pheatmap

pheatmap

Pretty heatmaps with clustering.

Basic Heatmap

library(pheatmap)

# From matrix
mat <- matrix(rnorm(100), nrow = 10)
rownames(mat) <- paste0("Gene", 1:10)
colnames(mat) <- paste0("Sample", 1:10)

pheatmap(mat)

Clustering

# With clustering (default)
pheatmap(mat, cluster_rows = TRUE, cluster_cols = TRUE)

# Without clustering
pheatmap(mat, cluster_rows = FALSE, cluster_cols = FALSE)

# Clustering method
pheatmap(mat, clustering_method = "complete")  # complete, average, ward.D2

# Clustering distance
pheatmap(mat, clustering_distance_rows = "euclidean")
pheatmap(mat, clustering_distance_cols = "correlation")

Colors

# Color palette
pheatmap(mat, color = colorRampPalette(c("blue", "white", "red"))(100))

# Breaks
pheatmap(mat, breaks = seq(-3, 3, length.out = 101))

# Color for NA
pheatmap(mat, na_col = "grey")

Annotations

# Row annotations
row_annotation <- data.frame(
  Group = c(rep("A", 5), rep("B", 5)),
  row.names = rownames(mat)
)

pheatmap(mat, annotation_row = row_annotation)

# Column annotations
col_annotation <- data.frame(
  Treatment = c(rep("Control", 5), rep("Treated", 5)),
  row.names = colnames(mat)
)

pheatmap(mat, annotation_col = col_annotation)

# Both
pheatmap(mat,
         annotation_row = row_annotation,
         annotation_col = col_annotation)

Annotation Colors

# Custom annotation colors
ann_colors <- list(
  Group = c(A = "red", B = "blue"),
  Treatment = c(Control = "white", Treated = "black")
)

pheatmap(mat,
         annotation_row = row_annotation,
         annotation_col = col_annotation,
         annotation_colors = ann_colors)

Display Options

pheatmap(mat,
  # Cell labels
  display_numbers = TRUE,
  number_format = "%.2f",
  number_color = "black",
  fontsize_number = 8,

  # Cell size
  cellwidth = 20,
  cellheight = 20,

  # Font sizes
  fontsize = 10,
  fontsize_row = 8,
  fontsize_col = 8,

  # Borders
  border_color = "grey60",

  # Legend
  legend = TRUE,
  legend_breaks = c(-2, 0, 2),
  legend_labels = c("Low", "Mid", "High")
)