100 lines
2.8 KiB
R
100 lines
2.8 KiB
R
# 列出所需的包
|
|
packages <- c("ComplexHeatmap", "circlize", "RColorBrewer", "dendextend", "dendsort", "gridBase")
|
|
|
|
# 检查并安装缺失的包
|
|
install_if_missing <- function(pkg) {
|
|
if (!requireNamespace(pkg, quietly = TRUE)) {
|
|
if (pkg == "ComplexHeatmap") {
|
|
if (!requireNamespace("BiocManager", quietly = TRUE)) {
|
|
install.packages("BiocManager")
|
|
}
|
|
BiocManager::install("ComplexHeatmap")
|
|
} else {
|
|
install.packages(pkg, dependencies = TRUE)
|
|
}
|
|
}
|
|
}
|
|
|
|
# 应用函数到每个包
|
|
sapply(packages, install_if_missing)
|
|
|
|
# 加载所有包
|
|
lapply(packages, library, character.only = TRUE)
|
|
|
|
# 加载绘图数据
|
|
data <- read.table(file = 'E:/hui.zhang/Drawpic/1.csv', header = TRUE, row.names = 1, sep = ',')
|
|
|
|
# 查看数据
|
|
head(data)
|
|
|
|
# 转化matrix格式矩阵及数据归一化
|
|
data <- as.matrix(data)
|
|
cir1 <- t(scale(t(data)))
|
|
|
|
# 处理 NA 值
|
|
cir1[is.na(cir1)] <- 0
|
|
|
|
# 查看归一化后的数据
|
|
head(cir1)
|
|
|
|
# 定义热图颜色梯度
|
|
mycol <- colorRamp2(c(-2.5, 0.3, 3.1), c("blue", "white", "red"))
|
|
mycol1 <- colorRamp2(c(-2, 0, 2), c("#003399", "white", "#cccc00"))
|
|
|
|
# 默认参数绘制普通热图
|
|
Heatmap(cir1, row_names_gp = gpar(fontsize = 6),
|
|
column_names_gp = gpar(fontsize = 8),
|
|
col = mycol,
|
|
name = "legend")
|
|
|
|
# 计算数据大小范围
|
|
range(cir1)
|
|
|
|
# 绘制基础环形热图
|
|
circos.heatmap(cir1, col = mycol)
|
|
circos.clear()
|
|
|
|
# 在circos.heatmap()中添加参数进行环形热图的调整和美化
|
|
circos.par(gap.after = c(30))
|
|
circos.heatmap(cir1, col = mycol,
|
|
dend.side = "inside",
|
|
rownames.side = "outside",
|
|
rownames.col = "black",
|
|
rownames.cex = 1.2,
|
|
rownames.font = 1.2,
|
|
bg.border = "black",
|
|
cluster = TRUE)
|
|
circos.clear()
|
|
|
|
# 聚类树的调整和美化
|
|
circos.par(gap.after = c(30))
|
|
circos.heatmap(cir1, col = mycol, dend.side = "inside",
|
|
rownames.side = "outside",
|
|
track.height = 0.28,
|
|
rownames.col = "black",
|
|
rownames.cex = 1.3,
|
|
rownames.font = 1.3,
|
|
cluster = TRUE,
|
|
dend.track.height = 0.18,
|
|
dend.callback = function(dend, m, si) {
|
|
color_branches(dend, k = 15, col = 1:15)
|
|
})
|
|
circos.clear()
|
|
|
|
# 添加图例标签等
|
|
lg <- Legend(title = "Exp", col_fun = mycol,
|
|
direction = c("vertical"))
|
|
grid.draw(lg)
|
|
|
|
# 添加列名
|
|
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
|
|
if (CELL_META$sector.numeric.index == 1) {
|
|
cn <- colnames(cir1)
|
|
n <- length(cn)
|
|
circos.text(rep(CELL_META$cell.xlim[2], n) + convert_x(0.5, "mm"),
|
|
1:n + 5,
|
|
cn, cex = 0.6, adj = c(0, 0.5), facing = "inside")
|
|
}
|
|
}, bg.border = NA)
|
|
|
|
circos.clear() |