vivaldi (version 1.0.1)

snv_genome: snv_genome

Description

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

Usage

snv_genome(vardf)

Value

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

Arguments

vardf

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

Examples

# Example 1: Simple dataframe
df <- data.frame(sample = c("m1", "m1", "m1", "m1", "m1",
                            "m2", "m2", "m2", "m2", "m2"),
			    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_genome(df)

# Example 2: Sample dataframe
snv_genome(example_filtered_SNV_df)