Function reference • STarlight

All functions
`STCompR-class`	Spatial transcriptomic comparison class (STCompR).
`STGrid-class`	Spatial transcriptomic analysis class (STGrid).
`as_matrix(<STGrid>)`	Convert the bin_mat slot of an STGrid object into an x/y matrix (e.g. to be displayed using image())
`as_matrix()`	Convert the bin_mat slot of an STGrid object into an x/y matrix (e.g. to be displayed using image())
`bin_mat(<STGrid>)`	The binned matrix stored in a STGrid object.
`bin_size(<STGrid>)`	The size of the bins stored in an STGrid object
`bin_x(<STGrid>)`	X bins of a STGrid object.
`bin_y(<STGrid>)`	Y bins of a STGrid object.
`cc_neighborhood(<STGrid>)`	Find the neighbors of a Connected Component.
`check_features_exist(<STGrid>)`	Check all specified features exist in an STGrid object.
`check_this_file()`	Check file existence and optionally create directory
`cmp_bar_plot(<STCompR>)`	Create a barplot to show counts for selected features.
`cmp_boxplot(<STCompR>)`	Create a boxplot/jitter plot to show molecule counts distribution.
`cmp_counts_st()`	Compare feature counts across multiple STGrid objects.
`cmp_images()`	Compare Images
`compute_k_ripley(<STGrid>)`	Estimate Ripley's reduced second moment function for each feature in a spatial grid.
`compute_module_score(<STGrid>)`	From a list of feature (e.g gene) modules, compute a score (e.g. mean value) accross bins.
`connected_components(<STGrid>)`	Given a Feature and an STGrid object, Label and Store Connected Components.
`control_list()`	Generate a Control Gene List with Similar Distribution
`coord(<STGrid>)`	The coordinates stored in a STGrid object
`create_hull(<STGrid>)`	Create a Hull around a Feature component of an STGrid
`dist_st()`	Compare distribution of features across various STGrid objects.
`example_dataset()`	Load/download a Seurat or ClusterSet example dataset.
`feat_names(<STCompR>)`	The features stored in a STCompR object
`feat_names(<STGrid>)`	The features stored in an STGrid object
`fov_selection()`	Interactive Visual Feature Picker
`feature_contrast(<STGrid>)`	Gene Contrast Analysis for an STgrid object.
`get_coord(<STGrid>)`	The x/y coordinates of features from a STGrid object.
`get_verb_level()`	Get the current verbosity level.
`hc_tree(<STGrid>)`	Create a tree from an STGrid object
`load_spatial()`	Create a Spatial Transcriptomic Grid class (STGrid)
`meta(<STGrid>)`	Extract meta slot of an STGrid object
`meta_names(<STGrid>)`	The names of meta informations stored in a STGrid object
`multi_feat_contrast(<STGrid>)`	Multi-Gene contrast analysis for an STGrid object.
`nb_feat(<STCompR>)`	The number of features stored in a STCompR object
`nb_feat(<STGrid>)`	The number of features stored in a STGrid object
`nb_items(<STGrid>)`	The number of x/y items (e.g. molecules or cells) stored in a STGrid object
`order_feat_by_ripley(<STGrid>)`	Returns features ordered by Ripley's K-function
`plot_rip_k(<STGrid>)`	Call the Ripley's k function.
`re_bin(<STGrid>)`	Re-bin a STGrid object.
`reload_pac()`	Reload STarlight (used for development).
`rm_controls(<STGrid>)`	Remove control (Blank-*) features from a STGrid object.
`row_names(<STGrid>)`	Row names of a STGrid object.
`set_verb_level()`	Set the verbosity level for the STarlight package
`show_st_methods()`	List the method for the STGrid object.
`spatial_image(<STGrid>)`	Color-coded representation of the object (e.g. molecules) density
`spatial_plot(<STGrid>)`	Plot x/y coordinates of molecules
`stat_test(<STCompR>)`	The normalized counts and test results of a STCompR object.
`stcompr()`	Create a STCompR compare class to compare two sets of STGrid objects.
`stgrid_from_data_frame()`	Create an STGrid from a data.frame
`sum_of_counts()`	Compute the Sum of Counts
`summary(<STGrid>)`	The summary() method of a STGrid object
`tab(<STGrid>)`	The number of items (molecules/cells) per features (gene/cell-type).
`table_st(<STGrid>)`	The number of items (e.g molecules) per feature of an STGrid object.
`write_coord(<STGrid>)`	Write object coordinates.

Reference

All functions