Figure S6. Integration of multiplexed error-robust fluorescence in situ hybridization (MERFISH) mouse liver and kidney data with Tabula Muris Senis scRNA-seq using Harmony and Symphony.
(A) Spatial plot of MERFISH mouse liver dataset, colored by cell type annotations predicted by Symphony. (B) Spatial plot of MERFISH mouse kidney dataset, colored by cell type annotations predicted by Symphony. Qualitatively, the results are similar to the scANVI results (Figs 6D and 7D), reproducing the structure of the liver (Fig 6D) and the artifactual population of podocytes in the kidney medulla (Fig 7D). (C) Confusion matrix of MERFISH cell type annotations between the manual method and Symphony predictions for the mouse liver. The rows for other endothelial cells and hepatocytes (“o-EC” and “o-hep”) are blank because none of the manual annotations were in these groups. In addition, the row for bile duct epithelial cells (“BD-EC”) is noisy because none of the scRNA-seq reference cells possessed this annotation. (D) Confusion matrix of MERFISH cell type annotations between the manual method and Symphony predictions for mouse kidney. Like with scANVI (Figs 6F and 7F), Symphony generally is consistent with manual annotation, as can be seen by the higher values along the main diagonal. However, Symphony produces slightly more off-diagonal values than scANVI and also misclassifies podocytes and pericytes (Fig S6D) just like scANVI.