Description
Spatial Analysis of Vectra Immunoflourescent Data.
Description
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>.
README.md
spatialTIME 
The goal of spatialTIME is to perform basic analysis and plotting of IF data from Vectra.
Installation
You can install spatialTIME from GitHub with:
# install.packages("devtools")
devtools::install_github("fridleylab/spatialTIME")
Usage
spatialTIME currently implements both univariate and bi-variate Ripley’s K analyses. The basis of the spatialTIME functions is the creation of the mif object.
x <- create_mif(clinical_data = example_clinical,
sample_data = example_summary,
spatial_list = example_spatial,
patient_id = "deidentified_id", sample_id = "deidentified_sample",
clean_columns = TRUE)
x
## 229 patients spanning 229 samples and 5 spatial data frames were found
Additional resources
For a more in-depth description of the methods used, please see the included vignette.
For a point-and-click resource that performs related analyses please check out iTIME.