Getting Started with canvasXpress in R

Isaac Neuhaus

2016-12-22

Overview

canvasXpress was developed as the core visualization component for bioinformatics and systems biology analysis at Bristol-Myers Squibb. It supports a large number of visualizationsto display scientific and non-scientific data. canvasXpress also includes a simple and unobtrusive user interface to explore complex data sets, a sofisticated and unique mechanism to keep track of all user customization for Reproducible Research purposes, as well as an ‘out of the box’ broadcasting capability to synchronize selected data points in all canvasXpress plots in a page. Data can be easily sorted, grouped, transposed, transformed or clustered dynamically. The fully customizable mouse events as well as the zooming, panning and drag’n drop capabilities are features that make this library unique in its class.

canvasXpress can be now simply used within R at the console to generate conventional plots, in R-Studio or seamlessly embeded in Shiny web applications. An full-fledged example of the canvasXpress library including the mouse events, zooming, and broadcasting capabilities is included in this package in the shiny directory. This canvasXpress R library was created with the htmlwidgets package.

Examples

Scatter 3D Plot

data <- t(iris[,1:4])
varAnnot <- as.matrix(iris[,5])
colnames(varAnnot) <- "Species"
canvasXpress(t(data), varAnnot=varAnnot, graphType='Scatter3D', colorBy='Species')
Scatter3D

Scatter3D

Scatter 2D Plot

data <- t(iris[,1:4])
varAnnot <- as.matrix(iris[,5])
colnames(varAnnot) <- "Species"
canvasXpress(t(data), varAnnot=varAnnot, scatterPlotMatrix=1, colorBy='Species')
Scatter2D

Scatter2D

Boxplot

data <- t(iris[,1:4])
smpAnnot <- as.matrix(iris[,5])
colnames(smpAnnot) <- "Species"
canvasXpress(data, smpAnnot=smpAnnot, graphType='Boxplot', groupingFactors=list('Species'))
# or
canvasXpress(data, smpAnnot=smpAnnot, graphType='Boxplot', afterRender=list(list('groupSamples', list('Species'))))
Boxplot

Boxplot

Heatmap

data <- t(iris[,1:4])
smpAnnot <- as.matrix(iris[,5])
colnames(smpAnnot) <- "Species"
canvasXpress(data, smpAnnot=smpAnnot, graphType='Heatmap', smpOverlays=list('Species'), variablesClustered=TRUE, showSampleNames=FALSE)
Heatmap

Heatmap

Four-way Venn Diagram

vennData <- data.frame(A=57, B=12, C=67, D=72, AB=4, AC=67, AD=25, BC=67, BD=27, CD=38, ABC=69, ABD=28, ACD=52, BCD=46, ABCD=3)
canvasXpress(vennData=vennData, graphType='Venn', vennGroups=4, vennLegend=list(A="List1", B="List2", C="List3", D="List4"))
Venn

Venn

Additional Information

Additional information and many examples with the JavaScript canvasXpress library can be found here.