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01_Interaction_map.R
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executable file
·88 lines (78 loc) · 4.89 KB
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rm(list=ls())
library(dplyr)
lr_pair <- read.delim("./results_pp_dEpi_orgEpi/LR_Pair_mus_musculus.txt")
epithelial_ligand_mtx <- read.delim("./results_pp_dEpi_orgEpi/epithelial_ligand_mtx.txt")
epithelial_receptor_mtx <- read.delim("./results_pp_dEpi_orgEpi/epithelial_receptor_mtx.txt")
pp_apc_ligand_mtx <- read.delim("./results_pp_dEpi_orgEpi/pp_apc_ligand_mtx.txt")
pp_apc_receptor_mtx <- read.delim("./results_pp_dEpi_orgEpi/pp_apc_receptor_mtx.txt")
# pp_apcs : new cluster
# (2,4,6): ILC13 --> 2
# (1): MPs --> 1
# (0,3): DCs --> 0
# (5,9): B cell --> exclude
# (7): pDCs --> 4
# (8): ILC2 --> 3
a = data.frame(cluster = c(0,1,2,3,4), celltype = c("DCs","MPs","ILC13","ILC2","pDCs"))
a$cluster <- as.character(paste0("pp_R_",a$cluster))
write.table(a,file = './results_pp_dEpi_orgEpi/pp_apc_ident.txt', sep = '\t', row.names = F)
class(a$cluster)
pp_apc_ligand_mtx$ident <- pp_apc_receptor_mtx$ident %>% unname()
pp_apc_ligand_mtx <- pp_apc_ligand_mtx[pp_apc_ligand_mtx$ident != 5 &
pp_apc_ligand_mtx$ident != 9,]
pp_apc_receptor_mtx$ident <- pp_apc_receptor_mtx$ident %>% unname()
pp_apc_receptor_mtx <- pp_apc_receptor_mtx[pp_apc_receptor_mtx$ident != 5 &
pp_apc_receptor_mtx$ident != 9,]
pp_apc_ligand_mtx$ident <- gsub("^4$","2",pp_apc_ligand_mtx$ident)
pp_apc_ligand_mtx$ident <- gsub("^6$","2",pp_apc_ligand_mtx$ident)
pp_apc_ligand_mtx$ident <- gsub("^3$","0",pp_apc_ligand_mtx$ident)
pp_apc_ligand_mtx$ident <- gsub("^7$","4",pp_apc_ligand_mtx$ident)
pp_apc_ligand_mtx$ident <- gsub("^8$","3",pp_apc_ligand_mtx$ident)
pp_apc_ligand_mtx = droplevels(pp_apc_ligand_mtx)
pp_apc_ligand_mtx$ident <- as.numeric(pp_apc_ligand_mtx$ident)
pp_apc_ligand_mean_mtx <- pp_apc_ligand_mtx %>% group_by(ident) %>% summarise_all(funs(mean))
pp_apc_ligand_mtx2 <- pp_apc_ligand_mtx[,2:ncol(pp_apc_ligand_mtx)]
pp_apc_ligand_mtx2[pp_apc_ligand_mtx2>0] <- 1
pp_apc_ligand_mtx2 <- cbind(pp_apc_ligand_mtx[,1], pp_apc_ligand_mtx2)
colnames(pp_apc_ligand_mtx2)[1] <- "ident"
pp_apc_ligand_PA_mtx <- pp_apc_ligand_mtx2 %>% group_by(ident) %>% summarise_all(funs(mean))
pp_apc_receptor_mtx$ident <- gsub("^4$","2",pp_apc_receptor_mtx$ident)
pp_apc_receptor_mtx$ident <- gsub("^6$","2",pp_apc_receptor_mtx$ident)
pp_apc_receptor_mtx$ident <- gsub("^3$","0",pp_apc_receptor_mtx$ident)
pp_apc_receptor_mtx$ident <- gsub("^7$","4",pp_apc_receptor_mtx$ident)
pp_apc_receptor_mtx$ident <- gsub("^8$","3",pp_apc_receptor_mtx$ident)
pp_apc_receptor_mtx = droplevels(pp_apc_receptor_mtx)
pp_apc_receptor_mtx$ident <- as.numeric(pp_apc_receptor_mtx$ident)
pp_apc_receptor_mean_mtx <- pp_apc_receptor_mtx %>% group_by(ident) %>% summarise_all(funs(mean))
pp_apc_receptor_mtx2 <- pp_apc_receptor_mtx[,2:ncol(pp_apc_receptor_mtx)]
pp_apc_receptor_mtx2[pp_apc_receptor_mtx2 > 0] <- 1
pp_apc_receptor_mtx2 <- cbind(pp_apc_receptor_mtx[,1], pp_apc_receptor_mtx2)
colnames(pp_apc_receptor_mtx2)[1] <- "ident"
pp_apc_receptor_PA_mtx <- pp_apc_receptor_mtx2 %>% group_by(ident) %>% summarise_all(funs(mean))
#### Cell Identification Table
ident_vector <- epithelial_ligand_mtx$ident
ident_index = data.frame(ident = unique(ident_vector))
ident_index$cluster <- c(0,1,2,3,4,5,6,7,8)
rownames(ident_index) <- as.character(ident_index$ident)
#rownames(ident_index) <- ident_index$ident
#ident_index$new_cluster <- c(1,2,3,1,2,2,1,2,2,4,1,2,5,6)
#ident_index$new_ident <- c("entero","stem","endocrine","entero","stem","stem",
# "entero","stem","stem","goblet","entero","stem","paneth","tuft")
#clusters <- sapply(ident_vector, FUN = function(x) return(ident_index[x,][3]) )
#clusters <- clusters %>% unlist() %>% unname()
#epithelial_ligand_mtx$ident <- clusters
write.table(ident_index, file = './results_pp_dEpi_orgEpi/epi_ident.txt', sep = '\t')
epithelial_ligand_mtx$ident <-
sapply(epithelial_ligand_mtx$ident, FUN = function(x){ ident_index[x,]$cluster }) %>% unlist() %>% unname()
epithelial_ligand_mean_mtx <- epithelial_ligand_mtx %>% group_by(ident) %>% summarise_all(funs(mean))
epithelial_ligand_mtx2 <- epithelial_ligand_mtx[,2:ncol(epithelial_ligand_mtx)]
epithelial_ligand_mtx2[epithelial_ligand_mtx2 > 0] <- 1
epithelial_ligand_mtx2 <- cbind(epithelial_ligand_mtx[,1], epithelial_ligand_mtx2)
colnames(epithelial_ligand_mtx2)[1] <- "ident"
epithelial_ligand_PA_mtx <- epithelial_ligand_mtx2 %>% group_by(ident) %>% summarise_all(funs(mean))
epithelial_receptor_mtx$ident <- epithelial_ligand_mtx$ident
epithelial_receptor_mean_mtx <- epithelial_receptor_mtx %>% group_by(ident) %>% summarise_all(funs(mean))
epithelial_receptor_mtx2 <- epithelial_receptor_mtx[,2:ncol(epithelial_receptor_mtx)]
epithelial_receptor_mtx2[epithelial_receptor_mtx2 > 0] <- 1
epithelial_receptor_mtx2 <- cbind(epithelial_receptor_mtx[,1], epithelial_receptor_mtx2)
colnames(epithelial_receptor_mtx2)[1] <- "ident"
epithelial_receptor_PA_mtx <- epithelial_receptor_mtx2 %>% group_by(ident) %>% summarise_all(funs(mean))