SpatialEcoTyper composition plot

Plot SpatialEcoTyper composition across cell types, samples, or other metadata groups using scop's default plotting theme and palettes.

Usage

SpatialEcoTyperCompositionPlot(
  srt,
  se.by = "SpatialEcoTyper_SE",
  group.by = "CellType",
  sample.by = NULL,
  position = c("fill", "stack"),
  palette = "Spectral",
  palcolor = NULL,
  legend.position = "right",
  theme_use = "theme_scop",
  theme_args = list(),
  verbose = TRUE
)

Arguments

srt

A Seurat object.

se.by

Metadata column containing SpatialEcoTyper labels.

group.by

Metadata column used as the composition group.

sample.by

Optional metadata column used for faceting.

position

Bar position. "fill" shows fractions and "stack" shows counts.

palette, palcolor

Palette passed to palette_colors().

legend.position

Legend position.

theme_use

Theme function name. Default is "theme_scop".

theme_args

Additional arguments passed to the theme function.

verbose

Whether to print the message. Default is TRUE.

Value

A ggplot object.

Examples

counts <- matrix(
  c(3, 0, 1, 2, 0, 4, 1, 0, 2, 1, 3, 0),
  nrow = 3,
  byrow = TRUE
)
rownames(counts) <- c("EPCAM", "COL1A1", "PTPRC")
colnames(counts) <- paste0("spot", 1:4)
srt <- Seurat::CreateSeuratObject(counts)
#> Warning: Data is of class matrix. Coercing to dgCMatrix.
srt$SpatialEcoTyper_SE <- c("SE1", "SE1", "SE2", "SE2")
srt$CellType <- c("Epithelial", "Fibroblast", "Immune", "Epithelial")
srt$sample <- c("slice1", "slice1", "slice2", "slice2")

SpatialEcoTyperCompositionPlot(
  srt,
  group.by = "CellType",
  sample.by = "sample",
  position = "fill"
)