## R Under development (unstable) (2025-01-20 r87609)
+## R Under development (unstable) (2025-02-12 r87715)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
@@ -171,16 +171,16 @@ Session Info## [1] rmarkdown_2.29
##
## loaded via a namespace (and not attached):
-## [1] gtable_0.3.6 jsonlite_1.8.9 renv_1.0.11
+## [1] gtable_0.3.6 jsonlite_1.8.9 renv_1.1.1
## [4] dplyr_1.1.4 compiler_4.5.0 BiocManager_1.30.25
## [7] tidyselect_1.2.1 rvcheck_0.2.1 scales_1.3.0
## [10] yaml_2.3.10 fastmap_1.2.0 here_1.0.1
-## [13] ggplot2_3.5.1 R6_2.5.1 generics_0.1.3
-## [16] knitr_1.49 yulab.utils_0.1.9 tibble_3.2.1
+## [13] ggplot2_3.5.1 R6_2.6.1 generics_0.1.3
+## [16] knitr_1.49 yulab.utils_0.2.0 tibble_3.2.1
## [19] desc_1.4.3 dlstats_0.1.7 munsell_0.5.1
## [22] rprojroot_2.0.4 pillar_1.10.1 RColorBrewer_1.1-3
## [25] rlang_1.1.5 badger_0.2.4 xfun_0.50
-## [28] fs_1.6.5 cli_3.6.3 magrittr_2.0.3
+## [28] fs_1.6.5 cli_3.6.4 magrittr_2.0.3
## [31] rworkflows_1.0.6 digest_0.6.37 grid_4.5.0
## [34] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.3
## [37] glue_1.8.0 data.table_1.16.4 colorspace_2.1-1
diff --git a/pkgdown.yml b/pkgdown.yml
index fa82644..dab5727 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,7 +1,7 @@
-pandoc: 3.6.2
+pandoc: 3.6.3
pkgdown: 2.1.1
pkgdown_sha: ~
articles:
docker: docker.html
HPOExplorer: HPOExplorer.html
-last_built: 2025-01-25T01:38Z
+last_built: 2025-02-16T01:33Z
diff --git a/reference/add_.html b/reference/add_.html
index 5f2ac67..f82c4d8 100644
--- a/reference/add_.html
+++ b/reference/add_.html
@@ -652,7 +652,7 @@ Examples
phenos2 <- add_death(phenos = phenos)
#> Annotating phenos with AgeOfDeath.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Adding genes and disease IDs.
if (FALSE) { # \dontrun{
phenos <- load_phenotype_to_genes()
@@ -660,33 +660,33 @@ Examples
} # }
phenos <- load_phenotype_to_genes()
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
phenos2 <- add_evidence(phenos = phenos)
#> Annotating gene-disease associations with Evidence Score
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for:
-#> - 10514 diseases
-#> - 5171 genes
-#> + Version: 2025-01-25
+#> - 10630 diseases
+#> - 5300 genes
+#> + Version: 2025-02-16
phenotype_to_genes <- load_phenotype_to_genes()[seq(1000),]
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
phenos2 <- add_gene_frequency(phenotype_to_genes = phenotype_to_genes)
#> Annotating gene frequencies.
#> Reading cached RDS file: genes_to_phenotype.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
phenos <- example_phenos()
phenos2 <- add_genes(phenos = phenos)
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Adding genes and disease IDs.
phenos <- example_phenos()
phenos2 <- add_gpt_annotations(phenos)
#> Loading required namespace: piggyback
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
phenos <- example_phenos()
@@ -694,7 +694,7 @@ Examples
#> Adding term definitions.
phenotype_to_genes <- load_phenotype_to_genes()
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
phenos <- unique(phenotype_to_genes[,c("hpo_id","hpo_name")])
phenos2 <- add_hpo_id(phenos=phenos)
phenos <- example_phenos()
@@ -706,7 +706,7 @@ Examples
#> Adding information_content scores.
phenos <- load_phenotype_to_genes(3)[seq(1000)]
#> Reading cached RDS file: phenotype.hpoa
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
phenos2 <- add_mondo(phenos = phenos)
#> Loading required namespace: downloadR
#> Loading required namespace: echogithub
@@ -719,11 +719,11 @@ Examples
phenos2 <- add_ndisease(phenos = phenos)
#> Annotating phenos with n_diseases
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Reading cached RDS file: genes_to_phenotype.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Reading cached RDS file: phenotype.hpoa
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
phenos <- example_phenos()
phenos2 <- add_omop(phenos = phenos)
#> Annotating phenos with OMOP metadata.
@@ -733,11 +733,11 @@ Examples
phenos2 <- add_onset(phenos = phenos)
#> Annotating phenos with onset.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Adding genes and disease IDs.
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Extracting data for 24 descendents.
#> Computing gene counts.
#> