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Create a NG-CHM

This vignette demonstrates how to construct a simple NG-CHM and save it as a file that can be opened in the NG-CHM Viewer . The following sections are below:

Sample NG-CHM Data

This vignette uses an additional package of demo data, NGCHMDemoData , which can be installed from GitHub with remotes :

remotes::install_github('MD-Anderson-Bioinformatics/NGCHMDemoData', ref='main')

and loaded into the current environment:

library(NGCHMDemoData)

The sample data includes a matrix of mRNA expression data, TCGA.GBM.Expression, for 3540 genes (rows) and 169 samples (columns) from the Glioblastoma Multiforme TCGA data. In order to be used as the basis for an NG-CHM, a matrix should have both rownames and colnames. Here the rownames are genes and the colnames are TCGA sample identifiers:

TCGA.GBM.ExpressionData[1:4,1:2]
#           TCGA-06-0178-01A-01R-1849-01 TCGA-02-2483-01A-01R-1849-01
# TNFAIP8L3                   0.04324498                  -1.12556612
# SYK                        -0.12174522                   0.03007443
# C2                          0.07445546                  -0.21648993
# ACP5                        1.45195866                   0.12276042

The sample data also includes a vector of TP35 mutation status for the TCGA samples in the matrix. This data will be used to construct a covariate bar in Covariate Bars and Discrete Color Maps. In order to be used as the basis for a covariate bar, a vector should have at least one name in common with the colnames of the matrix.

TCGA.GBM.TP53MutationData[1:2]
# TCGA-06-0178-01A-01R-1849-01 TCGA-02-2483-01A-01R-1849-01 
#                        "WT"                        "MUT"

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Creating a NG-CHM

Using the data loaded above, the chmNew() function can be used to create an NG-CHM:

library(NGCHM)
hm <- chmNew('tcga-gbm', TCGA.GBM.ExpressionData)

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Export to File

The NG-CHM created above can be exported to two different file types:

  1. A stand-alone HTML file that can be emailed to collaborators and opened in a standard browser.
  2. A ‘.ngchm’ file that can be opened in the NG-CHM Viewer .

Both methods use files from the NGCHMSupportFiles package referenced in the installation instructions. When loaded, NGCHMSupportFiles sets a two environment variables that point to these additional files.

library(NGCHMSupportFiles)

The NG-CHM can be exported as a stand-alone HTML file with the chmExportToHTML() funciton. The first argument is the NG-CHM created above. The second argument is the desired filename, and the third is a boolean dictating if any existing file of that name should be overwritten.

chmExportToHTML(hm,'tcga-gbm.html',overwrite=TRUE)

The file ‘tcga-gbm.html’ can be shared with collaborators and opened in a standard web browser.

Alternatively, .ngchm file can be created with the chmExportToFile() function.

chmExportToFile(hm,'tcga-gbm.ngchm',overwrite=TRUE)

The file ‘tcga-gbm.ngchm’ can be opened in the NG-CHM Viewer . NOTE: The filename must end with ‘.ngchm’ to open in the NG-CHM Viewer.

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