Supplementary Figure 3: Exploration of SC3 pipeline parameters
(a) Histogram of the d values where ARI>.95 is achieved for the downsampled (by a factor of 10, Methods) gold standard datasets from Fig. 1b. The black vertical lines indicate the interval d = 4-7% of the total number of cells N, showing high accuracy in the classification; (b) Histogram of the d values where ARI>.95 is achieved for the silver standard datasets from Fig. 1b. The black vertical lines indicate the interval d = 4-7% of the total number of cells N, showing high accuracy in the classification; (c) Exploration of the gene filter parameters (see Methods for more details). Dots represent individual clustering runs. Bars correspond to the median of the dots; (d) The effect of dropouts in the distance calculations step on the accuracy of SC3 clustering (Methods for more details). Dots represent individual clustering runs. Bars correspond to the median of the dots. Red and grey colours correspond to clustering with and without dropouts. The black line corresponds to ARI=0.8.
