snv_location {vivaldi}

snv_location

Description

Reads in the vcf dataframe and generates a plot showing the frequency and location of SNVs

Usage

snv_location(df)

Arguments

df

A rearranged dataframe

Value

A plot showing the location and frequency of SNVs found across samples

Examples

# Example 1:
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"),
                 POS = c(234, 266, 117, 134, 180,
                         234, 266, 199, 88, 180),
                 major = c("G", "G", "A", "A", "C",
                           "G", "G", "A", "G", "C"),
                 minor = c("A", "A", "G", "G", "T",
                           "A", "A", "G", "A", "T"),
                 ALT_TYPE = c("minor", "minor", "minor", "minor", "minor",
                              "minor", "minor", "minor", "major", "minor"),
                 minorfreq = c(0.010, 0.022, 0.043, 0.055, 0.011,
                               0.010, 0.022, 0.043, 0.055, 0.011),
                 majorfreq = c(0.990, 0.978, 0.957, 0.945, 0.989,
                               0.990, 0.978, 0.957, 0.945, 0.989)
)

df

snv_location(df)

# Example 2:

snv_location(example_filtered_SNV_df)