dimensionality_reduction_plot: Dimensionality reduction plot

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

Dimensionality reduction plot

Description

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

Usage

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")

TrigosTeam/SPIAT documentation built on Aug. 22, 2024, 7:50 p.m.