While using ggtree in rstudio, it shows error in some commands

Question

[abdul.suboor123]

I want to construct round tree for my protein sequences, I am new to rstudio. By searching about ggtree i got little idea but still facing problems. I give the command

 > ggplot(tree, aes(x, y)) + geom_tree() + theme_tree() + xlab("seq") + ylab("comp")

and I got this error, what does it mean?

Error in FUN(X[[i]], ...) : object 'node' not found

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[h.mon]

Could you provide a small example to reproduce the error?

[cpad0112]

and function to generate tree.

[Joe]

Can you also show your input tree. That error could suggest the tree is malformed.

[abdul.suboor123]

I am using my protein sequences of different species, I am using fastq file for it but it does not work. May be my file format is wrong. I want to know the pipeline for making round tree in rtsudio? I want to make a likelihood tree. I already mentioned above that I am new to R that is why I am facing problems. I will be thankful If someone mention the complete pipeline.

[Joe]

What do you mean you have a FASTQ of protein sequences? I very much doubt that...

You need to make your tree, before you pass it to ggplot. It will not construct the tree for you, only draw it.

[cpad0112]

Post few records from sequences file

[abdul.suboor123]

My problem is solved. The command that I have followed is given below.

> ggtree(tree1, layout = "rectangular") + geom_text2(data=d, aes(subset=!isTip, label=label, color="isTip"), hjust=1) + geom_tiplab(size=3, aes(angle=0)) + scale_color_manual(values=c("red", "firebrick")) + geom_hilight(22, "brown") + geom_hilight(20, fill = "steelblue") + geom_hilight(25, fill="darkgreen") + geom_hilight(32, fill="pink") + geom_hilight(30, fill="grey") + geom_hilight(31, fill="purple") + geom_hilight(29, fill="lightblue") + ggtitle("Protein Sequences correlation")