In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis

knitr::opts_chunk$set(echo = TRUE)

This script downloads the steinbock output of a small test dataset. The Github repository containing this data can be accessed here.

More specifically, we will use the 210308_ImcTestData dataset.

Download the steinbock output

Here, we will first download the output of the steinbock. For this, we an use the automatically generated Github assets.

cur_url <- "https://github.com/BodenmillerGroup/TestData/releases/download/v1.0.10/210308_ImcTestData_steinbock.tar.gz"

download.file(cur_url, "210308_ImcTestData_steinbock.tar.gz")
untar("210308_ImcTestData_steinbock.tar.gz")
unlink("210308_ImcTestData_steinbock.tar.gz")

Only copy the needed files

For reading in the single-cell features, we will only need to copy the .csv files and the folders containing the individual measurements.

files_of_interest <- c("panel.csv", "steinbock.sh", "images.csv")

folders_of_interest <- c("neighbors", "intensities", "regionprops")

lapply(folders_of_interest, function(x){
    dir.create(paste0("../extdata/mockData/steinbock/", x))
    file.copy(list.files(paste0("datasets/210308_ImcTestData/steinbock/", x, "_deepcell"), 
                         full.names = TRUE),
          paste0("../extdata/mockData/steinbock/", x), 
          overwrite = TRUE)
})

file.copy(paste0("datasets/210308_ImcTestData/steinbock/", files_of_interest),
          "../extdata/mockData/steinbock/", 
          overwrite = TRUE)
unlink("datasets/", recursive = TRUE)