Extended Data Fig. 3: Protein background in cells and empty droplets.
From: Joint probabilistic modeling of single-cell multi-omic data with totalVI
a-c, Histogram of log(protein counts + 1) in the SLN111-D1 dataset for B cells, T cells, and empty droplets (Methods) for CD19 (a), CD20 (b), and CD28 (c). d-f, Fraction of empty droplets, B cells, or T cells with > 0 UMIs detected for a given RNA (left, hatched) or protein (right, solid). RNA/proteins displayed are Cd19/CD19 (d), Ms4a1/CD20 (e), and Cd28/CD28 (f). g, Barcode rank plot for all barcodes detected in the SLN111-D1 dataset. Red lines at 20 and 100 RNA UMI counts indicate the lower and upper bounds, respectively, used to define empty droplets in (a-f). h, Performance of totalVI and a Gaussian mixture model (GMM) fit on all cells for each protein of the SLN111-D1 dataset to classify cell types by marker proteins (Methods). Receiver operating characteristic (ROC) curves shown for CD19 (B cells), CD20 (B cells), or CD28 (T cells). Area under the receiver operating characteristic curve (ROC AUC score) was calculated using as input either the totalVI foreground probability or GMM foreground probability where the indicated cell type was the positive population out of all B and T cells.
