Package: spatialTIME 1.3.4-5

Fridley Lab

spatialTIME: Spatial Analysis of Vectra Immunoflourescent Data

Visualization and analysis of Vectra Immunoflourescent data. Options for calculating both the univariate and bivariate Ripley's K are included. Calculations are performed using a permutation-based approach presented by Wilson et al. <doi:10.1101/2021.04.27.21256104>.

Authors:Jordan Creed [aut], Ram Thapa [aut], Christopher Wilson [aut], Alex Soupir [aut], Oscar Ospina [aut], Julia Wrobel [aut], Brooke Fridley [cph], Fridley Lab [cre]

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spatialTIME.pdf |spatialTIME.html✨
spatialTIME/json (API)

# Install 'spatialTIME' in R:

install.packages('spatialTIME', repos = c('https://fridleylab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fridleylab/spatialtime/issues

Datasets:

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

On CRAN:

6.16 score 4 stars 30 scripts 680 downloads 14 exports 64 dependencies

Last updated 7 months agofrom:391197e34d. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 10 2025
R-4.5-win	OK	Feb 10 2025
R-4.5-mac	OK	Feb 10 2025
R-4.5-linux	OK	Feb 10 2025
R-4.4-win	OK	Feb 10 2025
R-4.4-mac	OK	Feb 10 2025
R-4.3-win	OK	Feb 10 2025
R-4.3-mac	OK	Feb 10 2025

Exports:%>%bi_NN_G bi_pair_correlation bi_ripleys_k bi_ripleys_k_WSI create_mif dixons_s interaction_variable merge_mifs NN_G pair_correlation plot_immunoflo ripleys_k subset_mif

Dependencies:abind cli codetools colorspace cpp11 crayon deldir digest dixon dplyr fansi farver furrr future generics ggplot2 globals glue goftest gtable isoband labeling lattice lifecycle listenv magrittr MASS Matrix mgcv munsell nlme parallelly pbmcapply pillar pkgconfig polyclip purrr R6 RColorBrewer rlang rpart scales sp spatstat spatstat.data spatstat.explore spatstat.geom spatstat.linnet spatstat.model spatstat.random spatstat.sparse spatstat.univar spatstat.utils splancs stringi stringr tensor tibble tidyr tidyselect utf8 vctrs viridisLite withr

Introduction to spatialTIME

Rendered fromintro.Rmdusingknitr::rmarkdownon Feb 10 2025.

Last update: 2024-05-28
Started: 2020-10-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bivariate Nearest Neighbor G(r)	bi_NN_G
Bivariate Pair Correlation Function	bi_pair_correlation
Bivariate Ripley's K	bi_ripleys_k
Bivariate Ripley's K for Whole Slide Images	bi_ripleys_k_WSI
Calculate Count Based Measures and NN Measures of Spatial Clustering for IF data	compute_metrics
Create Multiplex Immunoflourescent object	create_mif
Dixon's S Segregation Statistic	dixons_s
Clinical variables of 229 patients	example_clinical
Example list of 5 spatial TMA data	example_spatial
Marker summaries of 229 samples	example_summary
Bivariate Interaction Variable	interaction_variable
Merge several MIF objects together	merge_mifs
Univariate Nearest Neighbor G(r)	NN_G
Univariate Pair Correlation Function	pair_correlation
Generate plot of TMA point process	plot_immunoflo
Calculate Ripley's K	ripleys_k
Subset mif object on cellular level	subset_mif