Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
Data Exploration
Data exploration using data available from the TCGA Data Tool paclet.
This loads the paclet.
In[1]:=
Needs["JaneShenGunther`TCGADataTool`"]
TCGA project exploration
Use data from GDCProject entities to visualize basic information about projects in the TCGA program.
Get all GDCProject entities for the TCGA program and their properties.
In[64]:=
tcgaProjectEntities=EntityList[EntityClass["GDCProject","TCGA"]]
Out[64]=
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
TCGA-CHOL
TCGA-LIHC
TCGA-DLBC
TCGA-BLCA
TCGA-ACC
TCGA-CESC
TCGA-PCPG
TCGA-PAAD
TCGA-MESO
TCGA-TGCT
TCGA-KIRP
TCGA-UVM
TCGA-UCS
TCGA-THYM
TCGA-COAD
TCGA-ESCA
TCGA-GBM
TCGA-KICH
TCGA-HNSC
TCGA-PRAD
TCGA-OV
TCGA-LUSC
TCGA-LAML
TCGA-LGG
TCGA-SARC
TCGA-BRCA
TCGA-READ
TCGA-LUAD
TCGA-STAD
TCGA-THCA
TCGA-KIRC
TCGA-SKCM
TCGA-UCEC
In[65]:=
properties={"ProjectID","CaseCount","TCIADataQ","FileSize"};tcgaProjectsMetadataSubset=EntityValue[tcgaProjectEntities,properties,"PropertyAssociation"];
In[65]:=
tcgaProjectsMetadataSubset〚;;3〛
Out[67]=
{ProjectIDTCGA-CHOL,CaseCountGDC51,TCIA0,TCIADataQFalse,FileSizeTotalFileSize,ImageTotalFileSize,TextTotalFileSize,ProjectIDTCGA-LIHC,CaseCountGDC377,TCIA97,TCIADataQTrue,FileSizeTotalFileSize,ImageTotalFileSize,TextTotalFileSize,ProjectIDTCGA-DLBC,CaseCountGDC58,TCIA0,TCIADataQFalse,FileSizeTotalFileSize,ImageTotalFileSize,TextTotalFileSize}
96.7764
GB
95.1052
GB
1.67123
GB
627.952
GB
611.982
GB
15.9699
GB
55.7289
GB
53.9161
GB
1.81283
GB
In[68]:=
PieChart[ ReverseSort@Counts[tcgaProjectsMetadataSubset〚All,"TCIADataQ"〛], SectorOriginTop,LabelingFunction"RadialCenter", PlotLabel"TCGA projects that have TCIA data", ChartLabelsNone,ChartLegendsAutomatic]
Out[68]=
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In[72]:=
BarChart[Sort@Association[Query[All,#ProjectID#["CaseCount"]["GDC"]&]@tcgaProjectsMetadataSubset],BarOriginLeft,ImageSize600,FrameTrue,GridLinesAutomatic,FrameLabel{"TCGA Projects on GDC portal","# GDC Cases"},ChartLabelsAutomatic,LabelingFunctionRight,PlotLabel"Number of GDC cases per TCGA project"]
Out[72]=
Contents cannot be rendered at this time; please try again later
Plot TCGA project file sizes broken down by GDC file type.
In[76]:=
BarChart[Sort@(Association[Query[All,#ProjectID#["FileSize"]&]@tcgaProjectsMetadataSubset]/.q_QuantityRound[UnitConvert[q,"Terabytes"],.001]), BarOriginLeft,ImageSize600,FrameTrue,GridLinesAutomatic, FrameLabel{"TCGA Projects on GDC portal","GDC File Size (TB)"},ChartLabels{Automatic,None},ChartLegendsPlaced[Automatic,Below], LabelingFunctionAutomatic,PlotLabel"GDC file size per TCGA project",BarSpacing{0,1}]
Out[76]=
TCGA-CESC patient coverage
Use example data for TCGA-CESC project to get a visualization of how many patients have data for each data subcategory.
Load example data for TCGA-CESC project.
