library(reactable)
signature_matrix_adeno <- readRDS("~/new_data/signature_matrix_adeno.rds")
signature_matrix_adeno <- as.data.frame(signature_matrix_adeno)
reactable(signature_matrix_adeno) #7093 gene
filtered_genes <- signature_matrix_adeno[signature_matrix_adeno$Neutrophils > 2.0000 & 
                              apply(signature_matrix_adeno[, colnames(signature_matrix_adeno) != "Neutrophils"], 1, max) <= 2.0000, ]

reactable(filtered_genes) #42 gene
library(biomaRt)
mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
ensembl_ids <- rownames(filtered_genes)
gene_conversion <- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), 
                         filters = "ensembl_gene_id", 
                         values = ensembl_ids, 
                         mart = mart)
filtered_genes$Gene_Name <- gene_conversion$hgnc_symbol[match(rownames(filtered_genes), gene_conversion$ensembl_gene_id)]
rownames(filtered_genes) <- filtered_genes$Gene_Name
filtered_genes$Gene_Name <- NULL
reactable(filtered_genes)

#filter

neutrophil_exp <- signature_matrix_adeno$Neutrophils  
other_cells_exp <- rowMeans(signature_matrix_adeno[, colnames(signature_matrix_adeno) != "Neutrophils"])
luad_filtered_genes <- signature_matrix_adeno[neutrophil_exp > 1.9 * other_cells_exp, ]
reactable(luad_filtered_genes) #670 gene