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. Author manuscript; available in PMC: 2022 Jul 5.
Published in final edited form as: Nat Methods. 2021 Nov 1;18(11):1333–1341. doi: 10.1038/s41592-021-01282-5

Fig. 3 ∣. Evaluation of dimension reduction methods for single-cell chromatin data.

Fig. 3 ∣

a, UMAP representations of reduced-dimension single-cell DNA accessibility data for LSI (Signac), SCALE and SnapATAC for the full dataset and with the total number of counts per cell downsampled to 20% of the total counts. b, Runtimes for each of the dimension reduction methods profiled. CisTopic CGS, cisTopic collapsed Gibbs sampling; cisTopic Warp: cisTopic Warp-LDA. c, Mean k-NN cell type purity (k = 100) and (d) mean Silhouette score for each cell type in the dataset, for each dimension reduction method and downsampling level. For each box-plot, n = 20 points (cell types). For each box-plot, n = 6 points (cell types). Box-plot lower and upper hinges represent first and third quartiles. Upper/lower whiskers extend to the largest/smallest value no further than 1.5× the interquartile range. Data beyond the whiskers are plotted as single points.