How to create a heatmap in R, you must convert a numerical matrix into a data frame that ggplot2 can interpret.

Use the melt function from the reshape package for that.

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library(reshape) set.seed(123) m <- matrix(round(rnorm(200), 2), 10, 10) colnames(m) <- paste("Col", 1:10) rownames(m) <- paste("Row", 1:10) # Transform the matrix in long format df <- melt(m) colnames(df) <- c("x", "y", "value")

head(df)

x y value 1 Row 1 Col 1 -0.56 2 Row 2 Col 1 -0.23 3 Row 3 Col 1 1.56 4 Row 4 Col 1 0.07 5 Row 5 Col 1 0.13 6 Row 6 Col 1 1.72

## Heat map with geom_tile

When using geom_tile in ggplot2, a heap map can be produced by giving categorical variables to the x and y inputs and a continuous variable to the fill argument of the aes function.

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# install.packages("ggplot2") library(ggplot2) ggplot(df, aes(x = x, y = y, fill = value)) + geom_tile()

**Square tiles**

Be aware that the tiles may not be squared depending on the size of the plotting window. Use cood_fixed if you wish to keep them square.

library(ggplot2) ggplot(df, aes(x = x, y = y, fill = value)) + geom_tile() + coord_fixed()

**Border customization**

With colour, lwd, and linetype, respectively, you can change the border colour, line width, and line style of the tiles.

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library(ggplot2) ggplot(df, aes(x = x, y = y, fill = value)) + geom_tile(color = "white", lwd = 1.5, linetype = 1) + coord_fixed()

**Adding the values**

Additionally, you may use the geom_text function to add values over tiles while giving a number variable as the label argument for the aes function.

ggplot(df, aes(x = x, y = y, fill = value)) + geom_tile(color = "black") + geom_text(aes(label = value), color = "white", size = 4) + coord_fixed()

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**Color palette**

There are three options for altering the heat map’s default colour scheme.

**scale_fill_gradient**

ggplot(df, aes(x = x, y = y, fill = value)) + geom_tile(color = "black") + scale_fill_gradient(low = "white", high = "red") + coord_fixed()

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**scale_fill_gradient2**

ggplot(df, aes(x = x, y = y, fill = value)) + geom_tile(color = "black") + scale_fill_gradient2(low = "#075AFF", mid = "#FFFFCC", high = "#FF0000") + coord_fixed()

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**scale_fill_gradientn**

ggplot(df, aes(x = x, y = y, fill = value)) + geom_tile(color = "black") + scale_fill_gradientn(colors = hcl.colors(20, "RdYlGn")) + coord_fixed()

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