Error when plotting phylo.to.map

[jhill1]

When plotting phylo to map, I get the following error:

plot(xx,type="phylogram")
Error in xy.coords(x, y) : 'x' and 'y' lengths differ

'direct' method works fine.

Some graphics are output, but the tree looks like it needs rotating 180 (see attached).

Happy to send the input files if necessary via email.

Jon

[liamrevell]

This might be as simple as resizing the plotting device or the text of the plot labels, as I know there can be issues when the tree & labels don't fit in the plotting device as intended.
Yes - please feel free to send me the input files and your script and I will look into it.

• Liam

[rwness]

I am getting the same error message. The 'direct' shape works but with phylogram the plot is only partially drawn and no connecting lines are drawn. I tried, rerooting, removing branch lengths and shortening the labels to single letters.

Did you work out a general solution to this problem?

require(phytools)
tree <-read.tree('nexus23.NoEuro.nwk')
plotTree(tree)
latlong <-read.table("LatLong.invented.txt", header = T)
#convert column 1 to rownames and remove column 1
rownames(latlong) <- latlong$Strain
latlong <- latlong[,2:3]
#This works:
phylo.to.map(tree, latlong,type="direct",ylim=c(38.32,49.12), xlim=c(-141.7, -60.27))
# This does not:
phylo.to.map(tree, latlong,type="phylogram",rotate=T,ylim=c(38.32,49.12), xlim=c(-141.7, -60.27))

objective: 0
objective: 0
objective: 0
objective: 0
objective: 0
objective: 0
objective: 0
objective: 0
Error in xy.coords(x, y) : 'x' and 'y' lengths differ

[alexweisberg]

I get this same error when plotting a cophylo plot. The same code works for some trees, however others give this error when I attempt to plot them.
obj<-cophylo(multi2di(tree1),multi2di(tree2), rotate.multi=FALSE)
pdf(paste0("Figure_", treefilename ,".pdf"),width=18,height=10)
plot(obj)
dev.off()
Rotating nodes to optimize matching...
Done.
Error in xy.coords(x, y) : 'x' and 'y' lengths differ
Calls: plottree ... makelinks -> lines -> lines.default -> plot.xy -> xy.coords
Execution halted
The pdf file contains a partial cophylo plot without labels or lines.

EDIT: This happens when I have a cophylo plot with duplicate taxa in one of the trees (the tip labels are modified from strain_locus to strain once loaded with ape, so there are identical tip labels). When I drop the duplicates the plot is correct. I guess I could make the labels unique and manually create the association matrix to include both.

[liamrevell]

My suspicion is this has to do with supplying the assoc matrix as a data frame, or, in the case of phylo.to.map, the geographic coordinates in a data frame instead of a matrix. Could this be the case?

[jhill1]

It is in my case. Had a look at the code:
all_otulocs = matrix(0, nrow = length(all_otus), ncol=2)
all_otulocs = data.frame(all_otulocs)

So, yep, passing a data.frame not a matrix. Thanks.

[biosapo666]

Hi Liam
i obtain this

Error in coords[cw$tip.label, 2:1] : subscript out of bounds

[k-sanchez]

Hi Liam, I'm getting this error every time I want to plot my tree on a map:

Error in aggregate.data.frame(as.data.frame(x), ...) : 
  arguments must have same length

Note: I load my coordinate file as read.csv; both the number of rows in the coordinate file and the number of terminals in the tree are the same

Thanks!

[architasharma23]

I was getting this error too
Error in aggregate.data.frame(as.data.frame(x), ...) :
arguments must have same length

How to solve it - convert your dataframe/csv into a matrix
map <- read.csv("Coordinates.csv", header = T, row.names = 1)
matrix = as.matrix(map)