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ggplot2 heatmap with "spectral" palette
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doInstall <- TRUE # Change to FALSE if you don't want packages installed. | |
toInstall <- c("ggplot2", "reshape2", "RColorBrewer") | |
if(doInstall){install.packages(toInstall, repos = "http://cran.us.r-project.org")} | |
lapply(toInstall, library, character.only = TRUE) | |
# Generate a random matrix | |
# This can be any type of numeric matrix, | |
# though we often see heatmaps of square correlation matrices. | |
nRow <- 9 | |
nCol <- 16 | |
myData <- matrix(rnorm(nRow * nCol), ncol = nCol) | |
rownames(myData) <- letters[1:nRow] | |
colnames(myData) <- LETTERS[1:nCol] | |
# Replace with numbers that actually have a relationship: | |
for(ii in 2:ncol(myData)){ myData[, ii] <- myData[, ii-1] + rnorm(nrow(myData)) } | |
for(ii in 2:nrow(myData)){ myData[ii, ] <- myData[ii-1, ] + rnorm(ncol(myData)) } | |
# 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$Var1 <- factor(longData$Var1, names(sort(with(longData, by(value, Var1, mean))))) | |
longData$Var2 <- factor(longData$Var2, names(sort(with(longData, by(value, Var2, mean))))) | |
# Define palette | |
myPalette <- colorRampPalette(rev(brewer.pal(11, "Spectral")), space="Lab") | |
zp1 <- ggplot(longData, | |
aes(x = Var2, y = Var1, 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() | |
print(zp1) |
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Is there any way to set 0 to the light yellow? Or should I standardized the value?