Fig. 2: The performance of TrimNN on spatial omics. | Nature Communications

Fig. 2: The performance of TrimNN on spatial omics.

From: TrimNN: characterizing cellular community motifs for studying multicellular topological organization in complex tissues

Fig. 2: The performance of TrimNN on spatial omics.The alternative text for this image may have been generated using AI.

A Simulations of missing cell effects on CC motifs, represented as the Spearman correlation between abundance rankings of all the possible motifs before and after simulated noises at cell proportions of 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, and 0.5 within CC motifs in size-1, size-2, size-3, size-4, and size-5 (n = 100). B Simulations of cell coordinate shifting effects on CC motifs, represented as the Spearman correlation between abundance rankings of all the possible motifs before and after simulated noises with different levels of noises of 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, and 0.5 at cell proportions of 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, and 0.5 within CC motifs in size-1, size-2, size-3, size-4, and size-5 (n = 100). C Simulations of cell-type misclassification effects on CC motifs, represented as the Spearman correlation between abundance rankings of all the possible motifs before and after simulated noises at cell proportions of 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, and 0.5 within CC motifs in size-1, size-2, size-3, size-4, and size-5 (n = 100). D Benchmarking the performance of TrimNN, TrimNN-RGIN, and NSIC on independent simulated data for subgraph matching (n = 3000). The X-axis represents different sizes of CC motifs, and the Y-axis indicates the MCC (Matthews Correlation Coefficient) values. E Performance comparison of TrimNN, TrimNN-RGIN, and NSIC in identifying occurrences of CC motifs in diverse simulated datasets. The Y-axis is the RMSE (Root Mean Square Error) value. F Scalability of TrimNN. The X-axis represents the size of the triangulated graph, and the Y-axis indicates the runtime on a workstation equipped with an Intel Xeon Gold 6338 CPU and 80 G RAM. G Ablation tests on performance comparison adding the positional encoding of TrimNN model (n = 3000). The X-axis represents different sizes of CC motifs, and the Y-axis indicates the MCC values. CC: cellular community. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles. The whiskers extend to the most extreme data points without outliers, and the outliers are plotted individually as circles. Source data are provided as a Source Data file.

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