Fig. 3

Classification performance across the PbmcBench datasets. a Heatmap showing the median F1-scores of the supervised classifiers for all train-test pairwise combination across different protocols. The training set is indicated in the gray box on top of the heatmap, and the test set is indicated using the column labels below. Results shown to the left of the red line represent the comparison between different protocols using sample pbmc1. Results shown to the right of the red line represent the comparison between different samples using the same protocol, with pbmc 1 used for training and pbmc2 used for testing. Boxplots on the right side of the heatmap summarize the performance of each classifier across all experiments. The mean of the median F1-scores, also used to order the classifiers, is indicated in the boxplots using a red dot. Boxplots underneath the heatmap summarize the performance of the classifiers per experiment. For SCINA_DE, Garnett_DE, and DigitalCellSorter_DE, different numbers of marker genes were tested. Only the best result is shown here. b Median F1-score of the prior-knowledge classifiers on both samples of the different protocols. The protocol is indicated in the gray box on top of the heatmap, and the sample is indicated with the labels below. Classifiers are ordered based on their mean performance across all datasets