Enhancement: Configurable colour mapping for edit-graph - Githubissues

peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool

https://thapbi-pict.readthedocs.io/

MIT License

8 stars 2 forks source link

Enhancement: Configurable colour mapping for edit-graph #556

Open peterjc opened 1 year ago

peterjc commented 1 year ago

Currently the node colours in the edit-graph output are assigned using a hard-coded genus mapping, defined here:

https://github.com/peterjc/thapbi-pict/blob/v0.14.1/thapbi_pict/edit_graph.py#L33

https://github.com/peterjc/thapbi-pict/blob/v0.14.1/thapbi_pict/edit_graph.py#L476

In words

Unassigned - "#808080" # grey
Multiple genera - "#FF8C00" # dark orange
Oomycetes; Peronosporales:
- Phytophthora - "#FF0000", # Red
- Peronospora - "#00FF00", # Lime
- Hyaloperonospora - "#0000FF", # Blue
- Bremia - "#FFFF00", # Yellow
- Pseudoperonospora - "#00FFFF", # Cyan
- Plasmopara - "#FF00FF", # Magenta
- Nothophytophthora - "#800000", # Maroon
- Peronosclerospora - "#808000", # Olive
- Perofascia - "#008000", # Green
- Paraperonospora - "#800080", # Purple
- Protobremia - "#008080", # Teal
Nematoda:
- Globodera - "#FF0000", # Red
- Heterodera - "#00FF00", # Lime
synthetic - "#FFA500", # Orange
Any other genus - "#8B0000" # dark red

It would be nice to offer a user defined genus:color mapping as an optional argument. e.g. as a TSV file?

As a workaround, the user may alter the XGMML output display once loaded into CytoScape,