pheatmap交互

最近ComplexHeatmap更新可以將pheatmap對象進行參數(shù)轉(zhuǎn)換。新增的ComplexHeatmap::pheatmap()的功能與pheatmap::pheatmap()完全一致辖佣，其返回一個Formal class Heatmap對象，這意味著我們可以使用ComplexHeatmap中的其他函數(shù)對其進行操作并繪制更加復雜的熱圖。

# 模擬數(shù)據(jù)
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 = "")

# 整理注釋信息
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 = "")

ann_colors = list(
  Time = c("white", "firebrick"),
  CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
  GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E")
)

# 繪圖
p1 = pheatmap(test, name = "mat1")
p2 = rowAnnotation(foo = anno_barplot(1:nrow(test)), border = F)
p3 = pheatmap(test, name = "mat2", 
              col = colorRampPalette(c("navy", "white", "firebrick3"))(50))
# or you can simply specify as
# p3 = pheatmap(test, name = "mat2", col = c("navy", "white", "firebrick3"))
p1 + p2 + p3

ComplexHeatmap::pheatmap

ComplexHeatmap::Heatmap主體熱圖參數(shù)

繪制熱圖首先需要準備已經(jīng)標準化的二維矩陣作為輸入蚁堤，可以出圖后我們就需要對主體部分進行修改幔戏，一些比較常用的參數(shù)包括單元格（顏色，邊界旬渠，大小等）俱萍，行/列聚類（是否聚類，是否展示聚類樹告丢，聚類樹的位置枪蘑，大小，顏色等），行/列注釋（行/列名岳颇，位置照捡，大小，顏色话侧，角度等）栗精，圖注信息等。

在ComplexHeatmap主要使用了grid繪圖系統(tǒng)瞻鹏，使用gpar調(diào)整熱圖參數(shù)：

col 控制顏色
fill 控制填充色
alpha 控制透明度
lty 線的類型
lwd 線寬
fontsize 字符的大小

而unit參數(shù)則主要控制一些距離參數(shù)悲立，包括子圖間的空隙row/column_gap = unit(1, "mm")，熱圖的長寬heatmap_width/height = unit(1, "npc")新博，聚類樹的高度row/column_dend_width/height = unit(10, "mm")以及文字的最大長度row/column_names_max_width/height = unit(6, "cm")等

控制聚類信息的參數(shù)：

cluster_columns薪夕，cluster_rows 指定是否聚類
show_row_dend，show_column_dend 是否展示聚類結(jié)果（進行聚類）
row_names_side赫悄，column_names_side 聚類樹位置（"left"原献，"right"，"top"涩蜘，"bottom"）
clustering_method_rows嚼贡，clustering_method_columns 聚類方法
row_dend_width，column_dend_height 聚類樹寬/高
row_km同诫，column_km 按聚類結(jié)果拆分熱圖

控制單元格的參數(shù)：

col = circlize::colorRamp2(c(-2, 0, 2), c("navy", "white", "firebrick3")) 顏色粤策。
rect_gp = gpar(col= "white") 指定單元格邊界顏色
border 指定熱圖邊界顏色

控制行/列標簽的參數(shù)：

row_labels，column_labels 行/列標簽
show_column_names误窖，show_row_names 是否顯示列/行名
row_names_side``coolumn_names_side 顯示行/列名的位置（"left"叮盘，"right"，"top"霹俺，"bottom"）
row_names_gp``column_names_gp 控制行/列名大腥岷稹（gpar(fontsize = 12)）
row_names_rot``column_names_rot 控制行/列名的角度

控制整體圖形的參數(shù)：

heatmap_width = unit(1, "npc")，heatmap_height = unit(1, "npc") 圖形高/寬度
row_gap = unit(1, "mm")丙唧，column_gap = unit(1, "mm") 子圖空隙

