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. 2023 May 18;26(6):106877. doi: 10.1016/j.isci.2023.106877

Figure 4.

Figure 4

Evaluation of the scHPL classifier

(A) Boxplot of median F1 scores (y axis) computed over 6-folds in three different scenarios (x axis). From left to right, scHPL trained with MKA∗, Azimuth’s label transfer using the HubMAP reference available33 and Azimuth’s label transfer using MKA∗ as reference. Each dot corresponds to the median F1 score computed across cell populations for a given training and validation set (i.e. MKA∗ and each of the annotated datasets in MKA respectively).

(B–D) Confusion matrices normalized by class support size, computed using the predicted annotations by scHPL and our Atlas reference (B), the transferred labels from Azimuth’s human kidney reference.32 (C) or the transferred labels from Azimuth using our reference (D). Higher values indicate higher agreement between predicted and true cell labels.

(E–H) UMAP plot of the Miao21 dataset colored by the original cell types (after manual re-annotation) (E), by the predicted cell types from the learned classification tree (F), by the transferred cell types from the Azimuth human reference (G) and by the transferred labels using Azimuth with our Atlas reference (H). IC: Intercalated Cell, ICA: Intercalated Cell Type A, ICB: Intercalated Cell Type B, Endo: Endothelial Cell, Fib: Fibroblast, Macro: Macrophage, B lymph: B lymphocyte, Stroma: Stroma cell, NK: Natural Killer, T lymph: T lymphocyte, PT: Proximal Tubule, PTS1: Proximal Tubule Segment 1, PTS2: Proximal Tubule Segment 2, PTS3: Proximal Tubule Segment 3, PTS3T2: Proximal Tubule Segment 3 Type 2, PC: Principal Cell, PEC: Parietal Epithelial Cell, Per: Pericyte, DCT: Distal Convoluted Tubule, ATL: Ascending Thin Limb of Henle, MD: Macula Densa, LOH: Loop of Henle, CTAL: Thick Ascending Limb of Henle in Cortex, MTAL: Thick Ascending Limb of Henle in Medulla, CNT: Connecting Tubule, Podo: Podocyte, DTL: Descending Thin Limb of Henle, MC: Mesangial Cell, Neutro: Neutrophil, Asc-Vas-Recta (Asc VR): Ascending Vasa Recta, Desc-Vas-Recta (Desc VR): Descending Vasa Recta, Glom Endo: Glomeruli Endothelial.