examples/Interacting_Vignette.md

In PFPrzytycki/CellWalkR: An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements

Interacting with your cellWalk object

Pawel F. Przytycki 2021-07-01

Once a cellWalk object has been created, downstream analysis can be performed using an interactive interace. Several additional R packages are required for the interface to function:

install.packages("shiny")
install.packages("plotly")
install.packages("ggplot2")
install.packages("reshape2")

Once required packages are installed, an interface can be launched as follows:

launchViz(cellWalk)

To be able to compute label scores for bulk data, the cellWalk object will need to raw ATAC data to be associated with it:

cellWalk <- storeMat(cellWalk, ATACMat, peaks)

Alternatively, if label scores for bulk data have already been computed (as desribed in the main vignette), they can be added to the cellWalk object before launching the vizualization:

cellWalk <- storeBulk(cellWalk, bulkPeaks, labelScores)

PFPrzytycki/CellWalkR documentation built on Oct. 26, 2023, 1:50 p.m.