ggplot2 heatmap with "spectral" palette

Heatmap.R

heatmapdata <- read.csv("~/Subsystem_by_Phylum-absolute.csv", sep="\t", check.names=FALSE)

row.names(heatmapdata) <- heatmapdata$Phylum

hmdata <- heatmapdata[,2:29]

myData <- data.matrix(hmdata)

# For melt() to work seamlessly, myData has to be a matrix.
longData <- melt(myData)
head(longData, 20)

# Optionally, reorder both the row and column variables in any order
# Here, they are sorted by mean value
longData$Phylum <- factor(longData$X1, names(sort(with(longData, by(value, X1, mean)))))
longData$Subsystem <- factor(longData$X2, names(sort(with(longData, by(value, X2, mean)))))

# Define palette
myPalette <- colorRampPalette(rev(brewer.pal(11, "Spectral")))

zp1 <- ggplot(longData,aes(x = Subsystem, y = Phylum, fill = value))
zp1 <- zp1 + geom_tile()
zp1 <- zp1 + scale_fill_gradientn(colours = myPalette(100))
zp1 <- zp1 + scale_x_discrete(expand = c(0, 0))
zp1 <- zp1 + scale_y_discrete(expand = c(0, 0))
zp1 <- zp1 + coord_equal()
zp1 <- zp1 + theme_bw()
zp1 <- zp1 + theme(axis.text.x=element_text(angle=-90, hjust=0))
print(zp1)