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

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NGCHM R package

NGCHM is an R package for creating Next-Generation Clustered Heat Maps. Next-Generation Clustered Heat Maps (NG-CHMs) allow for a dynamic exploration of heat map data in a web browser.

Our YouTube Video presents a brief overview of NGCHM usage and functionality.

Click Start Here! in the main menu to learn how to create an NG-CHM like the one below.

NG-CHM of Breast Cancer (BRCA) Data from The Cancer Genome Atlas (TCGA)

library(NGCHMDemoData)
library(NGCHMSupportFiles)
library(NGCHM)
unadjustedColorMap <- chmNewColorMap(c(6.4,10,14), c('mediumblue','snow','firebrick'))
rowCenteredColorMap <- chmNewColorMap(c(-2,0,2), c('#9933ff','#f0f0f0','#228B22'))
unadjustedLayer <- chmNewDataLayer('Unadjusted', TCGA.BRCA.ExpressionData, unadjustedColorMap)
rowCenteredData <- t(scale(t(TCGA.BRCA.ExpressionData)))
rowCenteredLayer <- chmNewDataLayer('Row-Centered', rowCenteredData, rowCenteredColorMap)
hm <- chmNew('TCGA BRCA Expression', unadjustedLayer, rowCenteredLayer)
covariateBar <- chmNewCovariate('TP53 Mutation',TCGA.BRCA.TP53MutationData)
hm <- chmAddCovariateBar(hm, 'column', covariateBar)
hm <- chmAddAxisType(hm, 'row', 'bio.gene.hugo')
hm <- chmAddAxisType(hm, 'column', 'bio.tcga.barcode.sample.vial.portion.analyte.aliquot')

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

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

MD-Anderson-Bioinformatics/NGCHM-R documentation built on April 1, 2024, 12:34 p.m.