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Plot the mean-dispersion trend from getHVG().

Source: R/getHVG.R
plotHVG.Rd

Visualises each eligible gene's dispersion against its mean expression, overlaid with the fitted lowess trend, and highlights the selected highly variable genes. Requires getHVG to have been run with a fitted trend (i.e. more eligible genes than requested HVGs).

Usage

plotHVG(
  spe,
  pt.size = 0.6,
  pt.alpha = 0.6,
  cols = c("grey70", "firebrick"),
  line.col = "blue"
)

Arguments

spe

A SpatialExperiment processed by getHVG.

pt.size

Point size. Default 0.6.

pt.alpha

Point alpha (0-1). Default 0.6.

cols

Length-2 vector of colours for non-HVG and HVG points. Default c("grey70", "firebrick").

line.col

Colour of the fitted trend line. Default "blue".

Value

A ggplot object (dispersion vs mean expression, both on log10 axes).

Examples


data("xenium_bc_spe")
spe <- getHVG(spe, n = 100)
plotHVG(spe)