Scatter plots of the per-cell QC metrics against each other. — plot_metrics

One panel per pair in pairs, colored by sample. No legend, since this only ever runs on a single sample - see filter_cells(). Pairs are a curated list rather than every combination of a metric vector, since that would make the panel count quadratic in the number of metrics (5 metrics -> 10 panels via combn()) and most pairs are not biologically meaningful together.

Usage

plot_metrics_correlations(
  x,
  pairs = list(c("total_counts", "detected_genes"), c("pct_mito", "detected_genes"),
    c("pct_mito", "pct_ribo")),
  group_by = "orig.ident",
  color_scheme = NULL,
  file = NULL,
  width = 16,
  height = 5
)

Arguments

x: Seurat object.
pairs: A list of length-2 character vectors, c(feature1, feature2), one per panel.
group_by: Metadata column to color the points by.
color_scheme: (optional) Named vector of colors. Defaults to the "samples" scheme, named by the sorted levels of group_by.
file: Path to save the plot to. NULL returns it without writing. Parent directories are created as needed.
width, height: Saved size in inches. The default is wide and short: one square panel per pair of metrics, side by side.

Value

A combined plot, one panel per pair.