Seurat can help you find markers that define clusters via differential expression. By default, it identifes positive and negative markers of a single cluster (specified in ident.1 ), compared to all other cells. FindAllMarkers automates this process for all clusters, but you can also test groups of clusters vs. each other, or against all cells. Seurat is great for scRNAseq analysis and it provides many easy-to-use ggplot2 wrappers for visualization. However, this brings the cost of flexibility. For example, In FeaturePlot, one can specify multiple genes and also split.by to further split to multiple the conditions in the meta.data. If split.by is not NULL, the ncol is ignored so you can not arrange the grid.