Scatter / hex plot of two features against each other

Plots two features against each other (typical use case: protein vs mRNA on ADT/RNA data). Each feature may carry a _rna or _adt suffix to select its modality independently; unsuffixed features fall back to modality. With geom = "density" points are coloured by 2D KDE, with geom = "hex" cells are binned into hexagons.

Usage

feature_scatter_plot_sc(
  object,
  feature_1,
  feature_2,
  geom = c("density", "hex"),
  remove_zeros = TRUE,
  smoothness = 10,
  bins = 60,
  modality = c("rna", "adt"),
  point_size = 2.5,
  point_alpha = 0.5,
  raster = NULL,
  raster_dpi = c(512, 512),
  palette = c("viridis", "sequential", "spectral", "diverging")
)

Arguments

object

A single cell class.

feature_1

String. First feature (x-axis), optionally _rna / _adt suffixed.

feature_2

String. Second feature (y-axis), optionally _rna / _adt suffixed.

geom

String. "density" or "hex" (default: "density").

remove_zeros

Boolean. Drop cells where both features are zero (default: TRUE).

smoothness

Numeric. Bandwidth multiplier for the KDE (default: 10). Only used for geom = "density".

bins

Numeric. Number of hex bins (default: 60). Only used for geom = "hex".

modality

String. Fallback modality for unsuffixed features. One of c("rna", "adt").

point_size

Numeric. Point size for density plots (default: 2.5).

point_alpha

Numeric. Alpha for density plots (default: 0.5).

raster

Optional boolean. Shall the plot be rasterised. If NULL and n_cells > 1e5, defaults to TRUE. Only applies to geom = "density".

raster_dpi

Two numerics. Pixel resolution for rasterised plots (default: c(512, 512)).

palette

String. Continuous palette for the density / count scale. One of c("viridis", "sequential", "spectral", "diverging"), see bx_colors().

Value

A ggplot object.