Fig. 5: Cell contact networks.
From: Temporo-spatial cellular atlas of the regenerating alveolar niche in idiopathic pulmonary fibrosis
a–c Output for Cell Contact Network (CCN) for alveolar epithelial -immune cell pairs, depicting pairs of cell type A (here. alveolar epithelial cell types) that are in contact with at least one of cell type B (here, immune cell types) at a frequency greater than expected under complete spatial randomness (CSR), and where z score between observed and random contact has p < 0.05 (shown as bubbles). Broken circles Identify pairs of alveolar epithelial cell-immune cell types (we have not included pairs containing _UD cell types). Immune-immune or epithelial- epithelial pairings. Pairs with ‘UD’ cell clusters are not circled. Left upper quadrant - ‘anchor cells’ are alveolar epithelial cell; right lower quadrant output mirrors the left upper quadrant but ‘anchor cells’ are immune cell types. d–f CCN network for all cell type pairs showing ‘communities’ of directly contacting cell pairs (grey and lime coloured spaces). Connecting lines join cell type pairs that are in direct contact with each other with greater frequency than complete spatial randomness, and with z scores that have FDR q values < 0.05. Size of nodes represents number of cells per mm2, thickness of lines represents number of contacts between cell types A and B. Grey spaces—communities of immune cells (purple nodes); lime spaces—communities of alveolar epithelial cells (yellow nodes). Note we have included the UD’s in the network to show all cell types. Broken circles highlight ABI_b-DC ADJ and CD206hi macrophage pairs, which at all stages, link up aberrant alveolar epithelial communities with immune cell communities. Source data are available in Source Date File.
