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kmer-ord visualise

Generate static plots from a kmer-ord SQLite/SpatiaLite database.

This command provides:

  • embedding visualisations (UMAP, t-SNE, etc.)
  • feature distributions
  • categorical comparisons

Usage

kmer-ord visualise [OPTIONS]

Required arguments

Parameter Flag Type Default Description
Database path -d, --db path — SQLite/SpatiaLite database generated by project or cluster

Plot selection

Parameter Flag Type Default Description
Embedding plots --embeddings / --no-embeddings bool True Enable/disable embedding plots
Feature plots --features / --no-features bool True Enable/disable feature plots

Embedding visualisation

Parameter Flag Type Default Description
Embedding mode --embedding-mode string all Plot type: density, categorical, continuous, all
Max categories --max-categories int 10 Limit number of categories in categorical plots

Embedding modes

Mode Description
density Point density representation (useful for large datasets)
continuous Colour by numeric features
categorical Colour by categorical features
all Generate all plot types

Output

Plots are written to:

<output_dir>/plots/

plots/
├── embeddings/
│   ├── umap/
│   ├── tsne/
│   └── ...
├── features/
    ├── continuous/
    └── categorical/

Examples

Generate all plots

kmer-ord visualise \
  -d results/kmer-ord.sqlite

Only embedding plots

kmer-ord visualise \
  -d results/kmer-ord.sqlite \
  --no-features

Continuous-only embedding plots

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

When to use visualise

Use this command when you want to: auto generate figures inspect embeddings without launching the app quickly explore dataset structure

Use instead:

  • project: to generate embeddings
  • cluster: to assign cluster labels
  • bin: for interactive binning

See also: