msaplot | R Documentation |
visualize phylogenetic tree with multiple sequence alignment
msaplot(
p,
fasta,
offset = 0,
width = 1,
color = NULL,
window = NULL,
bg_line = TRUE,
height = 0.8
)
p |
tree view |
fasta |
fasta file that contains multiple sequence alignment information |
offset |
set the offset of MSA to tree |
width |
total width of alignment, compare to width of tree, defaults to 1, which means they are of the same length |
color |
set color of the tree |
window |
specific a slice of alignment to display |
bg_line |
whether to add background line in alignment, defaults to "TRUE" |
height |
height ratio of sequence, defaults to 0.8 |
tree view
Guangchuang Yu
For demonstration of this function, please refer to chapter 7.4 of Data Integration, Manipulation and Visualization of Phylogenetic Trees http://yulab-smu.top/treedata-book/index.html by Guangchuang Yu.
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