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.
In this example, a NG-CHM is created from the sample data described in Create a NG-CHM, and linkouts appropriate for the rows and columns are added.
First the needed packages are loaded and a basic NG-CHM is constructed from the sample data.
library(NGCHMDemoData) library(NGCHMSupportFiles) library(NGCHM) hm <- chmNew('tcga-gbm', TCGA.GBM.ExpressionData)
To add linkouts, the label type is specified for a given axis. The system will automatically apply appropriate linkouts when the NG-CHM is opened in the NGCHM Viewer .
The axis type is specified with chmAddAxisType(). The first argument is the NG-CHM. The second specifies if the axis is ‘row’ or ‘column’. The third argument is the type of axis. The available axis label types are listed in Available Axis Label Types below.
In this example, row labels correspond to genes, and are specified as HUGO gene symbols with
hm <- chmAddAxisType(hm, 'row', 'bio.gene.hugo')
The column labels in the demo data are full 28-character TCGA aliquot barcodes, and are specified with
hm <- chmAddAxisType(hm, 'column', 'bio.tcga.barcode.sample.vial.portion.analyte.aliquot')
As described in Creating a NG-CHM, the NG-CHM can be exported to a .ngchm or .html file with
When opening the file ‘tcga-gbm.ngchm’ in the NG-CHM Viewer , or the stand-alone ‘tcga-gbm.html’ file, appropriate gene linkouts will be available for the row labels, and TCGA bar codes available for the column labels..
In the above example, the axis type was ‘bio.gene.hugo’. The available axis types are: