Dimensionality reduction plot — dimensionality_reduction

Generates the dimensionality reduction plots (UMAP or tSNE) based on marker intensities. Cells are grouped by the categories under the selected column.

dimensionality_reduction_plot(
  spe_object,
  plot_type = "UMAP",
  scale = TRUE,
  perplexity = 30,
  feature_colname
)

Arguments

spe_object: SpatialExperiment object in the form of the output of format_image_to_spe.
plot_type: String. Choose from "UMAP" and "TSNE".
scale: Boolean. Whether scale the marker intensities.
perplexity: Numeric. Perplexity parameter of the Rtsne function (should be positive and no bigger than 3 * perplexity < n - 1, where n is the number of cells).
feature_colname: String. Specify the column name to group the cells.

Value

A plot

Examples

dimensionality_reduction_plot(SPIAT::simulated_image, plot_type = "TSNE",
feature_colname = "Phenotype")