R总给我惊喜
Hello!
First of all, I would like to thank you for this wonderful and very powerful package! I have tried to plot a phylogenetic tree with heatmap of associated matrix (with gheatmap).
I found that the row names of matrix doesn't exactly match to the tip names of tree in case if there is missing data in associated matrix.
In other words, if we have two species (e.g., Species198 and Species1981), but only one of them is represented in the associated matrix, we will have colored cells for both species in the heatmap.
Here is a reproducible example:
library(ggtree)
set.seed(111)
# Prepare a species list
tipss <- c("Fomes", "Rozella", "Saitoella", "Entorrhiza", "Cryptococcus", "Tremella", "Puccinia", "Amoeboaphelidium")
tipss <- c(tipss, "Species198", "Species1981")
# Generate random tree
trr <- ape::rtree(n = length(tipss), rooted = TRUE, tip.label = tipss)
# Generate associated data matrix for each species
abunds <- matrix(data = sample(1:100, size = 4*length(tipss)), nrow = length(tipss))
rownames(abunds) <- tipss
colnames(abunds) <- paste("Samp", 1:ncol(abunds), sep="")
# Remove data for some species
abunds <- abunds[-which(rownames(abunds) == "Species198"), ] # !! no information for this species
abunds <- abunds[-which(rownames(abunds) == "Cryptococcus"), ]
tt <- ggtree(trr) + geom_tiplab()
gheatmap(tt, abunds)
Here is the resulting picture:
You may see that heatmap cells are blank for Cryptococcus (as expected).
However, cells corresponding to Species198 are colored with Species1981 data (marked with red arrow).
With best regards,
Vladimir
有人在GitHub上对我报了这个bug，说我的gheatmap函数不是精确匹配，这不能够吧？！但可重复性的代码已经说明了一切，我翻一下代码，最终发现是R的问题，R再一次给了我们惊喜，比如下面演示的：
dd
Samp1 Samp2 Samp3 Samp4
Fomes 47 58 3 13
Rozella 100 83 27 18
Saitoella 36 51 78 63
Entorrhiza 70 32 43 16
Tremella 75 73 35 20
Puccinia 61 53 8 72
Amoeboaphelidium 95 66 92 19
Species1981 30 48 34 41
dd['Species198',]
Samp1 Samp2 Samp3 Samp4
Species1981 30 48 34 41
这就是问题之所在，当然这个bug我已经修正了，现在再使用gheatmap将不会有这个问题，但我们在使用R的时候，还是要小心哦，以后按名字取子集的时候，还是不要用[的好，R总是能给人惊喜，比如《你的数据被化了妆？》，以及集中吐槽的《R的诡异事件》，都值得重新温习一遍.
往期精彩