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. 2022 Feb 10;11:e71361. doi: 10.7554/eLife.71361

Figure 4. Topic modeling of EB cells.

(A) Structure plot showing the results of topic modeling at k = 6. Plot includes a random subset of 5,000 EB cells divided by Seurat cluster at resolution 0.1. (B) UMAP projection of cells colored by loading of topic 1. (C) Box plot showing the loading of topic 1 from the k = 6 topic analysis on each Seurat cluster at clustering resolution 0.1. (D) Box plot showing the loading of topic 1 from the k = 6 topic analysis on each Seurat cluster at clustering resolution 1. (E) Volcano plot showing genes differentially expressed between topic 1 and all other topics from the k = 6 topic analysis. Points are colored by the average count on the logarithmic scale.

Figure 4.

Figure 4—figure supplement 1. UMAP visualization of k = 6 topic loadings.

Figure 4—figure supplement 1.

Figure 4—figure supplement 2. Volcano plot showing genes differentially expressed in each topic from the k = 6 topic analysis.

Figure 4—figure supplement 2.

Points are colored by the average count on the logarithmic scale. The top 10 driver genes of each topic are labeled.
Figure 4—figure supplement 3. Topic loadings on Seurat clusters across clustering resolutions.

Figure 4—figure supplement 3.

Bar plots show the loading of each topic (from the k = 6 analysis) on each Seurat cluster at resolution 0.1 (A), resolution 0.5 (B), resolution 0.8 (C), and resolution 1 (D).