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R/scImmuCC.R

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+#' @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  a 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
+#' library(GSVA)
+#' library(Seurat)
+
+scImmuCC_Layered <- function(count,Non_Immune=TRUE){
+
+  # if (!requireNamespace("GSVA", quietly = TRUE)) {
+    BiocManager::install("GSVA")
+  # }
+  # if (!requireNamespace("Seurat", quietly = TRUE)){
+    install.packages("Seurat")
+  # }
+  data("./data/layer1_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")
+  data("./data/layer0_genelist.rda",package="scImmuCC")
+
+
+  if(Non_Immune==TRUE){
+
+    layer0_result <- scImmuCC_main(count,layer0_genelist,"Layer0")
+    immune <- layer0_result[which(layer0_result[,2]=="Immune"),]
+    count_immune <- count[,immune[,1]]
+    ssGSEA_result <- scImmuCC_main(count_immune,layer1_genelist,"Layer1")
+    seurat_result <- seurat_Heatmap(count,layer1_genelist,ssGSEA_result,"Layer1")
+
+  }else{
+
+    ssGSEA_result <- scImmuCC_main(count,layer1_genelist,"Layer1")
+    seurat_result <- seurat_Heatmap(count,layer1_genelist,ssGSEA_result,"Layer1")
+  }
+
+  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,"Layer2_Tcell")
+    seurat_Tcell <- seurat_Heatmap(sub_count_Tcell,Tcell_genelist,ssGSEA_Tcell,"Layer2_Tcell")
+
+    cell_type2 <- unique(ssGSEA_Tcell[,2])
+
+    if("CD4_T" %in% cell_type){
+      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,"Layer3_CD4")
+      cells <- length(sub_count_CD4[2,])
+      if(cells>50){
+        seurat_CD4 <- seurat_Heatmap(sub_count_CD4,CD4_genelist,ssGSEA_CD4,"Layer3_CD4")
+      }
+
+    }
+
+
+    if("CD8_T" %in% cell_type){
+      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,"Layer3_CD4")
+      cells <- length(sub_count_CD8[2,])
+      if(cells>50){
+        seurat_CD8 <- seurat_Heatmap(sub_count_CD8,CD8_genelist,ssGSEA_CD8,"Layer3_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,"Layer2_Bcell")
+    cells <- length(sub_count_Bcell[2,])
+    if(cells>50){
+       seurat_Bcell <- seurat_Heatmap(sub_count_Bcell,Bcell_genelist,ssGSEA_Bcell,"Layer2_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,"Layer2_DC")
+    cells <- length(sub_count_DC[2,])
+    if(cells>50){
+      seurat_DC <- seurat_Heatmap(sub_count_DC,DC_genelist,ssGSEA_DC,"Layer2_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,"Layer2_NK")
+    cells <- length(sub_count_NK[2,])
+    if(cells>50){
+      seurat_NK <- seurat_Heatmap(sub_count_NK,NK_genelist,ssGSEA_NK,"Layer2_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,"Layer2_Monocyte")
+    cells <- length(sub_count_Mono[2,])
+    if(cells>50){
+      seurat_Mono <- seurat_Heatmap(sub_count_Mono,Monocyte_genelist,ssGSEA_Mono,"Layer2_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,"Layer2_Macrophage")
+    cells <- length(sub_count_Mac[2,])
+    if(cells>50){
+      seurat_Mac <- seurat_Heatmap(sub_count_Mac,Macrophage_genelist,ssGSEA_Mac,"Layer2_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,"Layer2_ILC")
+    cells <- length(sub_count_ILC[2,])
+    if(cells>50){
+      seurat_ILC <- seurat_Heatmap(sub_count_ILC,ILC_genelist,ssGSEA_ILC,"Layer2_ILC")
+    }
+  }
+}