url <-  "https://galaxyweb.umassmed.edu/pub/class/data.tsv"
#install a package
#install.packages("RCurl")
library(RCurl)
file <- textConnection(getURL(url))

# or download the file and read like below
# file <- "~/Downloads/data.tsv"
data <- read.table(file,sep="\t", header=TRUE, row.names=1)

columns <- c("exper_rep1","exper_rep2","exper_rep3",
             "control_rep1","control_rep2","control_rep3")

View(data)

data <- data[, columns]

avgX <- rowMeans(data[, c("exper_rep1","exper_rep2","exper_rep3")])
#or
#avgX <- rowMeans(data[, 1:3])

avgY <- rowMeans(data[, c("control_rep1","control_rep2","control_rep3")])

avgall <- cbind(avgX, avgY)

colnames(avgall) <- c("Treat", "Control")

gdat<-data.frame(avgall)

ggplot() +
    geom_point(data=gdat, aes_string(x="Treat", y="Control"),
               colour="grey", alpha=6/10, size=3) +
    scale_x_log10() +scale_y_log10()

head(data)
conds <- factor(c("Treat", "Treat", "Treat", "Control", "Control", "Control") )
    
source("https://galaxyweb.umassmed.edu/pub/class/funcs.R")

de_res <- runDESeq(data, columns, conds,
          padj=0.01, log2FoldChange=2, non_expressed_cutoff=10)

#dim(de_res$res_selected)

#write.table(rownames(de_res$res_detected), "~/Downloads/deres.txt",  
#    quote = FALSE, col.names = FALSE, row.names=FALSE)

overlaid_data <- overlaySig(gdat, de_res$res_selected)

#head(overlaid_data)

ggplot() +
    geom_point(data=overlaid_data, aes_string(x="Treat", y="Control",
                     colour="Legend"), alpha=6/10, size=3) +
    scale_colour_manual(values=c("All"="darkgrey","Significant"="red"))+
    scale_x_log10() +scale_y_log10()


sel_data<-data[rownames(de_res$res_selected),]
dim(sel_data)
norm_data<-getNormalizedMatrix(sel_data, method="TMM")

ld <- log2(sel_data+0.1)
cldt <- scale(t(ld), center=TRUE, scale=TRUE);
distance<-dist(cldt, method = "euclidean")
plot(hclust(distance, method = "complete"),
     main="Euclidean", xlab="")

cld <- t(cldt)
heatmap.2(cld, Rowv=TRUE,dendrogram="column",
          Colv=TRUE, col=redblue(256),labRow=NA,
          density.info="none",trace="none", cexCol=0.8);