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Visualising embeddings

The visualise command generates static plots from a kmer-ord database.

It is typically used to inspect embeddings and feature distributions before interactive binning.

When to use visualisation

Use visualise when you want to:

  • quickly inspect embeddings without launching the interactive app
  • generate figures for reports or publications
  • explore feature distributions across embeddings

Example

kmer-ord visualise \
  -d results/kmer-ord.sqlite \
  --embedding-mode all

What it does

  • loads embeddings and features from the database
  • generates a series of plots
  • saves them as image files

Plots

Embedding plots

visualise read distributions in embedding space

  • density plots: highlight read density
  • categorical plots: colour by distrete features
  • continous plots: colour by numeric features

feature plots

Summaries of feature distributions across reads.

Embedding modes

The --embedding-mode option controls how embeddings are rendered

Mode Description
density Density-based visualisation
categorical Colour by categorical features
continuous Colour by numeric features
all Generate all plot types

Use all for exploration, and restrict modes when generating specific figures.

Output

All plots are saved to:

<output_dir>/plots/

Notes

visualise is complementary to the interactive app

  • use visualise for fast, static inspection
  • use bin for manual exploration and binning

See also: