plot_entropy {vDiveR}

Entropy plot

Description

This function plot entropy (black) and total variant (red) incidence of each k-mer position across the studied proteins and highlight region(s) with zero entropy in yellow. k-mer position with low support is marked with a red triangle underneath the x-axis line.

Usage

plot_entropy(
  df,
  host = 1,
  protein_order = "",
  kmer_size = 9,
  ymax = 10,
  line_dot_size = 2,
  base_size = 8,
  all = TRUE,
  highlight_zero_entropy = TRUE
)

Arguments

df

DiMA JSON converted csv file data

host

number of host (1/2)

protein_order

order of proteins displayed in plot

kmer_size

size of the k-mer window

ymax

maximum y-axis

line_dot_size

size of the line and dot in plot

base_size

word size in plot

all

plot both the entropy and total variants (pass FALSE in to plot only the entropy)

highlight_zero_entropy

highlight region with zero entropy (default: TRUE)

Value

A plot

Examples

plot_entropy(proteins_1host)
plot_entropy(protein_2hosts, host = 2)