Minimal working example for running Slingshot

slingshot_pseudotime_example.R

library(Seurat)
library(slingshot)
library(RColorBrewer)

# start with a Seurat object containing assay of normalised cell counts, with a PCA or TSNE
# for example:

#  > seuratobj
# An object of class Seurat
# features across 801 samples within 1 assay
# Active assay: RNA (832 features)
# 1 dimensional reduction calculated: pca




# Plot 1 : Plot slingshot pseudotime
slingshotObject <- slingshot(as.SingleCellExperiment(seuratobj))


colors <- rainbow(50, alpha = 1)
plot(reducedDims(slingshotObject)$PCA, col = colors[cut(slingshotObject$slingPseudotime_1,breaks=50)], pch=16, asp = 1)




# Plot 2 : Plot cell type with slingshot lineage calculation

# create matrix of PC_1, PC_2 values for each cell
cellLabels = as.double(seuratobj$seurat_clusters)
names(cellLabels) = labels(seuratobj$seurat_clusters)

# create matrix of PC_1, PC_2 values for each cell
reducedDimension = reducedDim(as.SingleCellExperiment(seuratobj))

# use slingshot to calculate lineage between cells in low dimensional space
lineage <- getLineages(reducedDimension, cellLabels)


# plot the cells by PC_1 and PC_2, and the lineage slingshot calculates
{plot(reducedDimension, col = brewer.pal(9,"Set1")[cellLabels], asp = 1, pch = 16)
lines(lineage, col = 'black')}