Prioritise targets grid

Plot the output of prioritise_targets as a grid.

prioritise_targets_grid(
  top_targets,
  res_class = HPOExplorer::gpt_annot_class(),
  n_per_class = 10,
  keep_severity_class = c("profound", "severe"),
  keep_physical_malformations = NULL,
  species_list = c("Homo sapiens", "Macaca mulatta", "Mus musculus", "Danio rerio",
    "Drosophila melanogaster", "Caenorhabditis elegans"),
  legend.position = "left",
  keep_ont_levels = NULL,
  width = 70,
  widths1 = c(1, 4),
  widths2 = c(1, 0.8),
  show_plot = TRUE,
  ...
)

Arguments

top_targets

output of prioritise_targets.

res_class

Output of the gpt_annot_class function.

n_per_class

Number of phenotypes per severity class to include.

keep_severity_class

Phenotypes to keep based on severity classes.

keep_physical_malformations

Phenotypes to keep based on physical malformation frequency (0=never, 1=rarely, 2=often, 3=always).

species_list

Species to include in orthologous genes grid.

legend.position

the default position of legends ("none", "left", "right", "bottom", "top", "inside")

keep_ont_levels

Only keep phenotypes at certain absolute ontology levels to keep. See add_ont_lvl for details.

width

Width of the saved plot.

widths1

Proportional widths of severity annotation heatmap (left subplot) and the top targets/orthologous genes grid (right subplot).

widths2

Proportional widths of the top targets/orthologous genes grid.

show_plot

Print the plot to the console.

...

Arguments passed on to HPOExplorer::plot_top_phenos

keep_descendants

Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step.

annotation_order

The order of the annotations to include.

split_by_congenital

Split the phenotypes by congenital onset (congenital = always/often, noncongenital = never/rarely).

axis.text.x

Whether to include x-axis text in top and bottom subplots.

Value

A named list with data and patchwork object.

Examples

top_targets <- MSTExplorer::example_targets$top_targets
out <- prioritise_targets_grid(top_targets = top_targets)
#> Mapping cell types to cell ontology terms.
#> Adding stage information.
#> Adding disease_name and disease_description.
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12
#> 383 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,753 phenotypes.
#> Assigning severity classes.
#> Adding level-2 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Ancestor metadata already present. Use force_new=TRUE to overwrite.
#> Translating ontology terms to ids.
#> Keeping descendants of 1 term(s).
#> 18,379 terms remain after filtering.
#> 1,150 associations remain after filtering.
#> Getting absolute ontology level for 19,025 IDs.
#> Adding disease_name and disease_description.
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 17 genes extracted.
#> Converting human ==> Macaca mulatta orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Macaca mulatta
#> 1 organism identified from search: 9544
#> Checking for genes without orthologs in Macaca mulatta.
#> Extracting genes from input_gene.
#> 7 genes extracted.
#> Extracting genes from ortholog_gene.
#> 7 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    -10 / 7 (-143%)
#> Total genes remaining after convert_orthologs :
#>    17 / 7 (243%)
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 17 genes extracted.
#> Converting human ==> Mus musculus orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Mus musculus
#> 1 organism identified from search: 10090
#> Checking for genes without orthologs in Mus musculus.
#> Extracting genes from input_gene.
#> 7 genes extracted.
#> Extracting genes from ortholog_gene.
#> 7 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    -10 / 7 (-143%)
#> Total genes remaining after convert_orthologs :
#>    17 / 7 (243%)
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 17 genes extracted.
#> Converting human ==> Danio rerio orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Danio rerio
#> 1 organism identified from search: 7955
#> Checking for genes without orthologs in Danio rerio.
#> Extracting genes from input_gene.
#> 7 genes extracted.
#> Extracting genes from ortholog_gene.
#> 7 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    -10 / 7 (-143%)
#> Total genes remaining after convert_orthologs :
#>    17 / 7 (243%)
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 17 genes extracted.
#> Converting human ==> Drosophila melanogaster orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Drosophila melanogaster
#> 1 organism identified from search: 7227
#> Checking for genes without orthologs in Drosophila melanogaster.
#> Extracting genes from input_gene.
#> 4 genes extracted.
#> Extracting genes from ortholog_gene.
#> 4 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    0 / 7 (0%)
#> Total genes remaining after convert_orthologs :
#>    7 / 7 (100%)
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 17 genes extracted.
#> Converting human ==> Caenorhabditis elegans orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Caenorhabditis elegans
#> 1 organism identified from search: 6239
#> Checking for genes without orthologs in Caenorhabditis elegans.
#> Extracting genes from input_gene.
#> 5 genes extracted.
#> Extracting genes from ortholog_gene.
#> 5 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Dropping 1 genes that have multiple input_gene per ortholog_gene (many:1).
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    -4 / 7 (-57%)
#> Total genes remaining after convert_orthologs :
#>    11 / 7 (157%)
#> Adding disease_name and disease_description.
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 13 genes extracted.
#> Converting human ==> Macaca mulatta orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Macaca mulatta
#> 1 organism identified from search: 9544
#> Checking for genes without orthologs in Macaca mulatta.
#> Extracting genes from input_gene.
#> 6 genes extracted.
#> Extracting genes from ortholog_gene.
#> 6 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    -4 / 7 (-57%)
#> Total genes remaining after convert_orthologs :
#>    11 / 7 (157%)
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 13 genes extracted.
#> Converting human ==> Mus musculus orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Mus musculus
#> 1 organism identified from search: 10090
#> Checking for genes without orthologs in Mus musculus.
#> Extracting genes from input_gene.
#> 7 genes extracted.
#> Extracting genes from ortholog_gene.
#> 7 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    -6 / 7 (-86%)
#> Total genes remaining after convert_orthologs :
#>    13 / 7 (186%)
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 13 genes extracted.
#> Converting human ==> Danio rerio orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Danio rerio
#> 1 organism identified from search: 7955
#> Checking for genes without orthologs in Danio rerio.
#> Extracting genes from input_gene.
#> 7 genes extracted.
#> Extracting genes from ortholog_gene.
#> 7 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    -6 / 7 (-86%)
#> Total genes remaining after convert_orthologs :
#>    13 / 7 (186%)
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 13 genes extracted.
#> Converting human ==> Drosophila melanogaster orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Drosophila melanogaster
#> 1 organism identified from search: 7227
#> Checking for genes without orthologs in Drosophila melanogaster.
#> Extracting genes from input_gene.
#> 2 genes extracted.
#> Extracting genes from ortholog_gene.
#> 2 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    0 / 7 (0%)
#> Total genes remaining after convert_orthologs :
#>    7 / 7 (100%)
#> Preparing gene_df.
#> data.table format detected.
#> Extracting genes from value.
#> 13 genes extracted.
#> Converting human ==> Caenorhabditis elegans orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Retrieving all organisms available in homologene.
#> Mapping species name: Caenorhabditis elegans
#> 1 organism identified from search: 6239
#> Checking for genes without orthologs in Caenorhabditis elegans.
#> Extracting genes from input_gene.
#> 4 genes extracted.
#> Extracting genes from ortholog_gene.
#> 4 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    -3 / 7 (-43%)
#> Total genes remaining after convert_orthologs :
#>    10 / 7 (143%)