kegg-map-kit
Colour KEGG pathway maps from a table of KEGG Ontology (KO) identifiers and render the result as SVG. A scriptable, SVG-producing counterpart to the KEGG Mapper Color tool.
Zero runtime dependencies — Python 3.10+ and the standard library.
Example
Glycolysis (ko00010) coloured from twelve values. Each box carries its EC
number redrawn on top of an opaque fill, so the caption stays legible at any
colour; the value is printed beneath; KO boxes with no data are grey; and the
colorbar is pinned to a fixed range so separate maps stay comparable.
kegg-map-kit ko00010 -i examples/demo.tsv -o glycolysis.svg \
--cmap coolwarm --vmin -2.5 --vmax 2.5 \
--box-labels ec --unmapped-color '#ececec' --label-values
The numbers in examples/demo.tsv are synthetic.
examples/glycolysis_vector.svg is the same
data through --mode vector: no bitmap at all, so it rasterises losslessly at
any resolution, at the cost of KEGG's arrows and decorations.
Install
uv tool install kegg-map-kit
# or
pip install kegg-map-kit
Use
kegg-map-kit ko00010 -i data.tsv -o map.svg
data.tsv holds a KO identifier per line, followed by either colours or numbers:
K00844 #ff0000
K01810 blue
K00845 #00ff00,#000000
The third line uses KEGG Mapper's bg,fg syntax: the second colour sets the
box's label colour in --mode vector. Fields may be separated by tabs, commas
or spaces, so a file written for KEGG Mapper works unchanged. Only whole lines
beginning with # are treated as comments; there are no trailing comments.
or values, which are mapped through a colormap and get a legend:
K00844 2.0 1.4
K01810 -1.5 -0.2
Several columns, or several KOs sharing one box, split that box into vertical slices (up to 12).
Options
| Flag | Default | Meaning |
|---|---|---|
--mode raster|vector |
raster |
raster embeds KEGG's map PNG and paints on top; vector redraws boxes from KGML alone |
--cmap NAME |
coolwarm |
coolwarm, RdBu, viridis, Reds, Blues |
--vmin / --vmax |
auto | Colour scale bounds. Diverging maps auto-scale symmetrically |
--opacity |
0.75 |
Overlay opacity in raster mode |
--offline |
off | Use the cache only, never the network |
--cache DIR |
$XDG_CACHE_HOME/kegg-map-kit, else ~/.cache/kegg-map-kit |
Cache location |
--kgml / --png |
— | Use local files instead of fetching |
--na-color COLOR |
— | Fill for blank cells; blank cells are skipped by default |
--unmapped-color COLOR |
— | Fill for KO boxes the input has no data for. Boxes carrying no KO at all (compounds, links to other maps) are left as KEGG drew them |
--box-labels ko|symbol|ec |
— | Repaint each box's caption on top of the fill, so an opaque colour stays readable. ec reproduces the string KEGG itself prints in the box. Implies --opacity 1.0 |
--box-label-color, --box-label-size |
auto, 7 |
Box label colour (default: auto black/white by fill darkness) and font size |
--blend normal|multiply |
normal |
multiply keeps KEGG's own captions legible under a translucent fill |
--label-values |
off | Print each value beneath its box. Value input only |
--label-size |
7 |
Font size for --label-values |
--no-legend, --no-links |
— | Suppress the colorbar / the links to KEGG |
-q |
off | Suppress the summary line |
Coloured boxes carry hover text and link to their KEGG entry page.
KEGG data is cached indefinitely under --cache; delete that directory to
refresh.
Exit codes
| Code | Meaning |
|---|---|
0 |
Success |
1 |
User error — bad pathway id, unusable command line, malformed input table, unknown colormap, --png with --mode vector, offline cache miss, KEGG 404, corrupt map image |
2 |
Network failure with no usable cache |
Exit 2 means the network, and only the network, so a script can retry on 2 and give up on 1.
Scope
v0.1.0 handles KO-level maps (ko#####) and colours rectangle entries only.
Compounds, organism-specific gene IDs, and the line-based global maps such as
ko01100 are not coloured.
Licence
MIT. KEGG data is © Kanehisa Laboratories and is subject to the KEGG terms of use; this tool only retrieves and renders it.
1 maintainer
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