Adding Linkouts

Source: vignettes/adding-linkouts.Rmd

This vignette demonstrates how to add linkouts to a NG-CHM. Linkouts allow for a deeper exploration of the NG-CHM data, for example by providing direct links to NCBI Databases, GeneCards, etc.

The needed packages are loaded and a basic NG-CHM is constructed from the sample data.

library(NGCHMDemoData)
library(NGCHM)
hm <- chmNew('tcga-brca', TCGA.BRCA.ExpressionData)

To add linkouts, the axis type is specified with chmAddAxisType(). For the demo data in this example, row labels correspond to genes, and are specified as HUGO gene symbols:

hm <- chmAddAxisType(hm, 'row', 'bio.gene.hugo')

The column labels in the demo data are full 28-character TCGA aliquot barcodes:

hm <- chmAddAxisType(hm, 'column', 'bio.tcga.barcode.sample.vial.portion.analyte.aliquot')

Resulting NG-CHM

Here is the resulting NG-CHM:

Available Axis Label Types

In the above example, the axis type was ‘bio.gene.hugo’. 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