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The pheatmap function in R, the pheatmap function gives you more control over the final plot than the standard base R heatmap does.

A numerical matrix holding the values to be plotted can be passed.

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# install.packages("pheatmap")
library(pheatmap)
# Data 
set.seed(123)
m <- matrix(rnorm(200), 10, 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)
# Heat map
pheatmap(m)

Normalization

If the matrix’s values are not normalized, you can use the scale parameter to normalize them by either the rows (“row”) or the columns (“column”) of the matrix.

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m <- matrix(rnorm(200), 10, 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)
# Heat map
pheatmap(m, scale = "column")

Values

Display_numbers = TRUE causes the values for each cell to be displayed. The text’s size and colour can both be changed.

pheatmap(m,
         display_numbers = TRUE,
         number_color = "black", 
         fontsize_number = 8)

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Number of clusters

With kmeans_k, the number of clusters can be altered. If there aren’t enough clusters, you can enlarge the cells using cellheight or cellwidth.

pheatmap(m, kmeans_k = 3, cellheight = 50)

Remove rows dendrogram

pheatmap(m, cluster_rows = FALSE)

Remove columns dendrogram

pheatmap(m, cluster_cols = FALSE)

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Remove dendrograms

pheatmap(m,
         cluster_cols = FALSE,
         cluster_rows = FALSE)

Border color

pheatmap(m, border_color = "black")

Color palette

pheatmap(m, color = hcl.colors(50, "BluYl"))

Legend breaks

heatmap(m, legend_breaks = c(-2, 0, 2))

Legend labels

pheatmap(m,
         legend_breaks = c(-2, 0, 2),
         legend_labels = c("Low", "Medium", "High"))

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Remove the legend

pheatmap(m, legend = FALSE)

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