Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
Data Visualization
It is possible to create various visualizations of the data downloaded using the .
This loads the paclet.
In[1]:=
Needs["JaneShenGunther`TCGADataTool`"]
Wolfram language statistical visualizations
TCGA project data is downloaded from the in the form of a list of , one for each patient in the project. It is possible to use built-in Wolfram language statistical visualization functions to explore the data.
Load TCGA-CESC example data structure and its description.
In[2]:=
dataStructure=
[{"TCGAProjectData","TCGACESCExceptGenomicDataAllPatients"}];
 | exampleDataTCGA |
Basic examples
Basic examples
of property Clinical::Patient::age_began_smoking_in_years
In[36]:=
ageBeginSmoking=
[dataStructure,"Clinical::Patient::age_began_smoking_in_years","DeleteMissing"True,"ListHandling"(If[ListQ[#],First[#],#]&)];
| pullDataSlice |
In[38]:=
Histogram[Flatten@Values[ageBeginSmoking],Automatic,"Probability",PlotRangeAll,FrameTrue,GridLinesAutomatic,PlotLabel"Age began smoking\n(years)"]
Out[38]=
of patient vital_status
In[86]:=
vitalStatusData=Flatten@Values@
[dataStructure,"Clinical::Patient::vital_status","DeleteMissing"True,"ListHandling"(If[ListQ[#],First[#],#]&)];
 | pullDataSlice |
In[88]:=
vitalStatusData〚;;3〛
Out[88]=
{Alive,Dead,Alive}
In[90]:=
PieChart[ Counts[vitalStatusData], SectorOriginTop,LabelingFunction"RadialCenter", PlotLabel"Clinical::Patient::vital_status", ChartLabelsNone,ChartLegendsAutomatic]
Out[90]=
 |
|
Plot age of initial pathologic diagnosis vs age began smoking.
In[94]:=
ageProperties=
[dataStructure,{"Clinical::Patient::age_at_initial_pathologic_diagnosis","Clinical::Patient::age_began_smoking_in_years"},"DeleteMissing"True,"ListHandling"(If[ListQ[#],First[#],#]&)];ageProperties〚;;2〛
| pullDataSlice |
Out[95]=
{Clinical::Patient::age_at_initial_pathologic_diagnosis34,Clinical::Patient::age_began_smoking_in_years21,Clinical::Patient::age_at_initial_pathologic_diagnosis50,Clinical::Patient::age_began_smoking_in_years12}
In[103]:=
ListPlot[ageProperties,PlotRangeAll,FrameTrue,FrameLabel{"age_at_initial_pathologic_diagnosis","age_began_smoking_in_years"},GridLinesAutomatic,GridLinesStyleLightGray]
Out[103]=
Additional examples
Additional examples
Distribution of the difference between age at diagnosis and age began smoking.
In[34]:=
ageProperties=
[dataStructure,{"Clinical::Patient::age_at_initial_pathologic_diagnosis","Clinical::Patient::age_began_smoking_in_years"},"DeleteMissing"True,"ListHandling"(If[ListQ[#],First[#],#]&)];
| pullDataSlice |
In[51]:=
ageProperties〚;;2〛
Out[51]=
{Clinical::Patient::age_at_initial_pathologic_diagnosis34,Clinical::Patient::age_began_smoking_in_years21,Clinical::Patient::age_at_initial_pathologic_diagnosis50,Clinical::Patient::age_began_smoking_in_years12}
In[52]:=
ageProperties=Merge[ageProperties,Identity]
Out[52]=
Clinical::Patient::age_at_initial_pathologic_diagnosis{34,50,43,63,51,25,41,34,80,49,42,37,56,51,35,64,55,33,56,49,35,36,45,57,27,37,78,69,61,54,47,47,50,43,36,58,46,44,65,34,68,47,65,21,85,48,33,38,51,40,29,63,34,42,46,24,42,46,38,44,33,53,54,26,32,31,58,79,45,35,24,48,38,38,60,55,37,53,74,43,54,46,32,47,51},Clinical::Patient::age_began_smoking_in_years{21,12,16,24,14,13,21,21,27,24,22,17,39,27,25,18,15,14,24,20,23,20,26,43,14,17,20,29,30,18,15,17,15,34,16,33,13,18,12,24,20,16,15,13,23,16,19,36,15,18,14,15,27,23,16,16,12,16,20,35,16,17,20,15,14,16,27,23,17,14,11,29,18,27,37,30,16,22,41,33,18,24,16,44,16}
In[53]:=
ageDifference=ageProperties["Clinical::Patient::age_at_initial_pathologic_diagnosis"]-ageProperties["Clinical::Patient::age_began_smoking_in_years"]
Out[53]=
{13,38,27,39,37,12,20,13,53,25,20,20,17,24,10,46,40,19,32,29,12,16,19,14,13,20,58,40,31,36,32,30,35,9,20,25,33,26,53,10,48,31,50,8,62,32,14,2,36,22,15,48,7,19,30,8,30,30,18,9,17,36,34,11,18,15,31,56,28,21,13,19,20,11,23,25,21,31,33,10,36,22,16,3,35}
In[57]:=
Histogram[ageDifference,Automatic,"Probability",PlotRangeAll,FrameTrue,GridLinesAutomatic,PlotLabel"Difference between\nage at diagnosis and age began smoking\n(years)"]
Out[57]=
Distribution of the difference between age at diagnosis and age began smoking, color coded by eastern cancer oncology group.
In[114]:=
patientData=
[dataStructure,{"Clinical::Patient::age_at_initial_pathologic_diagnosis","Clinical::Patient::age_began_smoking_in_years","Clinical::Patient::eastern_cancer_oncology_group"},"DeleteMissing"True,"ListHandling"(If[ListQ[#],First[#],#]&)];
| pullDataSlice |
In[115]:=
patientData〚;;2〛
Out[115]=
{Clinical::Patient::age_at_initial_pathologic_diagnosis50,Clinical::Patient::age_began_smoking_in_years12,Clinical::Patient::eastern_cancer_oncology_group1,Clinical::Patient::age_at_initial_pathologic_diagnosis43,Clinical::Patient::age_began_smoking_in_years16,Clinical::Patient::eastern_cancer_oncology_group2}
In[116]:=
groupedPatientData=GroupBy[patientData,#["Clinical::Patient::eastern_cancer_oncology_group"]&];
TCGADataTool visualizations
The TCGADataTool paclet includes custom visualizations for TCGA project data.
TCGADataTool specific visualization functions.
Create a swimmer plot for all patients treated with Cisplatin.
Plot overall survival rate.
Plot progression free survival rate.