JaneShenGunther/TCGADataTool | Paclet Repository

JaneShenGunther`TCGADataTool`

swimmerPlot

swimmerPlot [data]
	takes as input a list of Associations and returns a swimmer plot. Each input association corresponds to a patient and must contains a key for each relevant column needed for swimmer plot computation.

Details and Options



Examples

(10)

Basic Examples

(1)

Get the example data structure for project TCGA-CESC and select a valid patient UUID from that data structure:

In[1]:=

dataStructure=

exampleDataTCGA

[{"TCGAProjectData","TCGACESCExceptGenomicDataAllPatients"},"Data"];

Set the drug name for which we will display the swimmer plot and the properties needed to create the plot:

In[2]:=

drugName="cisplatin";propertiesToReturn="bcr_patient_uuid","Clinical::Patient::clinical_stage", "Clinical::Drug::drug_name","Clinical::Drug::days_to_drug_therapy_start","Clinical::Drug::days_to_drug_therapy_end","Clinical::Drug::measure_of_response"



;

Extract the data from the data structure about patients being treated with "Cisplatin":

In[3]:=

patients=

pullDataSlice

[dataStructure,propertiesToReturn,"FilterProperty""Clinical::Drug::drug_name","FilterFunction"(MemberQ[ToLowerCase[#],drugName]&)];

Restrict to the lines relative only to the drug of interest:

In[4]:=

patients=Map[With[{patientData=#,pos=Position[#["Clinical::Drug::drug_name"],s_String/;StringMatchQ[s,drugName,IgnoreCaseTrue]]},Join[patientData,"Clinical::Drug::drug_name"Extract[patientData["Clinical::Drug::drug_name"],pos],"Clinical::Drug::days_to_drug_therapy_start"Extract[patientData["Clinical::Drug::days_to_drug_therapy_start"],pos],"Clinical::Drug::days_to_drug_therapy_end"Extract[patientData["Clinical::Drug::days_to_drug_therapy_end"],pos],"Clinical::Drug::measure_of_response"Extract[patientData["Clinical::Drug::measure_of_response"],pos]]]&,patients];

Show result for a random sample of 10 patients:

In[5]:=