleSheet,
filename="IGVExample.html",basedirectory=getwd(),genome="mm9")
#sampleTable
Linking_id	Antibody	Species
EBF	EBF	ProB
H3K4me3	H3K4me3	ProB
H3K9ac	H3K9ac	ProB
RNAPol2	RNAPol2	ProB

#sampleMapping
#Bams
_Bam

#BigWigs
EBF_Bigwig	EBF
H3K4me3_Bigwig	H3K4me3
H3K9ac_Bigwig	H3K9ac
RNAPol2_Bigwig	RNAPol2

#Intervals
EBF_Interval	EBF

Simple Example

Simple Example

Integration with Rmarkdown HTML

FTP, local or Mixed modes

Local

XML

SampleSheet

Genomic Files 

  • All required files stored locally in default structure.

FTP, local or Mixed modes

FTP

XML

Sample Information

Genomic Files 

  • All file uploaded to ftp under user control.

FTP

Genomic Files 

Local

XML

SampleSheet

More Genomic Files

  • All files created by tracktables are local but  genomic files on an FTP
  • Mixed set-ups allow for user to combine local and FTP help data

Code to set up of different types

urlForFiles <- "https://github.com/ThomasCarroll/tracktables-Data/raw/master/"
# This will link to data and XMLs placed in github earlier.
# In practice a dedicated FTP would be required for larger files.
HTMLreport <- maketracktable(fileSheet=FileSheet,SampleSheet=SampleSheet,
filename="IGVEx4.html",genome="mm9",
basedirectory=urlForFiles,
full.xml.paths=T,
full.file.paths=T,
writedirectory=file.path(getwd(),"IGVDirectory")
)
HTMLreport <- maketracktable(fileSheet=FileSheet,
SampleSheet=SampleSheet,
filename="IGVEx3.html",
basedirectory=file.path(getwd(),"IGVDirectory"),
genome="mm9")

From FTP

From RelativePaths

igvDisplayParams <- igvParam(bigwig.autoScale = "false",
bigwig.minimum = 1,
bigwig.maximum = 5)

HTMLreport <- maketracktable(FileSheet,SampleSheet,"IGVex2.html",getwd(),"mm9",
colourBy="Antibody",
igvParam=igvDisplayParams)

Customisation

Casting Bioconductor objects into tracktables

  • Rapidly  evaluate results in browser
  • Supports GenomicRanges so far
  • row Metadata carried into table.
  • Standalone or integrated into report.

 

htmlpage <- makebedtable(Intervals,"EBF_PeaksTable.html",getwd())

Casting Bioconductor objects into tracktables

  • Want to create HTML reports from other objects.
    • Diffbind
    • DEseq2
    • EdgeR
    • any suggestions

Acknowledgements

  • Rory Stark (CRUK)
  • Sanjay Khadayate (MRC)
  • Whole MRC CSC team

Visualing

By tom carroll

Visualing

  • 535

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