tissue_maps: Anatomy maps
In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

tissue_maps

R Documentation

Anatomy maps

Description

Mappings from cell-type names to anatomy ontology terms in the HumanCellLandscape and DescartesHuman scRNA-seq datasets.

Usage

data("tissue_maps")

Format

data.table

Source

## Download standardised Seurat objects from CellXGene. obj_list <- list() obj_list[["DescartesHuman"]] <- readRDS("~/Downloads/db4d63ab-0ca3-4fa5-b0cf-34955227912d.rds") obj_list[["HumanCellLandscape"]] <- readRDS("~/Downloads/1b7484e3-83a0-47fe-847e-54d811a2adae.rds") cols <- c("tissue_ontology_term_id", "tissue", # "tissue_original", "cell_type_ontology_term_id", "cell_type") tissue_maps <- lapply(obj_list, function(obj){ select_cols <- cols[cols d <- data.table::as.data.table(obj@meta.data[,select_cols]) d[,cl_count:=.N, by=c("cell_type_ontology_term_id","cell_type")] unique(d) }) |> data.table::rbindlist(idcol = "ctd", fill=TRUE) data.table::setnames(tissue_maps, c("tissue_ontology_term_id","tissue", "cell_type_ontology_term_id","cell_type"), c("uberon_id","uberon_name", "cl_id","cl_name")) usethis::use_data(tissue_maps, overwrite = TRUE)

neurogenomics/MultiEWCE documentation built on April 22, 2024, 6:22 a.m.