Plot SpatialEcoTyper labels on spatial coordinates using scop's spatial plotting style.
Usage
SpatialEcoTyperSpatialPlot(
srt,
group.by = "SpatialEcoTyper_SE",
x.by = "X",
y.by = "Y",
image = NULL,
overlay_image = TRUE,
coord.cols = c(x.by, y.by),
palette = "Spectral",
palcolor = NULL,
theme_use = "theme_scop",
...
)Arguments
- srt
A Seurat object.
- group.by
Metadata column containing SpatialEcoTyper labels.
- x.by, y.by
Metadata coordinate columns used when no image coordinates are available.
- image
Name of the Seurat spatial image. If
NULL, the first image is used when present.- overlay_image
Whether to draw the spatial image beneath spots.
- coord.cols
Metadata coordinate columns used when no image is available.
- palette, palcolor
Palette passed to
palette_colors().- theme_use
Theme used. Can be a character string or a theme function. Default is
"theme_scop".- ...
Additional arguments passed to
SpatialSpotPlot().
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$X <- c(0, 1, 0, 1)
srt$Y <- c(0, 0, 1, 1)
srt$SpatialEcoTyper_SE <- c("SE1", "SE1", "SE2", "SE2")
srt$CellType <- c("Epithelial", "Fibroblast", "Immune", "Epithelial")
SpatialEcoTyperSpatialPlot(
srt,
overlay_image = FALSE,
coord.cols = c("X", "Y"),
pt.size = 4
)
