plot_conservationLevel {vDiveR}

Conservation Levels Distribution Plot

Description

This function plots conservation levels distribution of k-mer positions, which consists of completely conserved (black) (index incidence = 100%), highly conserved (blue) (90% <= index incidence < 100%), mixed variable (green) (20% < index incidence <= 90%), highly diverse (purple) (10% < index incidence <= 20%) and extremely diverse (pink) (index incidence <= 10%).

Usage

plot_conservationLevel(
  df,
  protein_order = "",
  conservation_label = 1,
  host = 1,
  base_size = 11,
  line_dot_size = 2,
  label_size = 2.6,
  alpha = 0.6
)

Arguments

df

DiMA JSON converted csv file data

protein_order

order of proteins displayed in plot

conservation_label

0 (partial; show present conservation labels only) or 1 (full; show ALL conservation labels) in plot

host

number of host (1/2)

base_size

base font size in plot

line_dot_size

lines and dots size

label_size

conservation labels font size

alpha

any number from 0 (transparent) to 1 (opaque)

Value

A plot

Examples

plot_conservationLevel(proteins_1host, conservation_label = 1,alpha=0.8, base_size = 15)
plot_conservationLevel(protein_2hosts, conservation_label = 0, host=2)