readImagefromTXT: Reads one or multiple .txt files into a CytoImageList object

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

Reads one or multiple .txt files into a CytoImageList object

Description

Reader function to generate Image objects in form of a CytoImageList container from .txt files.

Usage

readImagefromTXT(
  path,
  pattern = ".txt$",
  channel_pattern = "[A-Za-z]{1,2}[0-9]{2,3}Di",
  index_names = c("X", "Y"),
  BPPARAM = SerialParam()
)

Arguments

path	Full path to where the individual .txt files are located. This is usualy the path where the .mcd file is located.
pattern	pattern to select which files should be read in (default ".txt$").
channel_pattern	regular expression to select the channel names from the files.
index_names	exact names of the columns storing the x and y coordinates of the image
BPPARAM	parameters for parallelized reading in of images. This is only recommended for very large images.

Value

returns a CytoImageList object containing one Image object per .txt file.

Imaging mass cytometry .txt files

As part of the raw data folder, the Hyperion imaging system writes out one .txt file per acquisition. These files store the ion counts per pixel and channel.

This function reads these .txt files into a single CytoImageList object for downstream analysis. The pattern argument allows selection of all .txt files or a specific subset of files. The channelNames of the CytoImageList object are determined by the channel_pattern argument.

Author(s)

Nils Eling ([e-mail])

See Also

CytoImageList for the container

MulticoreParam for parallelized processing

Image for the multi-channel image object

vignette("cytomapper") for visualization of multi-channel images

Examples

path <- system.file("extdata/mockData/raw", package = "imcRtools")

# Read in all images
x <- readImagefromTXT(path)
x

# Read in specific files
y <- readImagefromTXT(path, pattern = "ROI_002")
y

# Read in other channelNames
z <- readImagefromTXT(path, channel_pattern = "[A-Za-z]{2}[0-9]{3}")
z

BodenmillerGroup/imcRtools documentation built on Oct. 30, 2024, 12:19 p.m.