Fig. 5
From: Decontamination of ambient RNA in single-cell RNA-seq with DecontX
Cluster similarity before and after decontamination. a tSNE of 19 cell clusters from the PBMC 4K dataset before decontamination. b Decontamination with DecontX improved separation on tSNE between different cell clusters. c The mean silhouette width was derived for each cluster before and after decontamination with DecontX. Each point represents the difference in the mean silhouette width for each cluster. All clusters except 17 showed an increase in silhouette width after decontamination. Cluster 17 was predicted to contain mostly doublets by Scrublet. Cluster 1 had only one cell and was not included in the analysis. d Predicted doublets had significantly higher levels of estimated contamination compared to singlets. The median contamination for doublets was 41.77% (7.32–95.08%) while the median for singlets was 7.02% (0.07–65.64%)