Fig. 2 | Nature Communications

Fig. 2

From: Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

Fig. 2

Pancreatic islet cell type composition in healthy and T2D human samples. a, b Benchmarking of deconvolution accuracy on bulk data constructed by combining together scRNA-seq samples. a The bulk data is constructed for 10 subjects from Segerstolpe et al. while the single-cell reference is taken from the same dataset. The cell type proportions of healthy subjects are estimated by leave-one-out single cell reference. The subject names are relabeled; the table shows average root mean square error (RMSD), mean absolute deviation (mAD), and Pearson correlation (R) across all samples and cell types. b The bulk data is constructed for 18 subjects from Xin et al. while the single cell reference is six healthy subjects from Segerstolpe et al. c Jitter plots of estimated cell type proportions for Fadista et al. subjects, color-coded by deconvolution method. Of the 89 subjects from Fadista et al., only the 77 that have recorded HbA1c level are plotted, and T2D subjects are denoted as triangles while non-diabetic subjects are denoted as dots. d HbA1c vs beta cell type proportions estimated by each of 4 methods. The reported p-values are from single variable regression β cell proportion ~HbA1c. Multivariable regression results are reported in Supplementary Table 1. Supplementary Figure 7 shows the deconvolution results of Fadista et al. with the inDrop data from Baron et al. as single-cell reference. The corresponding multivariable regression results are shown in Supplementary Table 2. Source data are provided as a Source Data file

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