控制圖注的參數(shù)：

show_heatmap_legend 是否展示圖注
heatmap_legend_param圖注參數(shù)（list(at = c(-2, 0, 2), labels =c(-2, 0, 2))#需要制定at和labels的list）

控制注釋的參數(shù)：

top_annotation = NULL
bottom_annotation = NULL
left_annotation = NULL
right_annotation = NULL

HeatmapAnnotation熱圖注釋

對于ComplexHeatmap來說愈魏，其主旨就是繪制復雜熱圖，所以對熱圖的注釋以及拼圖極其重視想际，對于*_annotation來說包括包括各種類型圖形和文字豐富結(jié)果培漏，并且還支持使用+（行）和%v%（列）對多個熱圖進行組裝。熱圖注釋是熱圖的重要組成部分胡本，它顯示與熱圖中的行或列關聯(lián)的其他信息牌柄。 ComplexHeatmap軟件包為設置注釋和定義新的注釋圖形提供了非常靈活的支持。注釋可以放在熱圖的四個側(cè)面侧甫，由top_annotation珊佣，bottom_annotation蹋宦，left_annotation和right_annotation參數(shù)。

四個參數(shù)的值應在HeatmapAnnotation類中咒锻，并應由HeatmapAnnotation（）函數(shù)構造冷冗，如果是行批注，則應由rowAnnotation（）函數(shù)構造虫碉。（rowAnnotation()和columnAnnotation()只是一個與HeatmapAnnotation(…贾惦，which=“row/column”)相同的輔助函數(shù)）。HeatmapAnnotation的簡單用法如下敦捧。

simple annotation 最常用的注釋樣式须板，它是類似于熱圖或網(wǎng)格的圖形，其中顏色用于映射到注釋值

ha = HeatmapAnnotation(
    # 指定annotation的名稱
    foo = cbind(a = 1:10, b = 10:1), 
    bar = sample(letters[1:3], 10, replace = TRUE),
    col = list(foo = col_fun, bar = c("a" = "red", "b" = "green", "c" = "blue")),    # 指定顏色兢卵，傳入list
    gp = gpar(col='white')    # 指定邊界顏色
    simple_anno_size = unit(1, "cm")    # 指定單元格大小
)

anno_block塊注釋更像一個顏色塊习瑰，用于在拆分熱圖的行或列時標識組別。

Heatmap(matrix(rnorm(100), 10), 
    top_annotation = HeatmapAnnotation(foo = anno_block(gp = gpar(fill = 2:4),
        labels = c("group1", "group2", "group3"), 
        labels_gp = gpar(col = "white", fontsize = 10))),
    column_km = 3,
    left_annotation = rowAnnotation(foo = anno_block(gp = gpar(fill = 2:4),
        labels = c("group1", "group2", "group3"), 
        labels_gp = gpar(col = "white", fontsize = 10))),
    row_km = 3)

anno_points 繪制散點圖秽荤，axis_param控制坐標軸參數(shù)甜奄，需要制定side(指定坐標軸展示的位置)，at(指定坐標)窃款，labels(指定標簽)

# 橫向散點圖
ha = HeatmapAnnotation(foo = anno_points(runif(10), ylim = c(0, 1),
    axis_param = list(
        side = "right",
        at = c(0, 0.5, 1), 
        labels = c("zero", "half", "one")
    ))
)

# 縱向散點圖
ha = rowAnnotation(foo = anno_points(runif(10), ylim = c(0, 1),
    width = unit(2, "cm"),
    axis_param = list(
        side = "bottom",
        at = c(0, 0.5, 1), 
        labels = c("zero", "half", "one"),
        labels_rot = 45
    ))
)

anno_lines繪制線圖课兄，可以使用add_points = TRUE加入散點圖，也可以使用smooth = TRUE繪制平滑后的曲線晨继，當設置smooth = TRUE會默認增加點圖

ha = HeatmapAnnotation(foo = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), 
    gp = gpar(col = 2:3), add_points = TRUE, pt_gp = gpar(col = 5:6), pch = c(1, 16)))

