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

knitr::opts_chunk$set(echo = TRUE)

This script downloads and subsets test IMC data that were acquired for general purpose testing. The Github repository containing this data can be accessed here.

More specifically, we will use the 210308_ImcTestData dataset.

Download the .txt files

Here, we will first download the raw data in form of .txt files. For this, we an use the automatically generated Github assets.

cur_url <- "https://github.com/BodenmillerGroup/TestData/releases/download/v1.0.2/210308_ImcTestData_raw.tar.gz"

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

Subset and move the data

Here, we will move the .txt files of one raw data file to the mockData folder

file.copy(list.files("datasets/210308_ImcTestData/raw/20210305_NE_mockData2/", pattern = ".txt$", full.names = TRUE),
          "../extdata/mockData/raw", overwrite = TRUE)
unlink("datasets/", recursive = TRUE)

Download the corresponding tiff files

Here, we will download the .tiff files asset.

cur_url <- "https://github.com/BodenmillerGroup/TestData/releases/download/v1.0.2/210308_ImcTestData_analysis_cpout_images.tar.gz"

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

And copy them to the right location.

file.copy("datasets/210308_ImcTestData/analysis/cpout/images/20210305_NE_mockData2_s0_a1_ac_fullFiltered.tiff",
          "../extdata/mockData/tiffs/", overwrite = TRUE)
unlink("datasets/", recursive = TRUE)