# Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

## Documentation for package ‘spatialGE’ version 1.2.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

compare_SThet | compare_SThet: Compares spatial autocorrelation statistics across samples
dim-method | dim: Prints the dimensions of count arrays within an STList object.
distribution_plots | per_unit_counts: Generates distribution plots of spot/cell meta data or gene expression
filter_data | filter_data: Filters cells/spots, genes, or samples
gene_interpolation | gene_interpolation: Spatial interpolation of gene expression
get_gene_meta | get_gene_meta: Extract gene-level metadata and statistics
load_images | load_images: Place tissue images within STlist
plot_counts | plot_counts: Generates plots for the distribution of counts
plot_image | plot_image: Generate a ggplot object of the tissue image
pseudobulk_dim_plot | pseudobulk_dim_plot: Plot PCA of pseudobulk samples
pseudobulk_heatmap | pseudobulk_heatmap: Heatmap of pseudobulk samples
pseudobulk_samples | pseudobulk_samples: Aggregates counts into "pseudo bulk" samples
show-method | show: Prints overview of STList oject.
spatial_metadata | spatial_metadata: Prints the names of the available spot/cell annotations
STclust | STclust: Detect clusters of spots/cells
STdiff | STdiff: Differential gene expression analysis for spatial transcriptomics data
STdiff_volcano | STdiff_volcano: Generates volcano plots from STdiff results
STenrich | STenrich
STgradient | STgradient: Tests of gene expression spatial gradients
SThet | SThet: Computes global spatial autocorrelation statistics on gene expression
STlist | STlist: Creation of STlist objects for spatial transcriptomics analysis
STlist-class | Definition of an STlist object class.
STplot | STplot: Plots of gene expression, cluster memberships, and metadata in spatial context
STplot_interpolation | STplot_interpolation: Visualize gene expression surfaces
summarize_STlist | summarize_STlist: Generates a data frame with summary statistics
summary-method | summary: Prints overview of STList oject.
tissue_names | tissue_names: Prints the names of the tissue samples in the STlist
transform_data | transform_data: Transformation of spatial transcriptomics data