Error in if (freq > 0.9) { : missing value where TRUE/FALSE needed

[limin321]

Hi all,

I want to create a graph combing the phylogenetic tree, fasta sequence, and some phenotypic traits.
When I first tried msaplot() to align the fasta sequence with the tree., there is no issue. Now I use ggmsa to align the tree with corresponding fasta file, it generates the following error message:
"Error in if (freq > 0.9) { : missing value where TRUE/FALSE needed"

Here is my r code:

tre <- read.tree("/Users/dklabuser/limin/data_analysis/pan-genome/genomic_comparison/pTi_roary_output/accessory_binary_genes.fa.newick")
n <- MRCA(tre, c("Tul003", "Teh002"))
tre <- root(tre,node = n)

p <- ggtree(tre, layout = "rectangular") +
  geom_tiplab(size=1.5) 

# rotate the tree for T-DNA right border alignment.
p <- flip(p, 6, 34) %>% flip(19,32)

nt_sequence <- system.file("extdata","/Users/dklabuser/limin/Dissertation_papers/dissertation/chapter4_genetic_diversity/RB_aln.fasta", package = "ggmsa")

ggmsa(nt_sequence,1,24,char_width = 0.5, color = "Chemistry_AA", seq_name = TRUE, use_dot = TRUE)

Here is the error message of the previous code:

Does anyone know what goes wrong with my codes? and how to solve this issue
Your help is greatly appreciated!

Best,
Limin

[nyzhoulang]

Hi, Limin

The input FASTA file dispenses with the need for system.file() function.

nt_sequence <- system.file("extdata","/Users/dklabuser/limin/Dissertation_papers/dissertation/chapter4_genetic_diversity/RB_aln.fasta", package = "ggmsa")

just specify the path directly, like this:
nt_sequence <- "/Users/dklabuser/limin/Dissertation_papers/dissertation/chapter4_genetic_diversity/RB_aln.fasta"

Best,
Lang

[limin321]

Hi, Limin

The input FASTA file dispenses with the need for system.file() function.

nt_sequence <- system.file("extdata","/Users/dklabuser/limin/Dissertation_papers/dissertation/chapter4_genetic_diversity/RB_aln.fasta", package = "ggmsa")

just specify the path directly, like this:
nt_sequence <- "/Users/dklabuser/limin/Dissertation_papers/dissertation/chapter4_genetic_diversity/RB_aln.fasta"

Best,
Lang

Hi, Lang,

Thank you so much! It works now. I actually follow the codes in the tutorial here https://github.com/YuLab-SMU/ggmsa

Now I want to graph the alignment with the tree, there is an error again, I follow the tutorial codes,

# to combine the above two trees into one
nt_sequence <- "/Users/dklabuser/limin/Dissertation_papers/dissertation/chapter4_genetic_diversity/RB_aln.fasta"

x <- readDNAStringSet(nt_sequence)
data1 = tidy_msa(nt_sequence)
p1 + geom_facet(geom = geom_msa, data = data1, panel = "msa", font = Null, color = "Chemistry_AA") +
  xlim_tree(1)

And there is an error again,

Any suggestion on what may cause this error?

Thank you so much!
Best,
Limin

[nyzhoulang]

p1 + geom_facet(geom = geom_msa, data = data1, panel = "msa", font = Null, color = "Chemistry_AA") + xlim_tree(1)

Null is illegal in R, pls using NULL instead of it.
Besides，we recommend the NT color scheme (color = "Chemistry_NT") when the input is DNA alignment.

[limin321]

p1 + geom_facet(geom = geom_msa, data = data1, panel = "msa", font = Null, color = "Chemistry_AA") + xlim_tree(1)

Null is illegal in R, pls using NULL instead of it.
Besides，we recommend the NT color scheme (color = "Chemistry_NT") when the input is DNA alignment.

Hi Lang,

Thank you so much. Everything works now. The graph is so beautiful!

Best,
Limin