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:
More advanced TODO:
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