Output files

Calling kaleidocell.get_html() writes a self-contained HTML report and a set of companion files to the same directory. All image paths are embedded as base64 in the HTML so the report can be shared as a single file.

File	Description	Condition
results.html	Self-contained tabbed HTML report with heatmap, metrics, UMAP scores, GSEA bar plots, gene tables, and violin plots.	Always
genes.csv	Long-format gene signature table with columns gene, mp, score. One row per gene per meta-program.	Always
heatmap.pdf	Cosine-similarity matrix coloured by cluster assignment.	Always
umap_scores.pdf	Panel of UMAP embeddings coloured by per-cell MP scores.	Requires mp_scores
gsea_{label}.csv	Significant GSEA terms for each GMT file, with columns MP, Term (and NES, FDR q-val for preranked GSEA).	When GSEA finds significant results
gsea_{label}_{MP}.pdf	Bar plot of top enriched terms for one MP × one GMT file. One PDF per MP per GMT file.	When GSEA finds significant results
violins_{obs_key}.pdf	Violin plots of MP score distributions across the categories in obs_key. One PDF per figure (each figure contains all MPs).	Requires obs

Example directory listing after a full run

results/
├── results.html
├── genes.csv
├── heatmap.pdf
├── umap_scores.pdf
├── gsea_GO_Biological_Process.csv
├── gsea_GO_Biological_Process_MP1.pdf
├── gsea_GO_Biological_Process_MP3.pdf
├── gsea_Hallmarks.csv
├── gsea_Hallmarks_MP1.pdf
├── gsea_Hallmarks_MP3.pdf
├── violins_Treatment.pdf
└── violins_Patients.pdf