Fig. 2: Benchmarking of sciCAN against other 5 existing integration methods.

a Integration evaluation by modality and cell-type silhouette scores across 5 datasets. x axis corresponds to modality silhouette score and y axis to cell-type silhouette score. Ideal integration should be located in the top right corner of each dot plot. To generate the dot plot, we randomly subsample 20% of the cell population to calculate both modality and cell-type silhouette scores for each method and each dataset. b Integration evaluation by F1 scores across 5 datasets. Upper panel corresponds to label transferring from RNA-seq to ATAC-seq (RtoA) while lower panel indicates label transferring from ATAC-seq to RNA-seq (AtoR). Boxplots are plotted based on F1 scores for all cell types in that dataset. The median value is marked with a horizontal line within the box, and the “X” mark represents the macro F1 score, which is the average of F1 scores for all cell types. Whiskers show minimum and maximum value and top and bottom of the box show 25th and 75th percentile respectively. c Benchmark ranking across 5 datasets. In each category, methods are ranked based on their scores from best (red, low number ranking) to worst (blue, high number ranking).