R/data.R

In BodenmillerGroup/SingleCellMapper: Visualization of highly multiplexed imaging data in R

#' Example SingleCellExperiment object
#'
#' This \linkS4class{SingleCellExperiment} object contains the expression values
#' of 5 proteins (rows) from 362 cells (columns) across 3 images. The data is
#' part of a imaging mass cytometry study on the progression of Type 1 diabetes
#' and therefore contains pancreas cells.
#'
#' @format A SingleCellExperiment object containing the raw and
#' arcsinh-transformed mean pixel counts per cell as well as associated cell-
#' and protein-specific metadata. Row names represent the names of the target
#' proteins and column names represent the image name and cell id of each cell.
#' \describe{
#' \item{colData}{Cell-specific metadata where rownames represent the
#' image name and cell id. It containins the
#' \enumerate{
#'     \item image number (ImageNb),
#'     \item cell number/identifier (CellNb),
#'     \item spatial position on the image (Pos_X, Pos_Y),
#'     \item the associated image name (ImageName, see
#'     \code{?"\link[cytomapper]{pancreasImages}"}),
#'     \item the associated mask name (MaskName, see
#'     \code{?"\link[cytomapper]{pancreasMasks}"}),
#'     \item a arbitrary cell-type label (CellType)
#'     \item a logical (Pattern) indicating exocrine cells
#' }
#' }
#' \item{rowData}{Protein-specific metadata where rownames represent
#' the names of the target proteins. It contains the
#' \enumerate{
#'     \item channel number (frame),
#'     \item metal tag of the antibody (MetalTag)
#'     \item Target (the expanded name of the targeted protein)
#'     \item clean_Target (the abbreviated name of the targeted protein)
#' }
#' }
#' \item{assays}{List of protein expression counts containing:
#' \enumerate{
#' \item the raw expression counts (counts):
#' mean pixel value per cell and protein
#' \item arcsinh-transformed raw expression counts
#' using a co-factor of 1 (exprs)
#' }
#' }
#' }
#'
#' @references
#' \href{https://www.sciencedirect.com/science/article/pii/S1550413118306910}{
#' Damond, N. et al., A Map of Human Type 1 Diabetes Progression by
#' Imaging Mass Cytometry, Cell Metabolism 29:3, 2019}
"pancreasSCE"

#' Example CytoImageList object of image files
#'
#' This \linkS4class{CytoImageList} object contains multi-channel stacks of
#' three images acquired by imaging mass cytometry. Each channel represents the
#' pixel-intensities of each of the 5 measured proteins. The data is part of a
#' imaging mass cytometry study on the progression of Type 1 diabetes and
#' contains pancreas cells.
#'
#' @format A CytoImageList object containing 3 \code{\linkS4class{Image}}
#' objects with 5 channels each. Channel names can be accessed via
#' \code{?\link{channelNames}}.
#'
#' @references
#' \href{https://www.sciencedirect.com/science/article/pii/S1550413118306910}{
#' Damond, N. et al., A Map of Human Type 1 Diabetes Progression by
#' Imaging Mass Cytometry, Cell Metabolism 29:3, 2019}
"pancreasImages"

#' Example CytoImageList object of segmentation masks
#'
#' This \linkS4class{CytoImageList} object contains single-channel images
#' representing the segmentation masks after preprocessing of imaging mass
#' cytometry data. The data is part of a imaging mass cytometry study on the
#' progression of Type 1 diabetes and contains pancreas cells.
#'
#' @format A CytoImageList object containing 3 \code{\linkS4class{Image}}
#' objects with 1 channel each. These images are the result to segmentation
#' and associated to the images stored in the
#' \code{\link[cytomapper]{pancreasImages}} object. Pixel values indicate the
#' numeric cell identifier while a value of 0 represents the image background.
#'
#' @references
#' \href{https://www.sciencedirect.com/science/article/pii/S1550413118306910}{
#' Damond, N. et al., A Map of Human Type 1 Diabetes Progression by
#' Imaging Mass Cytometry, Cell Metabolism 29:3, 2019}
"pancreasMasks"