Question received via GitHub https://github.com/Oshlack/splatter/issues/41

I was trying to simulate a differentiation, and followed the instructions for paths in Introduction to Splatter. However, when I then looked at the data with assay(sim.paths), I was greeted by a matrix where all columns (cells) had identical values. Am I doing something wrong? I was hoping to eventually simulate more complex lineage trees.

The code in question:

library(splatter)
sim.paths <- splatSimulate(method = "paths", verbose = FALSE)
sim.paths <- normalise(sim.paths)
View(assay(sim.paths))

When you run View(assay(sim.paths)) you are being shown the first matrix in the assays slot which contains some intermediate values.

To see the counts that have been produced you should use counts(sim.paths) or View(assay(sim.paths, "counts")).

A simple PCA plot coloured by the step along the path can also be helpful plotPCA(sim.paths, colour_by = "Step"). You should be able to see a trend from blue to yellow.

Thanks for giving Splatter a go, hope that helps!