In FridleyLab/spatialTIME: Spatial Analysis of Vectra Immunoflourescent Data

knitr::opts_chunk$set(
  echo = FALSE,
  collapse = TRUE,
  # fig.path = "man/figures/README-",
  out.width = "100%"
  )

library(spatialTIME)

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

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.

FridleyLab/spatialTIME documentation built on Aug. 9, 2024, 7:48 p.m.