如何在ComplexHeatmap中为行名添加上标并修改行注释图例标题？

问题描述 #

我使用以下R代码生成了ComplexHeatmap热图：

A = c(rep(100,22),rep(0,15),rep(10,12), rep(50,14))
B = c(rep(0,22),rep(8,15),rep(13,12), rep(82,14))
C = c(rep(0,22),rep(8,15),rep(13,6),rep(75,6), rep(82,14))
D  = c(rep(0,22),rep(8,15),rep(13,12), rep(82,14))
E = c(rep(100,22),rep(0,15),rep(10,12), rep(50,14))
F = c(rep(0,22),rep(8,15),rep(13,6),rep(75,6), rep(82,14))
G = c(rep(0,22),rep(8,15),rep(13,12), rep(82,14))
H = c(rep(80,22),rep(72,15),rep(5,12), rep(2,14))
df= data.frame(A,B,C,D,E,F,G, H)
correct_columnnames <- c("34T","56G", "45T","78T", "12F","25G","90F","78T")
colnames(df) <- correct_columnnames

split = c(rep(1,22),rep(2,15),rep(3,12), rep(4,14))
row_labels = c(rep("A",22),rep("B",15),rep("C",12), rep("D",14))
rowlabels= data.frame(row_labels)

row_labels = rowAnnotation(df = rowlabels,
                      col = list(row_labels = c("A"="#e48f1c","B"="#570c32","C"="#e5c616","C"="#d33b44", "D" = "#38ECF9")), 
                      annotation_legend_param = list(direction = "horizontal",
                                                     nrow = 1,
                                                     title = "Groups",
                                                     title_position = "topcenter",
                                                     legend_gp = gpar(fontsize = 14),
                                                     labels_gp = gpar(fontsize = 14)),
                      gp = gpar(col = "grey") )  


h1 = Heatmap(df, 
            clustering_method_columns = "average", 
            rect_gp = gpar(col = "grey", lwd = 1), 
            right_annotation = row_labels, 
            cluster_rows = FALSE, 
            heatmap_legend_param = list(legend_direction = "horizontal", 
                                        title = "M porcentage", 
                                        legend_width = unit(11, "cm"),
                                        title_position = "topcenter",
                                        at = c(0,10,20,30,40,50,60,70,80,90,100),
                                        labels = c(0,10,20,30,40,50,60,70,80,90,100),
                                        fontsize = 16),
            width = ncol(filtered_data)*unit(5, "mm"),
            height = nrow(filtered_data)*unit(5, "mm"),
            column_split = 7,
            column_title = NULL,
            row_split = split,
            row_title = NULL)

png("test.png",width=20,height=20, res = 300,  "in")
draw(h1,  heatmap_legend_side = "bottom", annotation_legend_side = "bottom" )
dev.off()

当前热图效果：

需要实现两个需求：

• 为热图的行名添加部分上标字符；
• 将行注释的图例标题修改为“行标签”（对应预期效果中的“row labels”）。

预期热图效果：

解决方案 #

关键修改点 #

1. 行名添加上标：借助grid包的expression语法构造带标的行名，在Heatmap函数中通过row_names参数指定。
2. 修改注释图例标题：直接修改rowAnnotation中annotation_legend_param的title参数为目标文本。
3. 修复原代码中未定义的filtered_data变量，以及png函数的语法错误。

修改后的完整代码 #

library(ComplexHeatmap)
library(grid)

# 构造数据
A = c(rep(100,22),rep(0,15),rep(10,12), rep(50,14))
B = c(rep(0,22),rep(8,15),rep(13,12), rep(82,14))
C = c(rep(0,22),rep(8,15),rep(13,6),rep(75,6), rep(82,14))
D  = c(rep(0,22),rep(8,15),rep(13,12), rep(82,14))
E = c(rep(100,22),rep(0,15),rep(10,12), rep(50,14))
F = c(rep(0,22),rep(8,15),rep(13,6),rep(75,6), rep(82,14))
G = c(rep(0,22),rep(8,15),rep(13,12), rep(82,14))
H = c(rep(80,22),rep(72,15),rep(5,12), rep(2,14))
df= data.frame(A,B,C,D,E,F,G, H)
correct_columnnames <- c("34T","56G", "45T","78T", "12F","25G","90F","78T")
colnames(df) <- correct_columnnames

split = c(rep(1,22),rep(2,15),rep(3,12), rep(4,14))
# 构造带标的行名，可根据需求修改上标内容
row_names <- c(rep(expression(A^1),22), 
               rep(expression(B^2),15), 
               rep(expression(C^3),12), 
               rep(expression(D^4),14))

rowlabels= data.frame(row_labels = c(rep("A",22),rep("B",15),rep("C",12), rep("D",14)))

# 修改行注释图例标题为“行标签”
row_labels = rowAnnotation(df = rowlabels,
                      col = list(row_labels = c("A"="#e48f1c","B"="#570c32","C"="#d33b44", "D" = "#38ECF9")), 
                      annotation_legend_param = list(direction = "horizontal",
                                                     nrow = 1,
                                                     title = "行标签",
                                                     title_position = "topcenter",
                                                     legend_gp = gpar(fontsize = 14),
                                                     labels_gp = gpar(fontsize = 14)),
                      gp = gpar(col = "grey") )  

h1 = Heatmap(df, 
            clustering_method_columns = "average", 
            rect_gp = gpar(col = "grey", lwd = 1), 
            right_annotation = row_labels, 
            cluster_rows = FALSE, 
            heatmap_legend_param = list(legend_direction = "horizontal", 
                                        title = "M porcentage", 
                                        legend_width = unit(11, "cm"),
                                        title_position = "topcenter",
                                        at = c(0,10,20,30,40,50,60,70,80,90,100),
                                        labels = c(0,10,20,30,40,50,60,70,80,90,100),
                                        fontsize = 16),
            width = ncol(df)*unit(5, "mm"),
            height = nrow(df)*unit(5, "mm"),
            column_split = 7,
            column_title = NULL,
            row_split = split,
            row_title = NULL,
            row_names_gp = gpar(fontsize = 10), # 可调整行名字体大小
            row_names = row_names)  # 指定带标的行名

# 修正png函数参数语法
png("test.png", width=20, height=20, res=300, units="in")
draw(h1, heatmap_legend_side="bottom", annotation_legend_side="bottom")
dev.off()

补充说明 #

• 行名的上标内容可灵活调整，例如用expression(A^"*")添加星号上标，或expression(A^"abc")添加字符上标；
• 若不需要统一上标，可单独为特定行设置自定义上标格式。

内容的提问来源于stack exchange，提问作者Juliana B C