R语言image函数画热图

image {graphics}

 

Display a Color Image

Description

Creates a grid of colored or gray-scale rectangles with colors corresponding to the values in z. This can be used to display three-dimensional or spatial data aka images. This is a generic function.

Usage

image(x, ...)

## Default S3 method:
image(x, y, z, zlim, xlim, ylim,
      col = hcl.colors(12, "YlOrRd", rev = TRUE),
      add = FALSE, xaxs = "i", yaxs = "i", xlab, ylab,
      breaks, oldstyle = FALSE, useRaster, ...)

### 样本数据
data <- matrix(abs(rnorm(50,0,0.1)), nrow = 10, ncol = 5, byrow = TRUE) 
m <- nrow(data)
n <- ncol(data)
colnames(data) <- paste0('y',1:n)
rownames(data)<- paste0('x',1:m)

### 设定绘图参数
breaks.frequency <- seq(from=min(data), to=max(data), 
                        length.out=m * n)
# myColors <- colorRampPalette(c("red", "blue"))

colPal = "BrBG" # palette name 调色板名称
# display.brewer.all()  # 显示所有调色板

# Creates nice looking color palettes especially for thematic maps
col_pal = RColorBrewer::brewer.pal(9, colPal)
# 返回插值一组给定颜色以创建新调色板的函数
myColors = grDevices::colorRampPalette(colors = col_pal)

### 绘制热图
par(fig=c(0,1,0,1))
image(1:nrow(data), 1:ncol(data), data,  
      breaks=breaks.frequency , # more breakpoint than colour 
      col=myColors(length(breaks.frequency)-1), 
      axes = FALSE, cex = 1.5, xlab = "", ylab = "",
      xlim = c(0,nrow(data)+6), ylim = c(0,ncol(data)))
# 加分割线
abline(h = 0:ncol(data) + 0.5, col = "white", lwd = 0.5)
abline(v = 0:nrow(data) + 0.5, col = "white", lwd = 0.5)

# 加文字
mtext(side = 2, at = 1:n, text = colnames(data),
      cex = 1, font = 3)
mtext(side = 3, at = 1:m, text = rownames(data),
      cex = 1, font = 3)

### 格子中绘制符号
pvalue <- c(0.01,0.05)
pvSymbols = c(46, 42)
sigSymbolsSize = 2
w = which(data < min(pvalue), arr.ind = TRUE)
points(w, pch = pvSymbols[2], col = "black", cex = sigSymbolsSize)
w = which(data < max(pvalue) & data > min(pvalue), arr.ind = TRUE)
points(w, pch = pvSymbols[1], col = "black", cex = sigSymbolsSize)

### 符号说明
points(x = m + 2, y = n-1, pch = pvSymbols[2], 
       cex = sigSymbolsSize)
text(x = m + 2, y = n-1, 
     paste0(" P < ", min(pvalue)), pos = 4, 
     cex = 0.8, adj = 0)
points(x = m + 2, y = n-2, 
       pch = pvSymbols[1], cex = sigSymbolsSize)
text(x = m + 2, y = n-2,
     paste0(" P < ", max(pvalue)), 
     pos = 4, cex = 0.8)
title(main = "heatmap", font.main = 4)

### 格子颜色图注legend
par(fig=c(0.1,0.9,0,1), new = TRUE)
image(x = c(0.9, 1), y = seq(0, 0.3, length.out = 200), 
      z = matrix(seq(0, 1, length.out = 200), nrow = 1), 
      col = col_pal, xlim = c(0, 1), ylim = c(0, 1), axes = FALSE, 
      xlab = NA, ylab = NA)
# 负对数并保留两位小数
data_label <- round(-log(seq(min(data), max(data), length.out = 7)),1)
atLims = seq(0, 0.3, length.out = 7)
axis(side = 4, at = atLims, # 坐标轴位置，刻度线标记的点
     tcl = -0.1, # 刻度长度
     labels = data_label, # 刻度文字标签
     las=2, # 标签是否平行于（=0）或垂直于（=2）坐标轴
     lwd = 0.5, cex.axis = 0.5, line = 0.2)
text(x = 0.85, y = 0.2, labels = "-log10(data)", 
     srt = 90, cex = 0.8, xpd = TRUE) 

参考：

https://zhuanlan.zhihu.com/p/505869908

https://www.cnblogs.com/xudongliang/p/6762618.html​​​​​​​