R语言——pheatmap包

载入包

library(pheatmap)

载入数据

data_frame = read.csv("file_path.csv",
                      header = T,  #将第行设为列名
                      )

# 将第一列设为行名
rownames(data_frame) = data_frame[,1]
data_frame = data_frame[,-1]   #删除第一列

绘制热图

pheatmap(data,
        scale="row",  #对行进行标准化
        border=TRUE,  #显示格子边框线与否
        border="white",  #设置边框颜色为白色
        cluster_cols = F, cluster_rows = F,   #行列聚类与否
        clustering_method = "average",  #设定不同聚类方法，默认为"complete",可以设定为'ward', 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'（"single"选择最近的点，"complete"选择最远的点，"average"选择所有点距离的平均值）
        clustering_distance_rows = "correlation",  #表示行聚类使用皮尔森相关系数聚类，默认为欧氏距离"euclidean"
        show_rownames = F, show_colnames = F,  #行列名称的显示与否
        legend = F,  #图例显示与否
        legend_breaks=c(-2,0,2),  #设置图例范围
        legend_labels = c("0", "1e-4", "1e-3", "1e-2", "1e-1", "1"),  #添加图例标签
        cellwidth = 15, cellheight = 12,   #设置cell大小
        fondsize = 2,  #设置字体大小
        fontsize_row = 8, fontsize_col=12,  #改变横向和纵向字体大小
        treeheight_col = 20, treeheight_row = 15,   #设置横向纵向的树高
        display_numbers = TRUE,  #在每个热图格子中显示相应的数值与否
        number_color = "blue",  #设置热图格子中显示数值字体的颜色
        number_format = "%.1e",  #设置热图格子中显示数值的格式
        display_numbers = matrix(ifelse(data > 5, "*", ""), nrow(data)),  #设置条件展示：大于5的格子显示*
        color = colorRampPalette(c("navy", "white", "firebrick3"))(50),  #定义颜色
        angle_col = "45",  #列标签角度改为45°
        gaps_row = c(10, 14),  #在第10列和第14列后设gap
        cutree_col = 2,  #根据聚类结果设gap
        labels_row = c("", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "Il10", "Il15", "Il1b"),  #展示行或者列的label
        annotation_col = group,  #以group数据框注释列分组，可进行多级注释
        ）

生成行列注释

# 列注释，列注释dataframe——group的行名为data的列名
group = rep(c("Immune control","immune clearance","immune tolerance","healthy control"),c(11,50,22,6))
group = data.frame(group = factor(group))
rownames(group) = colnames(M1_genes)
# 行注释类似，行注释dataframe的列名为data的行名