Extended Data Fig. 7: Robustness and validation of BayesPrism deconvolution.
(a) For each cell type, Spearman’s correlation of cell fraction across all spots was calculated between deconvolution using all available reads and 1 of 20 separate deconvolutions using the available reads downsampled to 90%. Points represent the mean of the 20 Spearman’s correlation calculations and error bars are the minimum and maximum correlation values. (b) Comparison of cell fractions across separately deconvolved serial sections. For all four biological samples, the average cell fraction for each cell type is plotted in the first serial section relative to the second. Trend line indicates a slope of 1. Spearman’s correlation is shown. (c) Comparison of average log cell fractions in each of 8 tissue sections using the standard scRNA-seq reference or the reference with tumor RNA substituted for KP-Tracer tumor cells. Trend line indicates a slope of 1. Spearman’s correlation is shown. (d, e). Examples of positive spots for certain populations of interest are associated with histological features. Images are from representative areas of control and Treg depleted tissue sections. Plots with positive spots display the same example areas in the top of each panel arrangement with the H&E stained image at lower resolution. (Br = bronchi; A/V = artery / vein; LV = lymphatic vessel). Analysis performed on (A-C) and images are representative of (D-E), one of two serial sections for each of four samples (DT and Ctrl two biological replicates each). One experiment was performed.
