Figure 3.

Unsupervised clustering on core genes. (A). The left UMAP plot colors each gene by cluster, assigned through unsupervised Leiden clustering. The right UMAP plot displays the percentage of contrasts in which the gene was upregulated on a spectrum of red (upregulated in all contrasts) to blue (downregulated in all contrasts). We can see that the green and orange clusters roughly encompass the up and downregulated genes. (B). Results of GO analysis on Leiden clusters 0 and 1. The bar colors correspond to cluster. Bar length represents the proportion of genes enriched with the term in the cluster, and the line plot represents the FDR of the enrichment. (C) Heatmap of contrasts (columns) by genes (rows). Contrasts are labelled based on the experiment’s cell fraction, and genes are labelled based on their Leiden cluster. We can see the general downregulation in the orange cluster and the upregulation in the green cluster. We can also see from this figure that the other clusters are generally caused by extreme deviations in one or two studies.