Customizing

Adding Custom Plots

The getMAFDashboard() function will accept a named list for adding arbitrary objects to the dashboard. Each item in the list will be displayed in separate tabs, and the name of the element will be used as the title of the tab.

Elements of the list can be:

• A boolean value: indicates whether or not to draw one of the preset plots provided by MAFDasoh
• A file path: any image format (or PDF)
• An R plot object: ggplot, plotly, ComplexHeatmap

This functionality can be used with or without providing a MAF file. When MAF data is not provided, the “Variant Table” tab of the dashboard is automatically omitted.

Toy example with iris data

library(ggplot2)
library(plotly)
library(ComplexHeatmap)

data(iris)

## Simple ggplot
myplot <- ggplot(iris) + geom_point(aes(x=Sepal.Length, y=Sepal.Width, color=Species))

## Save as PNG (provide absolute file path)
mycustomimage_png <- file.path(getwd(),"custom_ggplot.png")
ggsave(mycustomimage_png, plot=myplot, width=5, height=4)

## Save as PDF (provide absolute file path)
mycustomimage_pdf <- file.path(getwd(),"custom_ggplot.pdf")
ggsave(mycustomimage_pdf, plot=myplot, width=5, height=4)

## Convert ggplot to plotly
myplotly <- ggplotly(myplot)

## Make heatmap with ComplexHeatmap
hmdata <- t(iris[,1:4])
hmanno <- HeatmapAnnotation(df=data.frame(Species=iris[,5]))
myhm <- Heatmap(hmdata, bottom_annotation = hmanno)

## Customizable plotly from https://github.com/mtandon09/Dynamic_Plotly
source("https://raw.githubusercontent.com/mtandon09/Dynamic_Plotly/master/make_cutomizable_plotly.R")
custom_plotly <- make_customizable_plotly(iris)

## Put together objects/filepaths into a list
toyplotlist <- list("ggplot"= myplot,
                   "plotly"= myplotly,
                   "PNG"= mycustomimage_png,
                   "PDF"= mycustomimage_pdf,
                   "ComplexHeatmap"= myhm,
                   "Customizable"= custom_plotly
)

## Filename to output to
html_filename="toy_dash.html"

## Render dashboard
getMAFDashboard(plotList = toyplotlist,
                outputFileName = html_filename,
                outputFileTitle = "Iris")

Output

The output can be seen here.