snv_segment: snv_segment

In vivaldi: Viral Variant Location and Diversity

snv_segment

Description

Reads in a dataframe that has been arranged (arrange_data) and filtered (filter_variants) and outputs plots

Usage

snv_segment(vardf)

Arguments

vardf

A rearranged (arrange_data) and filtered (filtered_variants) vcf dataframe

Value

A bar plot showing the number of variants colored by their SNPEff annotation

Examples

# Example 1: Simple data
df <- data.frame(sample = c("m1", "m1", "m1", "m1", "m1",
                            "m2", "m2", "m2", "m2", "m2"),
  CHROM = c("PB1", "PB1", "PB2", "PB2", "PB2",
	           "PB1", "PB1", "PB2", "PB2", "PB2"),
  annotation = c("downstrean_gene_variant", "synonymous_variant",
		              "synonymous_variant", "stop_gained", "missense_variant",
		          	  "downstrean_gene_variant", "downstrean_gene_variant",
				          "synonymous_variant", "stop_gained", "missense_variant")
)

df

snv_segment(df)

# Example 2: Sample data
snv_segment(example_filtered_SNV_df)

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