Ronjon …2

# source('http://bioconductor.org/biocLite.R')
# biocLite('mogene10sttranscriptcluster.db')

load("~/Dropbox/RonjonOct2012/ronSub.RData")
library(annotate)
library(mogene10sttranscriptcluster.db)
glucoC = c("Cyp11a1", "Hsd3b1", "Cyp21", "Cyp11b1", "Hsd11b1", "H6pd", "Nr3c1")
sym = getSYMBOL(featureNames(ron.eset), "mogene10sttranscriptcluster")

match.all = function(x, vec) {
    ret = vector()
    for (i in x) ret = c(ret, which(vec == i))
    ret
}

glucoC.index = match.all(glucoC, sym)
glucoC.index

## 10585794 10500565 10429538 10361234 10518743 10458569 
##    32096    22826    15420     8244    24733    18422

sym[glucoC.index]

##  10585794  10500565  10429538  10361234  10518743  10458569 
## "Cyp11a1"  "Hsd3b1" "Cyp11b1" "Hsd11b1"    "H6pd"   "Nr3c1"

library(gplots)
hmap = as.matrix(t(exprs(ron.eset[glucoC.index, ])))

type = samp$type
type = as.vector(type)
type[type == "ResidentDCs"] <- "blue"
type[type == "MigratoryDCs"] <- "green"
type[type == "NonLymphoid"] <- "yellow"
type[type == "Precursors"] <- "red"
heatmap.2(hmap, trace = "n", scale = "c", labCol = glucoC, labRow = samp$heatmap_order, 
    Rowv = F, Colv = F, col = "bluered", RowSideColors = type, margins = c(7, 
        3))