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Create a new spatial map for spatial transcriptomics data

Source: R/make_escheR.R
make_escheR.Rd

make_escheR() is a generic function to initialize a ggplot object that contains a spatial map. Because the ggplot object saves the input spatial transcriptomics data, the transcriptomics data will be used in the following layering process to add more aesthestic components in the plot following the grammar of graphics and ggplot2 syntax.

Usage

make_escheR(object, spot_size = 2, ...)

# S3 method for SingleCellExperiment
make_escheR(object, spot_size = 2, dimred = "PCA", ...)

# S3 method for SpatialExperiment
make_escheR(object, spot_size = 2, dimred = NULL, y_reverse = TRUE, ...)

# S3 method for data.frame
make_escheR(object, spot_size = 2, .x, .y, ...)

Arguments

object

a data object that contains the spatial transcriptomics data. Currently only working for spatial transcriptomics data as SpatialExperiment objects.

spot_size

A numeric(1) specifying the size of the spot in the ggplot. Defaults to 2.

...

Reserved for future arguments.

dimred

String or integer scalar specifying the existing dimensionality reduction results to use.

y_reverse

(logical) Whether to reverse y coordinates, which is often required for 10x Genomics Visium data. Default = TRUE.

.x

the X-coordinate

.y

the Y-coordinate

Value

an ggplot object that contains the spatial transcriptomics data.

References

Guo B, Huuki-Myers LA, Grant-Peters M, Collado-Torres L, Hicks SC (2023). escheR: Unified multi-dimensional visualizations with Gestalt principles. Bioinformatics Advances, Volume 3, Issue 1, vbad179, doi:10.1093/bioadv/vbad179

Examples

library(STexampleData)
# SpatialExperiment Object
spe <- Visium_humanDLPFC()
#> see ?STexampleData and browseVignettes('STexampleData') for documentation
#> loading from cache
make_escheR(spe)


# SingleCellExperiment Object
sce <- SingleCellExperiment(counts(spe))
reducedDims(sce) <- list(
   # Example embedding
    EG = matrix(seq.int(1, ncol(spe)*2), ncol = 2)
    )
make_escheR(sce, dimred = "EG")

# data.frame Object
x <- spatialCoords(spe)[,1]
y <- spatialCoords(spe)[,2]
df <- colData(spe) |> data.frame()
make_escheR(object = df, .x = x , .y = y)