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Fig. 3 | BMC Bioinformatics

Fig. 3

From: scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

Fig. 3

Cell typing with different cell typing options in scTyper. a. A bar plot shows the proportion of cell type assignments by using the six methods according to the use of different cell typing methods (i.e., NTP, ES, and average values) and the inferCNV-based malignant cell typing. The results are also compared with that of the original study (Puram et al.). b. A heatmap shows the cell typing result with the gene expression levels of the 9 cell types of ‘Puram.2017.HNSCC.TME’. For each method, the assigned cell types are indicated by color bars (top). The inferred CNV values for each cell are shown (bottom). The cells with the CNV values greater than 90 percentile of the CNV values of immune cells were considered to have DNA copy number aberration and designated as malignant cells (red color bars). The malignant cells were assigned by cell typing methods (predicted as ‘Epithelial cell’) or CNV values (CNV values for reference cells > Q90, i.e., 86.44). c. Venn diagrams show the overlapped counts of the malignant cells assigned by the three cell typing methods without (top) or with (bottom) inferCNV analysis. The cell type assignment from the original study (Puram et al.) is also compared

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