R/pbmc.R

In chameleon: Automatic Colors for Multi-Dimensional Data

#' Sample scRNA data of PBMC metacells.
#'
#' This is a list with the following elements:
#'
#' `umis` - a matrix, containing ~1.5K metacells (rows), and for each one, the UMI count (# of
#' detected RNA molecules) for each of ~600 different "feature" genes (columns).
#'
#' `types` - a vector of cell type names assigned to each metacell using a supervised analysis
#' pipeline.
#'
#' `umap` - a matrix with 2 columns containing 2D UMAP x,y coordinates for each metacell.
#'
#' @docType data
#'
#' @usage data(pbmc)
#'
#' @format A list with the three elements described above.
#'
#' @keywords datasets
#'
#' @examples
#' data(pbmc)
#' fractions <- pbmc$umis / rowSums(pbmc$umis)
#' log_fractions <- log2(fractions + 1e-5)
#' type_colors <- chameleon::data_colors(log_fractions, group=pbmc$types)
#' plot(pbmc$umap, col=type_colors[pbmc$types], pch=19, cex=0.6)
#' legend('topleft', legend=names(type_colors), col=type_colors, lty=1, lwd=3, cex=0.8)
"pbmc"