Bug in gheatmap (not exact match to tip names)

[vmikk]

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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

[GuangchuangYu]

good catch and this is an unexpected surprise from R.

> 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

bug fixed.

[vmikk]

Great, It's working now!
Thank you.