R/project_management.R

In whtns/seuratTools: Tools for Managing Seurat Objects

#' Create a Table of single Cell Projects
#'
#' Uses a list of projects to create a matrix of single cell projects
#'
#' @param proj_list List of projects
#'
#' @return
#' @export
#'
#' @examples
create_proj_matrix <- function(proj_list) {
    proj_list <- unlist(proj_list)

    proj_tbl <- tibble::tibble(project_path = proj_list, project_name = fs::path_file(proj_list))

    patterns <- c("{date}-{user}-{note}-{species}_proj")

    proj_matrix <- unglue::unglue_data(proj_list, patterns) %>%
        dplyr::mutate(date = fs::path_file(date)) %>%
        dplyr::bind_cols(proj_tbl) %>%
        identity()

    primary_projects <-
        proj_matrix %>%
        dplyr::filter(!grepl("integrated_projects", project_path)) %>%
        dplyr::filter(stringr::str_count(project_name, "_") == 1) %>%
        identity()

    integrated_projects <-
        proj_matrix %>%
        dplyr::anti_join(primary_projects) %>%
        identity()

    proj_matrices <- list(primary_projects = primary_projects, integrated_projects = integrated_projects)

    return(proj_matrices)
}


#' Subset by new metadata
#'
#' Subset the seurat object using new metadata
#'
#' @param meta_path Path to new metadata
#' @param seu A seurat obejct
#'
#' @return
#' @export
#'
#' @examples
subset_by_meta <- function(meta_path, seu) {
    upload_meta <- readr::read_csv(meta_path, col_names = "sample_id") %>%
        dplyr::filter(!is.na(sample_id) & !sample_id == "sample_id") %>%
        dplyr::mutate(name = sample_id) %>%
        tibble::column_to_rownames("sample_id") %>%
        identity()

    upload_cells <- rownames(upload_meta)

    seu <- seu[, colnames(seu) %in% upload_cells]

    seu <- Seurat::AddMetaData(seu, upload_meta)

    return(seu)
}

#' Combine Loom Files
#'
#' @param projectPaths
#' @param newProjectPath
#'
#' @return
#' @export
#'
#' @examples
combine_looms <- function(projectPaths, newProjectPath) {
    # loom combine
    loompy <- reticulate::import("loompy")

    loom_filenames <- stringr::str_replace(fs::path_file(projectPaths), "_proj", ".loom")

    selected_looms <- fs::path(projectPaths, "output", "velocyto", loom_filenames)

    if (all(fs::is_file(selected_looms))) loompy$combine(selected_looms, newProjectPath)
}