#########################################################
## Plots Demo                                          ## 
## Author: Han-Ming Wu (hmwu@stat.sinica.edu.tw)       ## 
## Institute of Statistical Science, Academia Sinica   ## 
## http://www.sinica.edu.tw/~hmwu/                     ## 
## 2005/07/27                                          ## 
#########################################################


## Read Data
setwd("C:\\Program Files\\R\\rw2001\\WorkingData")
library(stats)
cell.matrix  <- read.table("TradCellCycle103_alpha.txt", header=TRUE)
n <- dim(cell.matrix)[1]
p <- dim(cell.matrix)[2]-2
cell.data <- cell.matrix[,3:p+2]
gene.name <- cell.matrix[,1]
gene.phase <- cell.matrix[,2]
phase <- unique(gene.phase)
phase.name <- c("G1", "S", "S/G2", "G2/M", "M/G1")

## standardized data
cell.sdata <- (cell.data-apply(cell.data, 1, mean))/sqrt(apply(cell.data, 1, var)) 

#Histogram
hist(cell.sdata[,1], br=12, col="lightblue", border="pink", labels = TRUE, main="Histogram for the exp. alpha14",
xlab="log ratio")

#Boxplot
boxplot(cell.sdata)
boxplot(cell.sdata[,1]~gene.phase, names=phase.name)

#Scatterplot matrix
pairs(cell.sdata[,1:5], col=phase)


## Data Image
cell.image <- as.matrix(t(cell.sdata[n:1,]))
RGcol <- maPalette(low = "green", high = "red", k = 50)
image(cell.image, xlab="Exp.", ylab="Genes", col = RGcol)


## Time Series Plots
number <- 1:n
par(mfrow=c(3,2))
for(i in 0:4){
    ts.plot(t(cell.sdata[number[gene.phase==i],]), xlab=phase.name[i+1])
}


### Name: maPalette
### Title: Microarray color palette
### Aliases: maPalette
### Keywords: color
### Author: Sandrine Dudoit <sandrine@stat.berkeley.edu>, Yee Hwa (Jean)
        Yang <yeehwa@stat.berkeley.edu>

maPalette <- function(low = "white",
                      high = c("green", "red"),
                      mid=NULL,
                      k =50)
{
    low <- col2rgb(low)/255
    high <- col2rgb(high)/255

    if(is.null(mid)){
        r <- seq(low[1], high[1], len = k)
        g <- seq(low[2], high[2], len = k)
        b <- seq(low[3], high[3], len = k)
      }
    if(!is.null(mid)){
      k2 <- round(k/2)
      mid <- col2rgb(mid)/255
      r <- c(seq(low[1], mid[1], len = k2),
             seq(mid[1], high[1], len = k2))
      g <- c(seq(low[2], mid[2], len = k2),
             seq(mid[2], high[2], len = k2))
      b <- c(seq(low[3], mid[3], len = k2),
             seq(mid[3], high[3], len = k2))
    }
    rgb(r, g, b)
}