Create an abundance/colocalization scatterplot

Create a scatter plot of the abundance values for two sets of markers from a Seurat object. The points (each corresponding to a cell) in the scatter plot are colored by the colocalization of the two markers.

Usage

AbundanceColocalizationPlot(
  object,
  markers_x,
  markers_y,
  shared_scales = TRUE,
  coord_fixed = TRUE,
  pt_size = c(1, 4),
  draw_origo = TRUE,
  layer = NULL,
  coloc_score = "pearson_z",
  colors = c("#1F395F", "#496389", "#728BB1", "#AABAD1", "gray90", "#E9AABF", "#CD6F8D",
    "#A23F5E", "#781534")
)

Arguments

object

A Seurat object.

markers_x, markers_y

A character vector of markers to plot along the x- and y-axis respectively.

shared_scales

Use the same scales for all plot panels.

coord_fixed

Fix the aspect ratio of the plot.

pt_size

Size or size range of the points.

draw_origo

Draw lines through the origin (0, 0) in the plot.

layer

Name of layer to fetch abundance data from. If NULL, the default layer is used.

coloc_score

Name of the colocalization score to plot.

colors

Colors to use for the colocalization score.

Value

A ggplot object.

Examples

library(pixelatorR)

# Load example data as a Seurat object
pxl_file <- system.file(
  "extdata/five_cells",
  "five_cells.pxl",
  package = "pixelatorR"
)
seur_obj <- ReadMPX_Seurat(pxl_file)
#> ✔ Created a 'Seurat' object with 5 cells and 80 targeted surface proteins

# Plot with data.frame
AbundanceColocalizationPlot(seur_obj, c("CD3E", "CD4"), c("CD19", "CD20"))
#> Warning: No layers found matching search pattern provided
#> Warning: data layer is not found and counts layer is used
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_point()`).