R Error '错误 seq.default(min(x, na.rm = T), max(x, na.rm = T), length = length(ColRamp)) : 'from'必须是有限数'

Question

我是 R 的新手，我有一个矩阵数据集，我想将其绘制为六边形颜色图。我已遵循此页面上概述的代码：

https://www.visualcinnamon.com/2013/11/how-to-create-hexagonal-heatmap-in-r

但是，我不断收到错误消息：

Error in seq.default(min(x, na.rm = T), max(x, na.rm = T), length = length(ColRamp)) : 'from' must be a finite number In addition: Warning message: In seq.default(min(x, na.rm = T), max(x, na.rm = T), length = length(ColRamp)) : NAs introduced by coercion

我的代码如下：

    library(RColorBrewer) 
    library(fields) 

    Hexagon <- function (x, y, unitcell = 1, col = col) {
    polygon(c(x, x, x + unitcell/2, x + unitcell, x + unitcell,
        x + unitcell/2), c(y + unitcell * 0.125,
                           y + unitcell * 0.875,
                           y + unitcell * 1.125,
                           y + unitcell * 0.875,
                           y + unitcell * 0.125,
                           y - unitcell * 0.125),
      col = col, border=NA)}

      Heatmap_Matrix = as.matrix("
      3 2   3   4   5   5   5   5
      4 2   3   4   5   5   5   5
      5 0   0   4   5   5   5   5
      7 2   3   8   8   8   8   8
      1 2   3   4   5   5   5   5
      6 0   3   4   5   5   5   5
      1 2   3   9   5   5   5   5
      1 2   3   4   7   7   7   7
      8 2   4   4   5   5   5   5
      1 0   8   4   3   3   3   3
      1 0   3   5   5   5   5   5
      9 2   3   4   5   5   5   5
      1 2   4   4   5   5   5   5
      1 0   3   4   2   2   2   2
      9 2   3   4   5   5   5   5")

      x <- as.vector(Heatmap_Matrix)

       SOM_Rows <- dim(Heatmap_Matrix)[1]
       SOM_Columns <- dim(Heatmap_Matrix)[2]

       par(mar = c(0.4, 2, 2, 7))

       plot(0, 0, type = "n", axes = FALSE, xlim=c(0, SOM_Columns),
       ylim=c(0, SOM_Rows), xlab="", ylab= "", asp=1)

       ColRamp <- rev(designer.colors(n=50, col=brewer.pal(9, "Spectral")))

       ColorCode <- rep("#FFFFFF", length(x)) #default is all white
       Bins <- seq(min(x, na.rm=T), max(x, na.rm=T), length=length(ColRamp))
       for (i in 1:length(x))
       if (!is.na(x[i])) ColorCode[i] <- ColRamp[which.min(abs(Bins-x[i]))]

       offset <- 0.5 
       for (row in 1:SOM_Rows) {
       for (column in 0:(SOM_Columns - 1))
       Hexagon(column + offset, row - 1, col = ColorCode[row + SOM_Rows * column])
       offset <- ifelse(offset, 0, 0.5)
       }  

       image.plot(legend.only=TRUE, col=ColRamp, zlim=c(min(x, na.rm=T), max(x, na.rm=T)))

我不太了解 R 编码，但我已经尝试了好几天来删除错误消息。这可能很简单，但我不知道。我基本上只是从上面的 link 复制代码。

如果有人知道错误是什么，我将不胜感激？

Answer 1

我认为这是关于您如何输入 Heatmap_Matrix。当我运行 str(x) 我看到它读为一长串字符（这是引号告诉它做的）。用逗号分隔数值是我的常规方法，或者如果数据很多，将其保存为制表符或逗号分隔的文本文件，例如excel 然后用 read.csv 等在 R 中读取它。

R Error '错误 seq.default(min(x, na.rm = T), max(x, na.rm = T), length = length(ColRamp)) : 'from'必须是有限数'

R Error 'Error in seq.default(min(x, na.rm = T), max(x, na.rm = T), length = length(ColRamp)) : 'from' must be a finite number'

numbers

r

colormap