From 97fdefab064f63642fa3ece05b807d29b459df31 Mon Sep 17 00:00:00 2001
From: Hui Lan <lanhui@zjnu.edu.cn>
Date: Wed, 4 Dec 2019 19:03:19 +0800
Subject: brain: add python and R code to local repository.

---
 Code/create_edges_k2.R | 136 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 136 insertions(+)
 create mode 100644 Code/create_edges_k2.R

(limited to 'Code/create_edges_k2.R')

diff --git a/Code/create_edges_k2.R b/Code/create_edges_k2.R
new file mode 100644
index 0000000..a044ed0
--- /dev/null
+++ b/Code/create_edges_k2.R
@@ -0,0 +1,136 @@
+# Last modified 13 August 2019
+
+TARGET_TF_FILE     <- "../Data/information/target_tf.txt"
+DATA_FILE          <- "../Data/history/expr/TPM.txt" # A TPM table
+AGINAME_FILE       <- "../Data/information/AGI-to-gene-names_v2.txt"
+CORR_THRESHOLD     <- 0.5
+MIN_SIZE           <- 100
+
+
+# Make sure we have required files
+if (! file.exists(TARGET_TF_FILE)) {
+   stop(sprintf('[create_edges2_k2.R] Unable to find %s', TARGET_TF_FILE))
+}
+
+if (! file.exists(DATA_FILE)) {
+   stop(sprintf('[create_edges_k2.R] Unable to find %s', DATA_FILE))
+}
+
+if (! file.exists(AGINAME_FILE)) {
+   stop(sprintf('[create_edges_k2.R] Unable to find %s', AGINAME_FILE))
+}
+
+
+####### Read data #########################################
+X             <- read.table(DATA_FILE, header=TRUE, check.names=FALSE)
+gene_id       <- X$gene_id
+X$gene_id     <- NULL
+row.names(X)  <- gene_id
+X             <- as.matrix(X)
+rna.sample.id <- colnames(X)
+
+target_tf  <- read.table(TARGET_TF_FILE, sep='\t', header=FALSE)
+target_tf  <- as.matrix(target_tf)
+targets    <- target_tf[,1]
+tfs        <- target_tf[,2]
+conditions <- target_tf[,3]
+
+agi        <- read.table(AGINAME_FILE, stringsAsFactors=F) # AGINAME_FILE cannot contain quotes
+#######################################################
+
+library(mixtools)
+options(max.print=999999999)
+output.file <- paste('../Data/history/edges/one_target/edges.txt', 'mixtools', format(Sys.time(), '%b.%d.%Y.%H%M%S'), sep='.')
+f <- file(output.file, 'w')
+
+for (i in 1:length(targets)) {
+    curr.date <- gsub('-','',Sys.Date())
+    id1 <- tfs[i]
+    id2 <- targets[i]
+    if (id1 %in% gene_id == F || id2 %in% gene_id == F) {
+        next
+    }
+
+    name1 <- agi$V2[which(agi$V1 == id1)]
+    name2 <- agi$V2[which(agi$V1 == id2)]	    
+
+    cond <- conditions[i]
+    x <- X[id1,]
+    y <- X[id2,]
+    x <- log(x+1)
+    y <- log(y+1)
+    index <- x < 0.01 | y < 0.01
+    x <- x[!index]
+    y <- y[!index]
+    if (length(x) < 3 | sd(x) < 0.1 | sd(y) < 0.1 ) {
+        next
+    }
+    r <- cor(x, y)
+    if (abs(r) >= CORR_THRESHOLD) {
+        s = sprintf('%s %s\t%s %s\t%4.2f\t%s\t%s\t%s\t%s\t%s\n', id2, name2,id1,name1, r, 'all', '.', cond, '.', curr.date)
+        #cat(s, file=result.file, sep='\n', append=T)
+        #cat(s, sep='\n')
+        #flush.console()
+	#write.table(s, file.name, quote=F, sep='', row.names=F, append=T, col.names=F)
+        next
+    }
+
+    k <- 2
+    N <- length(x)
+    tryCatch( em.out <- regmixEM(y, x, maxit=100, epsilon=1e-03, k=k), error=function(e) NULL )
+    if (length(em.out) == 0)  { # if there is an error when running regmixEM, we skip.
+        next
+    }
+
+    pos_r_max   <- -2
+    pos_r_N     <- 0
+    pos_r_index <- c()
+    pos_r_loglik <- -100000000
+
+    neg_r_max   <- 2
+    neg_r_N     <- 0
+    neg_r_index <- c()
+    neg_r_loglik <- -100000000
+
+    for (j in seq(1,k,1)) {
+
+        index <- which(max.col(em.out$posterior) == j)
+        size <- length(index)
+        r <- cor(em.out$x[index,2], em.out$y[index])
+
+        if (!is.na(r) && r >= CORR_THRESHOLD && size >= MIN_SIZE && r > pos_r_max && size > pos_r_N) {
+            pos_r_max <- r
+            pos_r_N   <- size
+            pos_r_index <- index
+            pos_r_loglik <- em.out$loglik
+        }
+        if (!is.na(r) && r <= -CORR_THRESHOLD && size >= MIN_SIZE && r < neg_r_max && size > neg_r_N) {
+            neg_r_max <- r
+            neg_r_N   <- size
+            neg_r_index <- index
+            neg_r_loglik <- em.out$loglik
+        }
+    }
+
+    if (pos_r_max > 0) {
+        sub.cond <- paste(rna.sample.id[pos_r_index], collapse=' ')
+	num.sub.cond <- length(rna.sample.id[pos_r_index])
+        s = sprintf('%s %s\t%s %s\t%4.2f\t%s\t%d\t%s\t%4.2f\t%s\t%4.2f\t%s\n', id2, name2, id1, name1, pos_r_max, 'mix', num.sub.cond, cond, pos_r_loglik, curr.date, pos_r_max, 'mixtool')
+        #cat(s, file=result.file, sep='\n', append=T)
+        #cat(s, sep='\n')
+	#write.table(s, file.name, quote=F, sep='', row.names=F, append=T, col.names=F)
+        cat(s, file=f, sep='')	
+    }
+    
+    if (neg_r_max < 0) {
+        sub.cond <- paste(rna.sample.id[neg_r_index], collapse=' ')
+	num.sub.cond <- length(rna.sample.id[neg_r_index])	
+        s = sprintf('%s %s\t%s %s\t%4.2f\t%s\t%d\t%s\t%4.2f\t%s\t%4.2f\t%s\n', id2, name2, id1, name1, neg_r_max, 'mix', num.sub.cond, cond, neg_r_loglik, curr.date, neg_r_max, 'mixtool')
+        #cat(s, file=result.file, sep='\n', append=T)
+        #cat(s, sep='\n')
+	#write.table(s, file.name, quote=F, sep='', row.names=F, append=T, col.names=F)
+        cat(s, file=f, sep='')
+    }
+}
+
+close(f)
\ No newline at end of file
-- 
cgit v1.2.1