Plot the distribution of evidence scores for gene-disease and gene-phenotype associations.

plot_evidence(
  metric = "evidence_score_sum",
  phenotype_to_genes = load_phenotype_to_genes(),
  show_plot = TRUE,
  save_path = NULL,
  height = NULL,
  width = NULL
)

Arguments

metric

Aggregated metric of evidence to assess.

phenotype_to_genes

Output of load_phenotype_to_genes mapping phenotypes to gene annotations.

show_plot

Show the plot.

save_path

Path to save interactive plot to as a self-contained HTML file.

height

Height of the heatmap body.

width

Width of the heatmap body.

Examples

out <- plot_evidence()
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for: 
#>  - 10514 diseases 
#>  - 5171 genes
#> + Version: 2024-12-19
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for: 
#>  - 10514 diseases 
#>  - 5171 genes
#> + Version: 2024-12-19
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12
#> Annotating gene-disease associations with Evidence Score
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for: 
#>  - 10514 diseases 
#>  - 5171 genes
#> + Version: 2024-12-19
#> Constructing HPO gene x phenotype matrix.
#> Annotating gene-disease associations with Evidence Score
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for: 
#>  - 10514 diseases 
#>  - 5171 genes
#> + Version: 2024-12-19
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.