plot_genome_stats: Plot statistics on genome assemblies on the NCBI

In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

Plot statistics on genome assemblies on the NCBI

Description

Plot statistics on genome assemblies on the NCBI

Usage

plot_genome_stats(ncbi_stats = NULL, user_stats = NULL)

Arguments

ncbi_stats

A data frame of summary statistics for a particular taxon obtained from the NCBI, as obtained with the function get_genome_stats.

user_stats

(Optional) A data frame with assembly statistics obtained by the user. Statistics in this data frame are highlighted in red if this data frame is passed. A column named accession is mandatory, and it must contain unique identifiers for the genome(s) analyzed by the user. Dummy variables can be used as identifiers (e.g., "my_genome_001"), as long as they are unique. All other column containing assembly stats must have the same names as their corresponding columns in the data frame specified in ncbi_stats. For instance, stats on total number of genes and sequence length must be in columns named "gene_count_total" and "sequence_length", as in the ncbi_stats data frame.

Value

A composition of ggplot objects made with patchwork.

Examples

# Example 1: plot stats on maize genomes on the NCBI
## Obtain stats for maize genomes on the NCBI
ncbi_stats <- get_genome_stats(taxon = "Zea mays")

plot_genome_stats(ncbi_stats)

## Plot stats
# Example 2: highlight user-defined stats in the distribution
## Create a data frame of stats for fictional maize genome
user_stats <- data.frame(
    accession = "my_lovely_maize",
    sequence_length = 2.4 * 1e9,
    gene_count_total = 50000,
    CC_ratio = 1
)

plot_genome_stats(ncbi_stats, user_stats)

almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.