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Plot VlnPlot for markers with minimum axis for joined marker plot as in (Macosko et al for retina)

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FFloWuenne
Last edited Aug 9, 2017
Created on Aug 9, 2017

This example uses Seurat’s `VlnPlot` to draw violin plots for a set of candidate marker genes (GAPDH, NANOG, ACTB) across cell populations, with a fixed y-max of 6 and no axis labels or ticks to focus on expression distributions. The code loops through each gene, builds a violin plot, and then removes all axis lines and text while flipping coordinates so the plots are horizontal. It demonstrates how to customize Seurat’s plotting defaults—using `point.size.use = -1` to suppress points, `remove.legend = TRUE`, and theme elements to create a minimal, clean visualization for comparing marker expression across clusters. The data source is an updated Seurat object (`expression_seurat.updated`).

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