treeMSA_plot: treeMSA_plot

In YuLab-SMU/ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

treeMSA_plot

Description

plot Tree-MSA plot

Usage

treeMSA_plot(
  p_tree,
  tidymsa_df,
  ancestral_node = "none",
  sub = FALSE,
  panel = "MSA",
  font = NULL,
  color = "Chemistry_AA",
  seq_colname = NULL,
  ...
)

Arguments

p_tree	tree view
tidymsa_df	tidy MSA data
ancestral_node	vector, internal node in tree. Assigning a internal node to display "ancestral sequences",If ancestral_node = "none" hides all ancestral sequences, if ancestral_node = "all" shows all ancestral sequences.
sub	logical value. Displaying a subset of ancestral sequences or not.
panel	panel name for plot of MSA data
font	font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'helvetical'. If font = NULL, only plot the background tile.
color	a Color scheme. One of 'Clustal', 'Chemistry_AA', 'Shapely_AA', 'Zappo_AA', 'Taylor_AA', 'LETTER', 'CN6', 'Chemistry_NT', 'Shapely_NT', 'Zappo_NT', 'Taylor_NT'. Defaults is 'Chemistry_AA'.
seq_colname	the colname of MSA on tree$data
...	additional parameters for 'geom_msa'

Details

'treeMSA_plot()' automatically re-arranges the MSA data according to the tree structure,

Value

ggplot object

Author(s)

Lang Zhou

YuLab-SMU/ggmsa documentation built on Dec. 18, 2024, 11:53 p.m.