Plot Case vs Control Methylation Fractions with Density-Weighted Points

This function generates a scatter plot of methylation fractions in case vs control samples from a modification DuckDB database table, with optional density shading and threshold lines.

Usage

plot_mod_diff_density(
  mod_db,
  table,
  thresh = c(0.2, 0.3),
  palette = "turbo",
  n_kde = 250
)

Arguments

mod_db

A path to the modification DuckDB database, or an open database connection object.

table

A string specifying the table name within the database, containing `mh_frac_case` and `mh_frac_control` columns.

thresh

A numeric vector of length 1 or 2 giving the positive and negative threshold values to draw as dashed red lines above and below the identity line (default is `c(0.2, 0.3)`). If `NULL`, no threshold lines are drawn.

palette

A string specifying the viridis color palette for density shading (default is `"turbo"`). Other options include `"viridis"`, `"plasma"`, `"cividis"`, etc.

size

A numeric value controlling point size in the plot (default is `0.8`).

Value

Invisibly returns the closed database connection object. The plot is printed to the current graphics device.

Details

This function visualizes the relationship between `mh_frac_case` and `mh_frac_control` methylation values by plotting them on a scatter plot. It optionally enhances visualization with local point density using the `ggpointdensity` package if available.

Features:

• If ggpointdensity is installed, point density is used to color points.

• If not installed, a fallback to plain transparent points is used.

• A solid black identity line (`y = x`) is added for reference.

• Optional threshold lines at ±`thresh` distance from the identity line are shown as red dashed lines.

The plot is limited to the [0, 1] range for both axes and uses a clean classic theme.

Examples

if (FALSE) { # \dontrun{
plot_mod_diff_density("my_data/my.mod.db", table = "chr5", thresh = c(0.25, 0.35))
} # }