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Fig. 2 | BMC Genomics

Fig. 2

From: Characterising genome architectures using genome decomposition analysis

Fig. 2

GDA analysis of the Plasmodium falciparum genome. A UMAP embedding (n = 5) and HDBSCAN2 clustering (c = 50) of 5kbp windows using simple features derived from the genome sequence (seq feature set). B Projection of clusters onto the chromosomes highlights the localisation of cluster 0 windows at the very ends of chromosomes, with cluster 1 windows adjacent to these and within the cores of some chromosomes. C Heatmap showing features enriched in each cluster with seq feature set. Colours indicate the relative value of the feature in each cluster (red = highest, blue lowest), icons indicate significance (‘∧’ = KS test greater p-value <  = 1e-20, ‘∨’ = KS test lesser p-value <  = 1e-20, ‘-’ = great and lesser p-values <  = 1e-20) (D) UMAP embedding (n = 20) and HDBSCAN2 clustering (c = 50) of 5kbp windows with seq + gene + rep + orth feature set. E Projection of clusters onto chromosomes shows that the additional features break the subtelomeric regions into four distinct regions and that two types of islands (clusters 3 and 4) interrupt the core (cluster 2) on some chromosomes. F Heatmap showing features enriched in each cluster with all features

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