In MD-Anderson-Bioinformatics/NGCHM-R: Next Generation Clustered Heat Maps

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

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:

library(NGCHMSupportFiles)
chmExportToHTML(hm,'tcga-brca-with-linkouts.html')

library('htmltools')
filePath = paste(getwd(),'/tcga-brca-with-linkouts.html',sep='')
htmltools::includeHTML(filePath)

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