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Plot mean expression of a gene vs other parameters and highlight specific genes using ggrepel

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FFloWuenne
Last edited Jul 26, 2017
Created on Jul 26, 2017

This example uses the scater package to calculate quality metrics for single-cell RNA-seq data, then plots mean gene expression against percent dropout and percent total expression. The ggplot2 code highlights a user-defined set of genes of interest in red, while ggrepel’s `geom_text_repel` labels those genes to avoid overlapping points. Two separate scatterplots are generated from the same `gene_info` data frame, each saved as an SVG, showing how specific genes relate to global expression distributions. The analysis relies on the `newSCESet` and `calculateQCMetrics` functions from scater to derive the plotted metrics.

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