#' @title scImmuCC_Layered.
#' @description Creating Hierarchical_annotation for scRNA-Seq data immune cell
#' @details Input takes a cells-genes matrix with cell unique barcodes as
#' column names and gene names as row names and returns the cells annotation
#' @param count  Matrix with cell unique barcodes as column names and gene names
#' as row names
#' @param Non_Immune Whether non-immune cells are included in the matrix
#' @return Data frames with the barcodes and cell types, and some maps
#' @import GSVA
#' @importFrom GSVA gsva
#' @import Matrix
#' @export
#' @examples test_data
scImmuCC_Layered <- function(count, Non_Immune = TRUE) {
  data("./data/cr0_genelist.rda", package = "scImmuCC")
  data("./data/cr1_genelist.rda", package = "scImmuCC")
  data("./data/Tcell_genelist.rda", package = "scImmuCC")
  data("./data/Bcell_genelist.rda", package = "scImmuCC")
  data("./data/DC_genelist.rda", package = "scImmuCC")
  data("./data/NK_genelist.rda", package = "scImmuCC")
  data("./data/Monocyte_genelist.rda", package = "scImmuCC")
  data("./data/Macrophage_genelist.rda", package = "scImmuCC")
  data("./data/ILC_genelist.rda", package = "scImmuCC")
  data("./data/CD4_genelist.rda", package = "scImmuCC")
  data("./data/CD8_genelist.rda", package = "scImmuCC")

  if (Non_Immune == TRUE) {
    cr0_result <- scImmuCC_main(count, cr0_genelist, "cr0")
    immune <- cr0_result[which(cr0_result[, 2] == "Immune"), ]
    count_immune <- count[, immune[, 1]]
    ssGSEA_result <- scImmuCC_main(count_immune, cr1_genelist, "cr1")
    seurat_result <- seurat_Heatmap(count, cr1_genelist, ssGSEA_result, "cr1")
  } else {
    ssGSEA_result <- scImmuCC_main(count, cr1_genelist, "cr1")
    seurat_result <- seurat_Heatmap(count, cr1_genelist, ssGSEA_result, "cr1")
  }

  cell_type <- unique(ssGSEA_result[, 2])

  if ("Tcell" %in% cell_type) {
    sub_ssGSEA_Tcell <- ssGSEA_result[which(ssGSEA_result[, 2] == "Tcell"), ]
    sub_count_Tcell <- count[, sub_ssGSEA_Tcell[, 1]]
    sub_count_Tcell <- as.matrix(sub_count_Tcell)
    ssGSEA_Tcell <- scImmuCC_main(sub_count_Tcell, Tcell_genelist, "cr2_Tcell")
    seurat_Tcell <- seurat_Heatmap(
      sub_count_Tcell, Tcell_genelist,
      ssGSEA_Tcell, "cr2_Tcell"
    )

    cell_type2 <- unique(ssGSEA_Tcell[, 2])

    if ("CD4_T" %in% cell_type2) {
      sub_ssGSEA_CD4 <- ssGSEA_Tcell[which(ssGSEA_Tcell[, 2] == "CD4_T"), ]
      sub_count_CD4 <- count[, sub_ssGSEA_CD4[, 1]]
      sub_count_CD4 <- as.matrix(sub_count_CD4)
      ssGSEA_CD4 <- scImmuCC_main(sub_count_CD4, CD4_genelist, "cr3_CD4")
      cells <- length(sub_count_CD4[2, ])
      if (cells > 50) {
        seurat_CD4 <- seurat_Heatmap(
          sub_count_CD4, CD4_genelist, ssGSEA_CD4,
          "cr3_CD4"
        )
      }
    }


    if ("CD8_T" %in% cell_type2) {
      sub_ssGSEA_CD8 <- ssGSEA_Tcell[which(ssGSEA_Tcell[, 2] == "CD8_T"), ]
      sub_count_CD8 <- count[, sub_ssGSEA_CD8[, 1]]
      sub_count_CD8 <- as.matrix(sub_count_CD8)
      ssGSEA_CD8 <- scImmuCC_main(sub_count_CD8, CD8_genelist, "cr3_CD8")
      cells <- length(sub_count_CD8[2, ])
      if (cells > 50) {
        seurat_CD8 <- seurat_Heatmap(
          sub_count_CD8, CD8_genelist, ssGSEA_CD8,
          "cr3_CD8"
        )
      }
    }
  }

