plot_JSD_logo: Calculate and plot the Jensen-Shannon divergence between 2...

In Ni-Ar/niar: Nice Interactive Analysis with R

Calculate and plot the Jensen-Shannon divergence between 2 sets of sequences contained in 2 data.frames

Description

Calculate and plot the Jensen-Shannon divergence between 2 sets of sequences contained in 2 data.frames

Usage

plot_JSD_logo(
  df1,
  df2,
  ID_col,
  alphabet,
  y_lims = c(-0.5, 0.5),
  max_JS_div_thrshld,
  anno_width = 0.75,
  highlight_colour = "grey74",
  axis_txt_size = 10,
  ttl_txt = NULL,
  ...
)

Arguments

df1	A data.frame with a column called Sequence and anther defined in ID_col. Use the wrapper fasta2df() to import a fasta file to a dataframe that is compatible with this function.
df2	A different data.frame with the same properties as df1.
ID_col	A character specifying the column name in df1 and df2 to be used as the sequence ID.
alphabet	A character vector containing the alphabet letters present in Sequence. Guessed by default from df1.
y_lims	A numeric vector of length 2 specifying the Y-axis min and max value. Default c(-0.5, 0.5)
max_JS_div_thrshld	The maximal absolute JS divergence threshold to consider a letter position to be highlighted by a vertical bar in the plot.
anno_width	A small number that defines how wide the vertical bar should be. Default 0.75.
highlight_colour	A colour name to fill the letter highlighting rectangle. Default grey74 with alpha = 0.5.
axis_txt_size	A number specifying the size of the axis text in the plot. Default 10.
ttl_txt	Some text in quotes specifying the plot title.
...	Advanced parameters passed to renumber_logo_seq_breaks.

Value

A ggplot sequence logo with the Jensen-Shannon divergence on the Y-axis.

Examples

plot_JSD_logo(df1 = clade1, df2 = clade2f, ID_col = 'Species',
              max_JS_div_thrshld = 0.2, anno_width = 0.5)

Ni-Ar/niar documentation built on Feb. 3, 2025, 9:25 a.m.