Package index • spatialTIME

Nearest Neighbor G

Univariate and Bivariate Nearest Neighbor G(r) functions

NN_G(): Univariate Nearest Neighbor G(r)
bi_NN_G(): Bivariate Nearest Neighbor G(r)

Ripley’s K

Univariate and Bivariate Ripley’s K functions

ripleys_k(): Calculate Ripley's K
bi_ripleys_k(): Bivariate Ripley's K
bi_ripleys_k_WSI(): Bivariate Ripley's K for Whole Slide Images (removed)

Pair Correlation

Univariate and Bivariate Pair Correlation functions

pair_correlation(): Univariate Pair Correlation Function
bi_pair_correlation(): Bivariate Pair Correlation Function

MIF Object Management

Functions for creating, merging, and subsetting Multiplex Immunoflourescent objects

create_mif(): Create Multiplex Immunoflourescent object
spatial_exp_to_mif(): Create Multiplex Immunoflourescent object from a SpatialExperiment object
merge_mifs(): Merge several MIF objects together
subset_mif(): Subset mif object on cellular level

Disk-backed MIF Objects

Keep per-cell spatial data in parquet files and read only the columns each computation needs, so peak memory scales with the number of workers rather than with the number of samples. Intended for whole slide images.

mif_to_disk(): Write a mif's spatial data to disk
open_mif(): Reopen a mif store written by mif_to_disk()
collect_mif(): Load a disk-backed mif's spatial data back into memory
verify_mif(): Re-probe every spatial file a mif points at

Other Spatial Statistics

dixons_s(): Dixon's S Segregation Statistic
interaction_variable(): Bivariate Interaction Variable
marker_freq_diff(): Marker Frequency Difference

Tissue Architecture

Density-based segmentation of a sample into tissue compartments

split_tissue(): Split a sample into tissue compartments by density difference

Visualization

plot_immunoflo(): Generate plot of TMA point process
plot_tissue_split(): Plot density-based tissue compartments alongside the density difference

Data

Example datasets included with the package

example_clinical: Clinical variables of 229 patients
example_spatial: Example list of 5 spatial TMA data frames
example_summary: Marker summaries of 229 samples

Internal

`%>%`: Pipe operator