In[120]:=
dataStructure=
[{"TCGAProjectData","TCGACESCExceptGenomicDataAllPatients"}];
 | exampleDataTCGA |
In[121]:=
dataScope=
[{"TCGAProjectData","TCGACESCExceptGenomicDataAllPatients"},"Metadata"]["DataScope"]
| exampleDataTCGA |
Out[121]=
{{Clinical,Patient},{Clinical,Drug},{Clinical,Radiation},{Clinical,NewTumorEvent},{Clinical,OtherMalignancyForm},{Clinical,FollowUp},{Clinical,NewTumorEventFollowUp},{Clinical,Ablation},{Biospecimen,Aliquot},{Biospecimen,Analyte},{Biospecimen,Auxiliary},{Biospecimen,DiagnosticSlide},{Biospecimen,Sample},{Biospecimen,Portion},{Biospecimen,Protocol},{Biospecimen,ShipmentPortion},{Biospecimen,Slide},{Biospecimen,SSFNormalControl},{Biospecimen,SSFTumorSample},{ScrapedData,RadiologicalImages},{ScrapedData,HistologicalImages},{ScrapedData,FollowUp},{ScrapedData,NewTumorEventFollowUp}}
Ignore Clinical::FollowUp and Clinical::NewTumorEventFollowUp subcategories since they are already covered by ScrapedData::FollowUp and ScrapedData::NewTumorEventFollowUp respectively.
In[122]:=
dataScope=DeleteCases[dataScope,Alternatives[{"Clinical","FollowUp"},{"Clinical","NewTumorEventFollowUp"}]];
Compute the number of patients covered by each data subcategory.
In[123]:=
patientsCovered=Flatten/@Thread[{dataScope,(Length[dataStructure]-Count[dataStructure〚All,Sequence@@#〛,_Missing])&/@dataScope}]
Out[123]=
{{Clinical,Patient,307},{Clinical,Drug,141},{Clinical,Radiation,177},{Clinical,NewTumorEvent,23},{Clinical,OtherMalignancyForm,8},{Clinical,Ablation,0},{Biospecimen,Aliquot,307},{Biospecimen,Analyte,307},{Biospecimen,Auxiliary,307},{Biospecimen,DiagnosticSlide,271},{Biospecimen,Sample,307},{Biospecimen,Portion,307},{Biospecimen,Protocol,307},{Biospecimen,ShipmentPortion,173},{Biospecimen,Slide,307},{Biospecimen,SSFNormalControl,305},{Biospecimen,SSFTumorSample,307},{ScrapedData,RadiologicalImages,54},{ScrapedData,HistologicalImages,307},{ScrapedData,FollowUp,248},{ScrapedData,NewTumorEventFollowUp,25}}
In[124]:=
patientsCovered=GroupBy[patientsCovered,First,Association[Rule@@@#〚All,2;;〛]&]
Out[124]=
ClinicalPatient307,Drug141,Radiation177,NewTumorEvent23,OtherMalignancyForm8,Ablation0,BiospecimenAliquot307,Analyte307,Auxiliary307,DiagnosticSlide271,Sample307,Portion307,Protocol307,ShipmentPortion173,Slide307,SSFNormalControl305,SSFTumorSample307,ScrapedDataRadiologicalImages54,HistologicalImages307,FollowUp248,NewTumorEventFollowUp25
Compute percentage of patients covered by each data subcategory.
In[125]:=
totalPatientsNumber=Length[dataStructure]
Out[125]=
307
In[126]:=
patientsCovered=Map["%"(Round[100.#/totalPatientsNumber]),"#"#&,patientsCovered,{2}]
Out[126]=
ClinicalPatient%100,#307,Drug%46,#141,Radiation%58,#177,NewTumorEvent%7,#23,OtherMalignancyForm%3,#8,Ablation%0,#0,BiospecimenAliquot%100,#307,Analyte%100,#307,Auxiliary%100,#307,DiagnosticSlide%88,#271,Sample%100,#307,Portion%100,#307,Protocol%100,#307,ShipmentPortion%56,#173,Slide%100,#307,SSFNormalControl%99,#305,SSFTumorSample%100,#307,ScrapedDataRadiologicalImages%18,#54,HistologicalImages%100,#307,FollowUp%81,#248,NewTumorEventFollowUp%8,#25
Visualize patient coverage by subcategory.