  if ("Bcell" %in% cell_type) {
    sub_ssGSEA_Bcell <- ssGSEA_result[which(ssGSEA_result[, 2] == "Bcell"), ]
    sub_count_Bcell <- count[, sub_ssGSEA_Bcell[, 1]]
    sub_count_Bcell <- as.matrix(sub_count_Bcell)
    ssGSEA_Bcell <- scImmuCC_main(sub_count_Bcell, Bcell_genelist, "cr2_Bcell")
    cells <- length(sub_count_Bcell[2, ])
    if (cells > 50) {
      seurat_Bcell <- seurat_Heatmap(
        sub_count_Bcell, Bcell_genelist,
        ssGSEA_Bcell, "cr2_Bcell"
      )
    }
  }

  if ("DC" %in% cell_type) {
    sub_ssGSEA_DC <- ssGSEA_result[which(ssGSEA_result[, 2] == "DC"), ]
    sub_count_DC <- count[, sub_ssGSEA_DC[, 1]]
    sub_count_DC <- as.matrix(sub_count_DC)
    ssGSEA_DC <- scImmuCC_main(sub_count_DC, DC_genelist, "cr2_DC")
    cells <- length(sub_count_DC[2, ])
    if (cells > 50) {
      seurat_DC <- seurat_Heatmap(
        sub_count_DC, DC_genelist, ssGSEA_DC,
        "cr2_DC"
      )
    }
  }

  if ("NK" %in% cell_type) {
    sub_ssGSEA_NK <- ssGSEA_result[which(ssGSEA_result[, 2] == "NK"), ]
    sub_count_NK <- count[, sub_ssGSEA_NK[, 1]]
    sub_count_NK <- as.matrix(sub_count_NK)
    ssGSEA_NK <- scImmuCC_main(sub_count_NK, NK_genelist, "cr2_NK")
    cells <- length(sub_count_NK[2, ])
    if (cells > 50) {
      seurat_NK <- seurat_Heatmap(
        sub_count_NK, NK_genelist, ssGSEA_NK,
        "cr2_NK"
      )
    }
  }

  if ("Monocyte" %in% cell_type) {
    sub_ssGSEA_Mono <- ssGSEA_result[which(ssGSEA_result[, 2] == "Monocyte"), ]
    sub_count_Mono <- count[, sub_ssGSEA_Mono[, 1]]
    sub_count_Mono <- as.matrix(sub_count_Mono)
    ssGSEA_Mono <- scImmuCC_main(
      sub_count_Mono, Monocyte_genelist,
      "cr2_Monocyte"
    )
    cells <- length(sub_count_Mono[2, ])
    if (cells > 50) {
      seurat_Mono <- seurat_Heatmap(
        sub_count_Mono, Monocyte_genelist,
        ssGSEA_Mono, "cr2_Monocyte"
      )
    }
  }

  if ("Macrophage" %in% cell_type) {
    sub_ssGSEA_Mac <- ssGSEA_result[which(ssGSEA_result[, 2] == "Macrophage"), ]
    sub_count_Mac <- count[, sub_ssGSEA_Mac[, 1]]
    sub_count_Mac <- as.matrix(sub_count_Mac)
    ssGSEA_Mac <- scImmuCC_main(
      sub_count_Mac, Macrophage_genelist,
      "cr2_Macrophage"
    )
    cells <- length(sub_count_Mac[2, ])
    if (cells > 50) {
      seurat_Mac <- seurat_Heatmap(
        sub_count_Mac, Macrophage_genelist,
        ssGSEA_Mac, "cr2_Macrophage"
      )
    }
  }

  if ("ILC" %in% cell_type) {
    sub_ssGSEA_ILC <- ssGSEA_result[which(ssGSEA_result[, 2] == "ILC"), ]
    sub_count_ILC <- count[, sub_ssGSEA_ILC[, 1]]
    sub_count_ILC <- as.matrix(sub_count_ILC)
    ssGSEA_ILC <- scImmuCC_main(sub_count_ILC, ILC_genelist, "cr2_ILC")
    cells <- length(sub_count_ILC[2, ])
    if (cells > 50) {
      seurat_ILC <- seurat_Heatmap(
        sub_count_ILC, ILC_genelist, ssGSEA_ILC,
        "cr2_ILC"
      )
    }
  }
}