Next-GenerationClusteredHeatMaps(NG-CHM)BradleyBroom andJohnWeinstein,

DepartmentofBioinformaticsandComputationalBiology,UTMDAndersonCancerCenter

A visualization tool for the dynamic exploration of large, omic data sets.

Visualization Features

• Easy-to-usenavigation• Flexiblezoomedviewsfor

inspectingsmalldetailsinlargedatasets

• Generatepublication-qualitygraphics

• Scalable• Highlyinteractive

Dynamic“Link-outs”• Can link-out from selected rows, columns, or matrix elements

• To other content specific resources,• E.g. NCBI, Genecards, Cancer Digital Slide Archive

• Content specific• Associate ‘types’ with row and column labels• ‘Link-out’ database indexed by type• Only matching link-outs included in a specific NG-CHM

• Or to dynamic analyses• E.g. Box Plot, Points Plot

• Five major types of resource links

AnExploratoryEnvironmentwithfivemajortypesofresourcelinks

CreatingNG-CHMs

Four“builder”levels:– GUI

• Newnon-quantitativeuser

• Experiencednon-quantitativeuser

– R• Quantitativeuser

– Specificationfiles• Systemdeveloper

RECENTDEVELOPMENTS

NewarchitectureNG-CHMs

• PreviousNG-CHMsystemarchitecture– Wasdesignedsixyearsago– Reliedheavilyonback-endserverfortilerendering– Didnotexploitrecentadvancesinwebbrowsers– Hadperformanceandscalingissues

• NewNG-CHMsystemarchitecture– Completere-designtotakeadvantageofnewbrowsercapabilities(e.g.WebGL)

– “TileGeneration”performedentirelyinbrowser– Farmoreresponsiveuserexperience

NewarchitectureNG-CHMs

• “Standalone”server-lessmodepossible– Nearly-allNG-CHMfunctionalityispresent

• Cannot“link-out”toserver-sidedynamiccomputations

– AllowsNG-CHMstobe:• Savedlocally(e.g.withotherprojectdata)• Attachedassupplementarymaterialtopapers• Sharedwithcolleaguesviaemail,websites,portals,etc.

NewarchitectureNG-CHMsintegratedwithGalaxy

• AddednewarchitectureNG-CHMstoGalaxy:– BigQueryInterface(forISB-CGCdataaccess)– NG-CHMBuildertool– NG-CHMVisualization

• Available– Asaready-to-runDockercontainer– FromtheGalaxyToolshed– FromGithub

• ExposesNG-CHMstoanewusercommunity

GalaxyNG-CHMBigQueryInterface(forISB-CGC)

GalaxyNG-CHMBuilder

GalaxyNG-CHMVisualizationTool

NewarchitectureTCGANG-CHMCompendium

http://tcga.ngchm.net/

NumerousImprovementstoNG-CHMViewer

• MoreuseroptionsforfinetuningPDFgeneration• ImprovedrenderingresponsivenessforlargeNGCHMs

• Abilitytocreateverylargeheatmaps(>20,000rows)– ContributeddendrogramcodetoRproject(inR3.4.0)

• AddednewfeaturestoNG-CHMs:– Canadd“cuts”(extrablankrows/columns)toheatmap– Canhighlightasmallnumberoftoprows/columnsinoverviewpane

• Numerousbugfixesandotherimprovements• Createdadditionaltutorialvideos

UPCOMINGPLANS

Upcomingplans

• ReleasenewarchitectureNG-CHMmanager• CompleteournewarchitectureNG-CHMcompendium

• Furtherincreaseviewerresponsivenessforverylargedatamatrices

• Developatablet-optimizeduserinterface• Collaborate

– Addlinksto/fromNG-CHMsfrom/toothertools– Createmoreadvancedtools&dataexchange

CreditsMDAndersonDeptofBioinformaticsandComputationalBiologyBradleyBroomJohnWeinsteinRehanAkbaniChrisWakefieldJamesMelott

InSilicoSolutionsMichaelRyanRobertBrownFutaIkedaMarkStucky

HobsonsDavidKane