Linkouts allow for a deeper exploration of the NG-CHM data by providing direct links to NCBI Databases, GeneCards, etc. This vignette demonstrates how to add linkouts to an NG-CHM.
These examples build on the setup from Getting Started.
Set Axis Type for Linkouts
To add linkouts, specify the axis type with
chmAddAxisType(). For the demo data in this example, row
labels correspond to genes, and are specified as HUGO gene symbols. The
column labels are full 28-character TCGA aliquot barcodes.
hm <- chmNew("tcga-brca", matrix_data)
hm <- chmAddAxisType(hm, "row", "bio.gene.hugo")
hm <- chmAddAxisType(hm, "column", "bio.tcga.barcode.sample.vial.portion.analyte.aliquot")Available Axis Types
The available axis types are:
- bio.gene.entrezid: NCBI Entrez Gene Identifier
- bio.gene.hugo: HUGO gene symbol
- bio.geo.acc: GEO accession id
- bio.go: Gene Ontology accession identifier
- bio.mdacc.pathwayid: PathwaysWeb pathway identifier
- bio.mirna: miRNA identifier
- bio.pathway.msigdb.name: msig DB pathway name
- bio.protein.uniprotid: Uniprot protein identifier
- bio.pubmed: PubMed identifier
- bio.tcga.barcode.sample: First 15 characters of TCGA aliquot barcode
- bio.tcga.barcode.sample.vial: First 16 characters of TCGA aliquot barcode
- bio.tcga.barcode.sample.vial.portion: First 19 characters of TCGA aliquot barcode
- bio.tcga.barcode.sample.vial.portion.analyte: First 20 characters of a TCGA aliquot barcode
- bio.tcga.barcode.sample.vial.portion.analyte.aliquot: Full 28 character TCGA aliquot barcode
- bio.transcript.ensembl: Ensembl transcript identifier
- bio.transcriptid: Entrez transcription identifier
- scholar: Google Scholar search term
- search: Generic search term