# Comparison between SparseSignatures and other methods on simulated data.

A) Bar and line plot showing, for each method, the number of simulations in which it selected each value of K (number of signatures). The x-axis shows values of K and the y-axis shows the number of times each value was selected. Each method was run on 50 simulated datasets. In all cases, the correct value of K was 4. B) Box plots showing the residual error for the solutions produced by each method, over 50 simulations. Residual error was measured as the mean squared error (MSE) in reconstructing the original count matrix. C) Box plots showing the fraction of variance in the count matrix explained by the solutions produced by each method, over 50 simulations. D) Box plots showing the cosine similarity in reconstructing the 3 non-background input signatures, over 50 simulations. E) Box plots showing the mean squared error in reconstructing the exposure values for the 3 non-background input signatures, over 50 simulations. F) Box plots showing the sparsity of the signatures produced by each method, over 50 simulations. Sparsity was measured as the fraction of cells in the signature matrix whose value is <10^{−3}. SS: SparseSignatures. SP: SigProfiler. SA: SignatureAnalyzer. SR: signeR. SS-BG: SparseSignatures without fixed background. Source data are provided in S2 Table.