Package index • SpatialFeatures

All functions

CountsMatrix(): Extract Counts Matrix from MoleculeExperiment based on Assay Type

EntropyMatrix(): Calculate the Entropy of a Counts Matrix

EntropySingleCellExperiment(): Create a SingleCellExperiment Object from a List of Data Frames

GenerateFeatureData(): Generate Feature Data Based on Assay Type Combining Various Polygon Assays

annuli_counts(): Convert cumulative counts in concentric polygons to annuli polygon counts

calculate_centroids(): Calculate centroids from boundaries

calculate_entropy(): Calculate entropy from a probability vector

check_if_me_boundaries(): Check that a MoleculeExperiment object is both valid and contains boundaries

compute_cell_entropy(): Compute entropy for a given matrix

countsprop(): Calculate prop for entropy

create_scaled_df_sub(): Create a scaled data frame

create_scaled_df_super(): Create a scaled data frame

create_sector_df(): Create sector data frame from circle data

create_sectors(): Create sectors from a given data frame

extract_boundaries(): Extract boundaries from a given object

extract_boundaries_and_centroids(): Extract boundaries and calculate centroids

extract_cell_segments(): Extract a submatrix corresponding to a segment from a matrix

generate_scale_factors_all(): Generate scale factors for all values of k

generate_scale_factors_all_outside(): Generate scale factors for all outside values of ks

get_cells(): Extract unique segments from matrix column names

loadBoundaries(): Load Boundaries to MoleculeExperiment Object

make_assay_data(): make assay data

matrix_entropy(): Compute entropy for the entire matrix

example_me: Example MoleculeExperiment data

modify_area_id(): Modify the area_id format

spatialFeatures(): Calculate SpatialFeatures from a MoleculeExperiment object