plot_shannon: plot_shannon

In vivaldi: Viral Variant Location and Diversity

plot_shannon

Description

Reads in a dataframe that has been arranged (arrange_data), filtered (filter_variants), and piped through the Shannon calculations (shannon_entropy) and outputs plots

Usage

plot_shannon(shannon_df)

Arguments

shannon_df

A dataframe that has been arranged (arrange_data), filtered (filter_variants), and piped through the Shannon calculations (shannon_entropy)

Details

The 'plot_shannon()' function takes the variant dataframe and generates three plots. 1. The Shannon entropy, or amount of diversity, at each position in the genome at which a variant was found. 2. The Shannon entropy summed over each segment 3. The Shannon entropy summed over each genome A higher value indicates more diversity.

Value

Three plots showing the nt Shannon, chrom Shannon, and full genome Shannon calculations

Examples

# Sample dataframe
df <- data.frame(sample = c("m1", "m2", "m1", "m2", "m1"),
                 CHROM = c("PB1", "PB1", "PB2", "PB2", "NP"),
                 POS = c(234, 234, 240, 240, 254),
                 minorfreq = c(0.010, 0.022, 0.043, 0.055, 0.011),
                 majorfreq = c(0.990, 0.978, 0.957, 0.945, 0.989),
                 SegmentSize = c(2280, 2280, 2274, 2274, 1809)
)

df

genome_size = 13133

# Modify the dataframe to add 5 new columns of shannon entropy data:
# 1. shannon_ntpos
# 2. chrom_shannon
# 3. genome_shannon
# 4. shannon_chrom_perkb
# 5. genome_shannon_perkb
shannon_df = shannon_entropy(df, genome_size)

# Plot
plot_shannon(shannon_df)

vivaldi documentation built on March 31, 2023, 9:20 p.m.