Plot a consensus NMF k sweep

Stability and relative reconstruction error against k, the standard cNMF diagnostic. Pick the k where stability is still high and the error curve has not yet flattened out. Values of k whose consensus step failed have no stability point.

Usage

# S3 method for class 'NmfKSweepResult'
plot(x, ...)

Arguments

x

NmfKSweepResult object.

...

Additional params. Currently unused.

Value

A ggplot2 object with the two curves side by side.

References

Kotliar et al., eLife, 2019

Examples

# stability against reconstruction error across k
sc <- demo_single_cells()
res <- nmf_k_sweep_sc(
  sc,
  k_range = 2:4,
  n_runs = 3L,
  nmf_consensus_params = params_nmf_consensus(density_threshold = 2),
  .verbose = FALSE
)
plot(res)


unlink(sc@dir_data, recursive = TRUE, force = TRUE)