pheatmap 热图示例（xhs:飞高高啦）

# 加载R包；
library(pheatmap)

# 查看当前目录的文件；
dir()

## [1] "COX模型.Rmd"           "heatmap_pheatmap.html" "heatmap_pheatmap.Rmd" 
## [4] "rsconnect"             "top30genesexp.csv"     "相关性网络图.R"

# 读入 CSV（用第1列做行名）
df <- read.csv("top30genesexp.csv", header = TRUE, row.names = 1, check.names = FALSE)
df <- as.matrix(df); storage.mode(df) <- "numeric"

# 查看数据的前6行，前6列；
df[1:6, 1:6]

##                 Ss_1    Ss_2    Ss_3    Bc_1    Bc_2    Bc_3
## MSTRG.15233  6715.10 5376.93 7079.48 3205.79 1733.16 1733.17
## Pp3c8_7680   6823.72 4798.55 4794.67 2047.43  962.95 1028.58
## Pp3c20_16230 4107.03 3442.52 9426.14 1738.24 1926.17 1142.52
## Pp3c13_6860  6436.62 4573.53 5095.80 1523.94 3597.34 1872.31
## Pp3c17_9180  6071.54 2842.33 3545.38 2015.36 2436.01 1997.46
## Pp3c4_16930  4386.64 4803.22 8170.27 2121.59 1014.94 2107.13

绘制热图

# 自定义颜色（负值蓝色，正值红色，中间白色）
mycol <- colorRampPalette(c("#4575B4", "white", "#D73027"))(100)

p <- pheatmap(df, scale = "row",
              border_color = "white", color = mycol,
              show_rownames = FALSE)
p

# 进化聚类树的高度设置(默认50 points)；
p2 <- pheatmap(df, scale = "row",
               border_color = "white", color = mycol,
               show_rownames = FALSE,
               legend_breaks = c(-2.5, -1.25, 0, 1.25, 2.5),
               legend_labels = c("-2.5","-1.25","0","1.25","2.5"),
               treeheight_row = 40,
               treeheight_col = 40)
p2

# 调整“横轴”字体方向与大小
p3 <- pheatmap(df, scale = "row",
               border_color = "white", color = mycol,
               show_rownames = FALSE,
               legend_breaks = c(-2.5, -1.25, 0, 1.25, 2.5),
               legend_labels = c("-2.5","-1.25","0","1.25","2.5"),
               treeheight_row = 40,
               treeheight_col = 40,
               fontsize = 6,
               fontsize_col = 8,
               angle_col = 90)
p3

添加标记（xhs:飞高高啦）

# 生成注释所用数据框（列注释）
ano_col <- data.frame(Cluster = factor(paste0('Cluster', cutree(p2$tree_col, 3))))
order  <- p3$tree_col$order
collab <- p3$tree_col$labels
row.names(ano_col) <- collab[order]

p4 <- pheatmap(df, scale = "row",
               border_color = "white", color = mycol,
               show_rownames = FALSE,
               legend_breaks = c(-2.5, -1.25, 0, 1.25, 2.5),
               legend_labels = c("-2.5","-1.25","0","1.25","2.5"),
               treeheight_row = 40,
               treeheight_col = 40,
               fontsize = 6,
               fontsize_col = 8,
               angle_col = 90,
               annotation_col = ano_col)
p4

# 类似的也可以生成行标记
ano_row <- data.frame(gene = factor(paste0('Cluster', cutree(p2$tree_row, 9))))
order1  <- p3$tree_row$order
rowlab  <- p3$tree_row$labels
row.names(ano_row) <- rowlab[order1]

p5 <- pheatmap(df, scale = "row",
               border_color = "white", color = mycol,
               show_rownames = FALSE,
               legend_breaks = c(-2.5, -1.25, 0, 1.25, 2.5),
               legend_labels = c("-2.5","-1.25","0","1.25","2.5"),
               treeheight_row = 40,
               treeheight_col = 40,
               fontsize = 6,
               fontsize_col = 8,
               angle_col = 90,
               annotation_col = ano_col,
               annotation_row = ano_row)
p5

添加基因名称（xhs:飞高高啦）

p6 <- pheatmap(df, scale = "row",
               border_color = "white", color = mycol,
               show_rownames = TRUE,          # 关键：显示行名（基因名）
               show_colnames = TRUE,
               labels_row = rownames(df),     # 可选：显式指定行标签
               fontsize_row = 8,              # 行名字号（可按需要调）
               fontsize_col = 8,
               angle_col = 90,
               legend_breaks = c(-2.5, -1.25, 0, 1.25, 2.5),
               legend_labels = c("-2.5","-1.25","0","1.25","2.5"),
               treeheight_row = 40,
               treeheight_col = 40,
               annotation_col = ano_col,
               annotation_row = ano_row,
               cellheight = 10)               # 可选：行高，避免名字挤在一起
p6

##小提示： - 如果基因名仍然拥挤：把 fontsize_row 再调小、或把代码块的 fig.height 再调大；也可以适当加大 cellheight。更多分析关注xhs：飞高高啦