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Generate a Histogram of Genotype Frequencies

Source: R/frequency_plot.R
frequency_plot.Rd

The function creates a histogram of genotype frequencies for each genotype category (e.g., "0", "1", "2") based on a frequency data frame. The function also returns the processed long-format data as an attribute. It will not work if your data is in A, H, B format. Use formater to change to dosage before using frequency_plot.

Usage

frequency_plot(freq_df)

Arguments

freq_df

Usually the output of freq. A data frame where rows represent markers or individuals, and columns represent genotype categories with their frequencies.

Value

A ggplot2 histogram visualizing the distribution of genotype frequencies. The processed long-format data is attached as an attribute (attr(output, "data")).

Details

  • Converts the input data frame to long format using pivot_longer().

  • Ensures correct ordering of genotype categories.

  • Generates a faceted histogram where each panel represents a genotype category.

  • Stores both the generated plot and the processed data but returns only the plot by default.

See also

freq()

Examples

# Example frequency data frame
freq_data <- data.frame(
  `0` = c(0.2, 0.3, 0.4),
  `1` = c(0.5, 0.4, 0.4),
  `2` = c(0.3, 0.3, 0.2),
  row.names = c("Marker1", "Marker2", "Marker3")
)

# Generate the frequency histogram
p <- frequency_plot(freq_data)
print(p)  # Display the plot
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.


# Access the processed long-format data
attr(p, "data")
#> # A tibble: 9 × 3
#>   Marker  Dosage Frequency
#>   <chr>   <fct>      <dbl>
#> 1 Marker1 NA           0.2
#> 2 Marker1 NA           0.5
#> 3 Marker1 NA           0.3
#> 4 Marker2 NA           0.3
#> 5 Marker2 NA           0.4
#> 6 Marker2 NA           0.3
#> 7 Marker3 NA           0.4
#> 8 Marker3 NA           0.4
#> 9 Marker3 NA           0.2