examples/SnapPlot.md

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

Plotting Data with SnapATAC

Pawel F. Przytycki 2022-01-05

We can look at the tSNE that is generated by SnapATAC directly from the chromatin accessibility data (download here).

library("SnapATAC")
snapData <- readRDS("SampleSnap.rds")

First we generate the embedding and plot the CellWalkR labels onto it:

snapData <- runViz(snapData, tmp.folder = tempdir())
plotViz(snapData, point.color = cellWalk$cellLabels, point.size = .5, legend.add = TRUE, point.alpha=0.8, text.add=FALSE)

Then we cluster the data and plot those clusters in the embedding:

snapData <- runCluster(snapData, tmp.folder=tempdir(), louvain.lib="R-igraph", seed.use=10)
plotViz(snapData,  point.color = snapData@cluster, point.size = .5, legend.add = TRUE, point.alpha=0.8, text.add=FALSE)

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