Create test matrix（造數據）

set.seed(6)
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")

正文從這裡開始

# Show text within cells
pheatmap(test, display_numbers = TRUE)
pheatmap(test, display_numbers = TRUE, number_format = "\\%.1e")
pheatmap(test, display_numbers = TRUE, display_numbers = matrix(ifelse(test > 5, "*", ""), nrow(test)))

• display_numbers = T 即Show text within cells

• number_format 可以格式輸出display_number

• 或者乾脆自定義一個matrix通過display_numbers參數進行display

# legend（圖例）的設置選項
pheatmap(test)  # p1
pheatmap(test, legend_breaks = -1:7)  # p2
pheatmap(test, legend_breaks = 1:6, legend_labels = c("6","6", "6", "6", "6", "6"))  # p3
pheatmap(test, legend_breaks = 9:14, legend_labels = c("6","6", "6", "6", "6", "6"))  # p4

• pheatmap函數會在內部算出legend的數值範圍，本例中大概是 -1:7

• 在數值範圍內，我們可以設定legend_breaks，以及對legend_breaks這個label的文本展示

• legend_breaks和legend_labels是有一個對應關係的，否則報錯如下

  Error in pheatmap(test, legend_breaks = 1:6, legend_labels =
  c(“6”, “6”, : Lengths of legend_breaks and legend_labels must be
  the same

• 假如我們的設定範圍超出，就如p4所示

# Fix cell sizes and save to file with correct size
pheatmap(test, cellwidth = 15, cellheight = 12, main = "Example heatmap")  # the title of the plot
pheatmap(test, cellwidth = 15, cellheight = 12, fontsize = 8, filename = "test.pdf")  # save to pdf

# Change angle of text in the columns (0, 45, 90, 270 and 315)
pheatmap(test, angle_col = "45")
pheatmap(test, angle_col = "0")

有關annotation

# Generate annotations for rows and columns（先造數據）
annotation_col = data.frame(
                    CellType = factor(rep(c("CT1", "CT2"), 5)), 
                    Time = 1:5
                )
rownames(annotation_col) = paste("Test", 1:10, sep = "")

annotation_row = data.frame(
                    GeneClass = factor(rep(c("Path1", "Path2", "Path3"), c(10, 4, 6)))
                )
rownames(annotation_row) = paste("Gene", 1:20, sep = "")

# Display row and color annotations
pheatmap(test, annotation_col = annotation_col, cluster_cols = F)

pheatmap(test, annotation_col = annotation_col, annotation_legend = FALSE, cluster_cols = F)

pheatmap(test, annotation_row = annotation_row, cluster_rows = F)

• annotation數據首先要組織成dataframe，dataframe中的rownames要和註釋項進行對應，
  而column就是要展示的註釋條，每個column都會生成一個註釋條來顯示

• annotation_col/row 預設會有legend配合展示，annotation_legend = FALSE可以去掉legend

# Specify colors （自定義註釋條顏色）
ann_colors = list(
    Time = c("white", "firebrick"),
    CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
    GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E")
)

pheatmap(test, annotation_col = annotation_col, annotation_colors = ann_colors)

pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = ann_colors)

• 註釋條顏色數據要組織成list（list的靈活性就在此處凸顯出來了），
  list中的每個元素名作為對應項（對應前述dataframe中的colnames），
  同時可以進一步為attribute指定顏色，例如
  CT1 = "#1B9E77", CT2 = "#D95F02"

參考資料

pheatmap幫助文檔