In epiviz/epivizWidgets: htmlwidgets based on the epiviz JS library

knitr::opts_chunk$set(cache=TRUE)

This is a prototype of embedding epiviz JS visualizations on Rmarkdown using the epivizWidgets package. This infrastructure is built on htmlwidgets.

Plotting an ExpressionSet. Compute average for tumor and normal, then make an MA plot.

require(epivizr)
require(antiProfilesData)

data(apColonData)

keep <- pData(apColonData)$SubType!="adenoma"
apColonData <- apColonData[,keep]
status <- pData(apColonData)$Status
Indexes <- split(seq(along=status),status)

exprMat <- exprs(apColonData)
mns <- sapply(Indexes, function(ind) rowMeans(exprMat[,ind]))
mat <- cbind(colonM=mns[,"1"]-mns[,"0"], colonA=0.5*(mns[,"1"]+mns[,"0"]))
assayDataElement(apColonData, "MA") <- mat
show(apColonData)

This is how it's used. apColonData is an ExpressionSet, columns specify which columns in assay MA are going to be plotted.

library(epivizWidgets)
epivizWidgets::scatterplot(apColonData, columns=c("colonA","colonM"), assay="MA")

TODO:

• add epiviz decorations (tool-tips, settings dialogs).
• fix issue with CSS styles

More advanced TODO:

• use the epiviz event infrastructure to implement highlight-on-hover.

epiviz/epivizWidgets documentation built on May 16, 2019, 8:18 a.m.