ha = HeatmapAnnotation(foo = anno_lines(runif(10), smooth = TRUE))

anno_barplot用于繪制條形圖烟阐，輸入數(shù)據(jù)為二維矩陣時，則轉(zhuǎn)變?yōu)槎逊e圖

# 繪制柱狀圖
ha = HeatmapAnnotation(foo = anno_barplot(seq(-5, 5), baseline = "min"))

# 繪制堆積圖
ha = HeatmapAnnotation(foo = anno_barplot(matrix(nc = 2, c(1:10, 10:1))))

柱狀圖

堆積圖

anno_boxplot繪制箱線圖

ha = HeatmapAnnotation(foo = anno_boxplot(m, height = unit(4, "cm"), 
    gp = gpar(fill = 1:10)))

anno_histogram繪制直方圖

# n_breaks控制顯示的柱子數(shù)量
ha = rowAnnotation(foo = anno_histogram(m, n_breaks = 20))

anno_density繪制密度圖

ha = rowAnnotation(foo = anno_density(m))

示例

# 示例數(shù)據(jù)
mat = readRDS(system.file("extdata", "measles.rds", package = "ComplexHeatmap"))

# 列注釋 頂部 條形圖
ha1 = HeatmapAnnotation(
  dist1 = anno_barplot(
    colSums(mat), 
    bar_width = 1, 
    gp = gpar(col = "white", fill = "#FFE200"), 
    border = FALSE,
    axis_param = list(at = c(0, 2e5, 4e5, 6e5, 8e5),
                      labels = c("0", "200k", "400k", "600k", "800k")),
    height = unit(2, "cm")
  ), show_annotation_name = FALSE)

# 行注釋 右側(cè) 條形圖
ha2 = rowAnnotation(
  dist2 = anno_barplot(
    rowSums(mat), 
    bar_width = 1, 
    gp = gpar(col = "white", fill = "#FFE200"), 
    border = FALSE,
    axis_param = list(at = c(0, 5e5, 1e6, 1.5e6),
                      labels = c("0", "500k", "1m", "1.5m")),
    width = unit(2, "cm")
  ), show_annotation_name = FALSE)

# 列注釋 底部 標簽注釋
year_text = as.numeric(colnames(mat))
year_text[year_text %% 10 != 0] = ""
ha_column = HeatmapAnnotation(
  year = anno_text(year_text, rot = 0, location = unit(1, "npc"), just = "top")
)

# 顏色
col_fun = colorRamp2(c(0, 800, 1000, 127000), c("white", "cornflowerblue", "yellow", "red"))

# 熱圖主體
ht_list = Heatmap(mat, name = "cases", col = col_fun, cluster_row_slices = 2, 
                  cluster_columns = F, show_row_dend = F, rect_gp = gpar(col= "white"), 
                  show_column_names = FALSE,
                  row_names_side = "left", row_names_gp = gpar(fontsize = 6),
                  column_title = 'Measles cases in US states 1930-2001\nVaccine introduced 1961',
                  top_annotation = ha1, bottom_annotation = ha_column,
                  heatmap_legend_param = list(at = c(0, 5e4, 1e5, 1.5e5), 
                                              labels = c("0", "50k", "100k", "150k"))) + ha2
draw(ht_list, ht_gap = unit(5, "mm"))

# 分割線
decorate_heatmap_body("cases", {
  i = which(colnames(mat) == "1961")
  x = i/ncol(mat)
  grid.lines(c(x, x), c(0, 1), gp = gpar(lwd = 2, lty = 2))
  grid.text("Vaccine introduced", x, unit(1, "npc") + unit(5, "mm"))
})

ComplexHeatmap繪制復雜熱圖

ComplexHeatmap繪制復雜熱圖

pheatmap交互

ComplexHeatmap::Heatmap主體熱圖參數(shù)

HeatmapAnnotation熱圖注釋

示例