# The pheatmap function in R

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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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