r - 热图返回错误: 'x' must be a numeric matrix, but x is a numeric matrix

Question

我正在尝试创建六个站点上物种丰富度的热图。
我有一个站点与物种的矩阵，其中有数字丰度数据。

但是，当我运行代码时，R返回一个错误，指出我的矩阵是非数字的。
谁能想到这个？我感到难过。

导出的数据框链接:log_mean_wide

加工:

lrc <- rainbow(nrow(log_mean_wide), start = 0, end = .3)
lcc <- rainbow(ncol(log_mean_wide), start = 0, end = .3)


logmap <- heatmap(log_mean_wide, col = cm.colors(256), scale = "column", 
               RowSideColors = lrc, ColSideColors = lcc, margins = c(5, 10),
               xlab = "species", ylab = "Site", 
               main = "heatmap(<Auckland Council MCI data 1999, habitat:bank>, ..., scale = \"column\")")

error message: Error in heatmap(log_mean_wide, Rowv = NA, Colv = NA, col = cm.colors(256), : 'x' must be a numeric matrix

log_heatmap <- heatmap(log_mean_wide, Rowv=NA, Colv=NA, col = cm.colors(256), scale="column", margins=c(5,10)) #same error

is.numeric(log_mean_wide) #[1] FALSE
is.character(log_mean_wide) #[1] FALSE
is.factor(log_mean_wide) #[1] FALSE
is.logical(log_mean_wide) #[1] FALSE
is.integer(log_mean_wide) #[1] FALSE

？!？!

dims <- dim(log_mean_wide)
log_mean_matrix <- as.numeric(log_mean_wide) 
dim(log_mean_matrix) <- dims

Error: (list) object cannot be coerced to type 'double'

str(log_mean_wide)将物种显示为数字，将站点显示为字符-为什么这不起作用？

storage.mode(log_mean_wide) <- "numeric" 

Error in storage.mode(log_mean_wide) <- "numeric" : (list) object cannot be coerced to type 'double'

Answer 1

有两个问题:

第一列log_mean_wide$Site是非数字的。

heatmap仅接受matrix作为输入数据(不接受data.frame)。

要解决这些问题，您可以执行以下操作(请注意，热图中有很多困惑情况):

# Store Site information as rownames
df <- log_mean_wide;
rownames(df) <- log_mean_wide[, 1];

# Remove non-numeric column
df <- df[, -1];

# Use as.matrix to convert data.frame to matrix
logmap <- heatmap(
    as.matrix(df),
    col = cm.colors(256),
    scale = "column",
    margins = c(5, 10),
    xlab = "species", ylab = "Site",
    main = "heatmap(<Auckland Council MCI data 1999, habitat:bank>, ..., scale = \"column\")")