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Abstract:
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Statistical work in neuroimaging has increased steadily over the years. As such, a large number of packages for neuroimaging analysis have been developed such as fmri, oro.nifti, AnalyzeFMRI, FIACH, ANTsR, and fslr. As the data are 3-dimensional, visualizing this data can be challenging. Plotting neuroimaging data in R has primarily been done using multiple views of slices of the brain, multiple views of the same area of the brain in different directions (x,y,z), or 3-dimensional rendering using packages such as rgl.
Neuroimaging visualization software exists, such as Mango, but does not interface easily with R, require third-party requirements.
The Mango software does have a pure JavaScript implementation, however, called Papaya. The goal of the papayar package (https://github.com/muschellij2/papayar) was to create a widget for R that allows users to pass images from R and create the necessary HTML to view the images using the Papaya library. This allows users to integrate interactive displays of neuroimage data into the capabilities present in R, such as embedding them into a report made with Rmarkdown and knitr, or a webpage with interactive controls using Shiny.
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