# Heatmap session 2010-10-19

library(ArrayExpress)
Atxn1Data = ArrayExpress("E-MEXP-886")
require(annotate)
?KEGG2heatmap
ls()
Atxn1Data
KEGG2heatmap("mmu04070", Atxn1Data, moe430a.db)
KEGG2heatmap("mmu04070", Atxn1Data, "moe430a.db")
KEGG2heatmap("mmu04070", Atxn1Data, "moe430a")
require(moe430a.db)
KEGG2heatmap("mmu04070", Atxn1Data, "moe430a")
Atnx1Data
Atxn1Data
Atxn1RMA = rma(Atxn1Data)
require(affy)
Atxn1RMA = rma(Atxn1Data)
Atxn1RMA
KEGG2heatmap("mmu04070", Atxn1Data, "moe430a")
KEGG2heatmap("mmu04070", Atxn1RMA, "moe430a")
KEGG2heatmap("04070", Atxn1RMA, "moe430a")
example(KEGG2heatmap)
KEGG2heatmap("04070", Atxn1RMA, "moe430a")
KEGG2heatmap("04070", Atxn1RMA, "moe430a", col=terrain.colors(12))
?heat.colors
KEGG2heatmap("04070", Atxn1RMA, "moe430a", col=rainbow(12))
KEGG2heatmap("04070", Atxn1RMA, "moe430a")
require(Heatplus)
KEGG2heatmap("04070", Atxn1RMA, "moe430a", col=RGBColVec(12))
dd = Atxn1Data
sampleNames(dd) 
pData(Atxn1Data)
sampleNames(dd) = pData(Atxn1Dataà$ Factor.Value..genotype.
sampleNames(dd) = pData(Atxn1Data)$Factor.Value..genotype.
sampleNames(dd) 
example(heatmap_plus)
KEGG2heatmap
KEGG2heatmap("04070", Atxn1RMA, "moe430a", col=RGBColVec(12), labCols= pData(Atxn1Dataà$ Factor.Value..genotype.)
)
KEGG2heatmap("04070", Atxn1RMA, "moe430a", col=RGBColVec(12), labCols= pData(Atxn1Data$Factor.Value..genotype.))
KEGG2heatmap("04070", Atxn1RMA, "moe430a", col=RGBColVec(12), labCols= pData(Atxn1Data)$Factor.Value..genotype.)
KEGG2heatmap("04070", Atxn1RMA, "moe430a", col=RGBColVec(12), labCol= pData(Atxn1Data)$Factor.Value..genotype.)
KEGG2heatmap("04730", Atxn1RMA, "moe430a", col=RGBColVec(12), labCol= pData(Atxn1Data)$Factor.Value..genotype.)
KEGG2heatmap("04540", Atxn1RMA, "moe430a", col=RGBColVec(12), labCol= pData(Atxn1Data)$Factor.Value..genotype.)
KEGG2heatmap("04070", Atxn1RMA, "moe430a")