Q (sonnet): Give me an OncoPrint for RTK genes in lung cancer, limited to driver events.

▶ resolve_and_route
{
 "studyKeywords": [
  "TCGA",
  "lung",
  "adenocarcinoma"
 ]
}

◀ result
{"success":true,"message":"Found 4 matching studies. Pick the best match (prefer TCGA → prefer PanCancer Atlas), use its metadata to call the appropriate navigation tool(s) and generate URLs immediately. Present other studies as alternatives.","data":{"totalCount":4,"studiesWithMetadata":[{"studyId":"luad_tcga","name":"Lung Adenocarcinoma (TCGA, Firehose Legacy)","sampleCount":586,"studyViewUrl":"https://www.cbioportal.org/study?id=luad_tcga","metadata":{"clinicalAttributeIds":["AGE","AJCC_CLINICAL_TUMOR_STAGE","AJCC_METASTASIS_CLINICAL_CM","AJCC_METASTASIS_PATHOLOGIC_PM","AJCC_NODES_CLINICAL_CN","AJCC_NODES_CLINICAL_CT","AJCC_NODES_PATHOLOGIC_PN","AJCC_PATHOLOGIC_TUMOR_STAGE","AJCC_STAGING_EDITION","AJCC_TUMOR_PATHOLOGIC_PT","ALK_ANALYSIS_TYPE","ALK_TRANSLOCATION_STATUS","ALK_TRANSLOCATION_VARIANT","CANCER_TYPE","CANCER_TYPE_DETAILED","CARBON_MONOXIDE_DIFFUSION_DLCO","DAYS_TO_COLLECTION","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DAYS_TO_PATIENT_PROGRESSION_FREE","DAYS_TO_SPECIMEN_COLLECTION","DAYS_TO_TUMOR_PROGRESSION","DFS_MONTHS","DFS_STATUS","DISEASE_CODE","ECOG_SCORE","ETHNICITY","EXTRANODAL_INVOLVEMENT","FEV1_FVC_RATIO_POSTBRONCHOLIATOR","FEV1_FVC_RATIO_PREBRONCHOLIATOR","FEV1_PERCENT_REF_POSTBRONCHOLIATOR","FEV1_PERCENT_REF_PREBRONCHOLIATOR","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","HISTOLOGICAL_DIAGNOSIS","HISTORY_IMMUNOLOGICAL_DISEASE","HISTORY_IMMUNOLOGICAL_DISEASE_OTHER","HISTORY_NEOADJUVANT_TRTYN","HISTORY_OTHER_MALIGNANCY","HISTORY_RELEVANT_INFECTIOUS_DX","HIV_STATUS","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","INITIAL_PATHOLOGIC_DX_YEAR","IS_FFPE","KARNOFSKY_PERFORMANCE_SCORE","KRAS_GENE_ANALYSIS_INDICATOR","KRAS_MUTATION","KRAS_MUTATION_IDENTIFIED_TYPE","LATERALITY","LOCATION_LUNG_PARENCHYMA","LONGEST_DIMENSION","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT_OTHER","METHOD_OF_SAMPLE_PROCUREMENT","MUTATION_COUNT","MUTATION_STATUS","MUTATION_TYPE","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","NUMBER_OF_LYMPHNODES_POSITIVE_BY_IHC","OCT_EMBEDDED","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER_METHOD_OF_SAMPLE_PROCUREMENT","OTHER_PATIENT_ID","OTHER_SAMPLE_ID","PATHOLOGY_REPORT_FILE_NAME","PATHOLOGY_REPORT_UUID","PERFORMANCE_STATUS_TIMING","PHARMACEUTICAL_TX_ADJUVANT","POS_LYMPH_NODE_LOCATION","PRIMARY_SITE_OTHER","PRIMARY_SITE_PATIENT","PROJECT_CODE","PROSPECTIVE_COLLECTION","PULMONARY_FUNCTION_TEST_INDICATOR","RACE","RADIATION_TREATMENT_ADJUVANT","RESIDUAL_TUMOR","RETROSPECTIVE_COLLECTION","SAMPLE_COUNT","SAMPLE_INITIAL_WEIGHT","SAMPLE_TYPE","SAMPLE_TYPE_ID","SEX","SHORTEST_DIMENSION","SMOKING_PACK_YEARS","SMOKING_YEAR_STARTED","SMOKING_YEAR_STOPPED","SOMATIC_STATUS","SPECIMEN_CURRENT_WEIGHT","SPECIMEN_FREEZING_METHOD","SPECIMEN_SECOND_LONGEST_DIMENSION","STAGE_OTHER","TARGETED_MOLECULAR_THERAPY","TIME_BETWEEN_CLAMPING_AND_FREEZING","TIME_BETWEEN_EXCISION_AND_FREEZING","TISSUE_SOURCE_SITE","TMB_NONSYNONYMOUS","TOBACCO_SMOKING_HISTORY_INDICATOR","TREATMENT_OUTCOME_FIRST_COURS … (6466 more chars)

▶ navigate_to_results_view
{
 "studyIds": [
  "luad_tcga_pan_can_atlas_2018"
 ],
 "genes": [
  "EGFR",
  "ALK",
  "MET",
  "ERBB2",
  "RET",
  "ROS1",
  "FGFR1",
  "KIT",
  "PDGFRA",
  "NTRK1"
 ],
 "tab": "oncoprint"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=EGFR%0AALK%0AMET%0AERBB2%0ARET%0AROS1%0AFGFR1%0AKIT%0APDGFRA%0ANTRK1&case_set_id=luad_tcga_pan_can_atlas_2018_all","url":"https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=EGFR%0AALK%0AMET%0AERBB2%0ARET%0AROS1%0AFGFR1%0AKIT%0APDGFRA%0ANTRK1&case_set_id=luad_tcga_pan_can_atlas_2018_all","data":{"studyIds":["luad_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"luad_tcga_pan_can_atlas_2018","name":"Lung Adenocarcinoma (TCGA, PanCancer Atlas)","sampleCount":566}],"genes":["EGFR","ALK","MET","ERBB2","RET","ROS1","FGFR1","KIT","PDGFRA","NTRK1"],"caseSetId":"luad_tcga_pan_can_atlas_2018_all","pageDescription":"Visual summary of alterations in queried genes across samples."}}

═ answer (success)
Note: the tool did not expose a driver-only alteration filter parameter for the OncoPrint tab, so the link above shows **all alterations** (not restricted to drivers). To limit the OncoPrint to putative driver events only, use the in-page control:

1. Open the link below.
2. In the OncoPrint toolbar, click **"Mutations"** → check **"Show only putative driver mutations"** (annotated via OncoKB/CIViC/hotspots, depending on portal configuration).
3. Similarly restrict CNA calls to putative drivers if that filter is available for this study.

**[View RTK Gene OncoPrint — Lung Adenocarcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=EGFR%0AALK%0AMET%0AERBB2%0ARET%0AROS1%0AFGFR1%0AKIT%0APDGFRA%0ANTRK1&case_set_id=luad_tcga_pan_can_atlas_2018_all)**

- **Study:** Lung Adenocarcinoma (TCGA, PanCancer Atlas) — 566 samples
- **RTK genes queried:** EGFR, ALK, MET, ERBB2, RET, ROS1, FGFR1, KIT, PDGFRA, NTRK1

If you'd like, I can also add lung squamous cell carcinoma (LUSC) to this panel, or run a query first to report driver-mutation frequencies numerically (using OncoKB driver annotations in the database) before you view the OncoPrint — let me know which cohort/scope you want.