Spatial Component Analysis for Spatial Sequencing Data

Documentation for package ‘SPACO’ version 1.0.1

create_SpaCoObject_from_KNN	create_SpaCoObject_from_KNN
denoised_projection_plot	Plot denoised gene expression
denoise_profiles	computes smoothed gene profiles of genes present in the data.
eigenMapMatMult	Multiply two matrices using Eigen library
feature_plot	Plot gene expression
read_10x_for_spaco	Read in 10x Visium spatial transcriptomics data
set_projection	Set projections of Spaco Object
seurat_to_spaco	Wrapper to transform existing Seurat object into an SpaCoObject.
SpaCo	SpaCo
SpaCoObject	Create a constructor function that creates an object of class SpaCoObject
Spaco_plot	Plot SPaCo meta genes.
spacs_to_seurat	transfer computed spatial components to existing Seurat object.
subset_non_neighbour_cells	Filtering function to remove cells without neighbours in defined distance from existing Seurat object to be conformable with existing SpaCoObject.
SVGTest	Compute the spatial variable genes of a SpaCoObject after runinng runSCA