Fig. 3: Comparisons between SPIDER and SOTA CCI methods on real PDAC dataset. | Nature Communications

Fig. 3: Comparisons between SPIDER and SOTA CCI methods on real PDAC dataset.

From: Finding spatially variable ligand-receptor interactions with functional support from downstream genes

Fig. 3

A Boxplot of six SVI-evaluation metrics, showing significantly higher scores of SPIDER-identified SVIs over those by SpatialDM, COMMOT, and stLearn, with those excluded as a baseline (n = 498 LRIs). The Geary score is again reversed. B Boxplot of the number of supporting svTFs per LRI among SPIDER svTF-supported LRIs, SpatialDM SVIs, stLearn and COMMOT LRIs (n = 374, 260, 346, and 320 LRIs, respectively). C Venn plot of svTF-supported LRIs, SpatialDM SVIs, and stLearn LRIs. D TSPAN14/15 signaling LRIs with their best supporting TF genes and correlations. E Barplot of the average number of ligands per receptor (left) and the average number of receptors per ligand (right) in three different LRI sets: SPIDER SVIs, SpatialDM SVIs, COMMOT and stLearn LRIs, and all LRIs in the database. F Barplot showing the number of TF supports for the top five SVI ranked by number of TF supports. G Dot plot of pathways enriched by each SVI and its supporting spatially variable TF genes. H Deconvoluted cell type annotations and the corresponding SPIDER SVIs with the five highest Pearson correlation coefficients. I Interaction patterns generated by LRIs identified by SPIDER and SpatialDM. J Heatmap of Pearson correlation coefficients between interaction patterns and PDAC region annotations, from SPIDER and SpatialDM, respectively. K Heatmap of pattern-indicated interaction between PDAC region annotations. PDAC: pancreatic ductal adenocarcinoma; corr: Pearson correlation coefficient. The boxplots display the median (center line), the 25th and 75th percentiles (box bounds), whiskers extending to the most extreme data points within 1.5 × the interquartile range, minima and maxima as the lowest and highest points within the whiskers, and outliers as individual points beyond the whiskers. The statistical significance of box plots is calculated using one-sided Mann-Whitney-Wilcoxon test with Benjamini-Hochberg correction, with the exact adjusted p-values listed in Supplementary Table 3 and the following significance annotations: ****: adjusted p-value ≤ 1.00e-04; ***: 1.00e-04  < adjusted p-value ≤ 1.00e-03; **: 1.00e-03  < adjusted p-value ≤ 1.00e-02; *: 1.00e-02  < adjusted p-value ≤ 5.00e-02. Source data are provided as a Source Data file.

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