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)
