Create a density scatter / pseudocolor plot.

Create a density scatter plot, also known as a pseudocolor plot, of two markers from a Seurat object. The points in the scatter plot are colored by the point density, determined by 2D kernel density estimation. Optionally, the plot can be faceted by one or two variables and a gate can be plotted.

Usage

DensityScatterPlot(
  object,
  marker1,
  marker2,
  facet_vars = NULL,
  plot_gate = NULL,
  scale_density = TRUE,
  margin_density = FALSE,
  coord_fixed = TRUE,
  pt_size = 1,
  alpha = 1,
  layer = NULL,
  grid_n = 500,
  colors = NULL,
  ...
)

Arguments

object

A Seurat object.

marker1

Marker to plot along the x-axis.

marker2

Marker to plot along the y-axis.

facet_vars

Variables to facet the plot by. If NULL, no faceting is done. If a character vector with 1 element, the plot is faceted by rows. If a character vector with 2 elements, the plot is faceted by rows and columns.

plot_gate

A data.frame with columns 'xmin', 'xmax', 'ymin', 'ymax' to plot a gate. This data.frame can also contain the variables in 'facet_vars' to plot different gates in different facets.

scale_density

Scale the density to the maximum density per facet.

margin_density

Add marginal density plots. Only supported when 'facet_vars' is NULL.

coord_fixed

Fix the aspect ratio of the plot. Only supported when 'margin_density' is FALSE.

pt_size

Size of the points.

alpha

Transparency of the points.

layer

Name of layer to plot. If NULL, the default layer is used.

grid_n

Number of grid points to calculate the density.

colors

Colors to use for the density plot. If NULL, the 'viridis' "turbo" palette is used.

...

Additional arguments to pass to 'MASS::kde2d'.

Value

A ggplot object.

Examples

library(pixelatorR)
library(Seurat)

# A mock-up Seurat Object
object <-
 CreateSeuratObject(counts = matrix(c(rpois(100000, 40),
                                      rpois(100000, 5))[sample(1:200000, 200000)],
                                    nrow = 100, ncol = 2000,
                                    dimnames = list(paste0("Feature", 1:100),
                                                    paste0("Cell", 1:2000))))
#> Warning: Data is of class matrix. Coercing to dgCMatrix.

object <-
  AddMetaData(object,
              metadata = data.frame(sample = rep(c("A", "B"), each = 1000),
                                    sample_type = rep(c("Unstimulated", "Stimulated"),
                                                      each = 500, times = 2),
                                    row.names = paste0("Cell", 1:2000)))

plot_gate <-
  data.frame(xmin = c(70, 75),
             xmax = c(150, 155),
             ymin = c(50, 50),
             ymax = c(150, 150),
             sample = c("A", "B"))


DensityScatterPlot(object,
                   marker1 = "Feature1",
                   marker2 = "Feature2",
                   facet_vars = "sample",
                   plot_gate = plot_gate,
                   layer = "counts")