msaplot: msaplot

In GuangchuangYu/ggtree: an R package for visualization of tree and annotation data

msaplot

Description

visualize phylogenetic tree with multiple sequence alignment

Usage

msaplot(
  p,
  fasta,
  offset = 0,
  width = 1,
  color = NULL,
  window = NULL,
  bg_line = TRUE,
  height = 0.8
)

Arguments

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

Value

tree view

Author(s)

Guangchuang Yu

References

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.

GuangchuangYu/ggtree documentation built on Oct. 31, 2024, 10:10 a.m.