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Generates and saves comprehensive visualization plots for specified genes.

savePlots.Rd

This function creates a multi-panel plot for each gene showing spatial expression patterns, pixel classifications, and correlation analysis. Each gene generates a four-panel figure that is saved as a PDF file.

Usage

savePlots(
  geneNames,
  spatialSimilarity,
  rastGexp,
  assayName = NULL,
  filePath = FALSE
)

Arguments

geneNames

Character vector. Names of genes to visualize and save.

spatialSimilarity

A list. Results from `spatialSimilarity()` containing similarity tables and analysis parameters.

rastGexp

A list of two SpatialExperiment objects. Rasterized gene expression data from the spatial experiments being compared.

assayName

A character string or numeric specifying the assay in the Spatial Experiment to use. Default is NULL. If no value is supplied for assayName, then the first assay is used as a default

filePath

Character. Directory path where PDF files will be saved.

Value

A list containing the arranged plot objects for each gene, with gene names as list element names. Each plot object is a four-panel arrangement showing:

  • Panel 1:Spatial expression plot for the first experiment.

  • Panel 2:Spatial expression plot for the second experiment.

  • Panel 3:Pixel classification plot showing similarity categories.

  • Panel 4:Linear regression scatter plot comparing expression between experiments.

Details

The function saves each gene's visualization as a PDF file named "gene_name.pdf" in the specified directory. Plot dimensions are set to 17 inches wide by 5 inches tall at 300 DPI resolution.

Examples

data(speKidney)
#' ##### Rasterize to get pixels at matched spatial locations #####
rastKidney <- SEraster::rasterizeGeneExpression(speKidney,
                assay_name = 'counts', resolution = 0.2, fun = "mean",
                BPPARAM = BiocParallel::MulticoreParam(), square = FALSE)
s <- spatialSimilarity(list(rastKidney$A, rastKidney$B))
plts <- savePlots("Gene", s, rastKidney)
#> Warning: package ‘patchwork’ was built under R version 4.3.3
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
plts
#> $Gene
#> Warning: Removed 15 rows containing missing values or values outside the scale range
#> (`geom_point()`).

#>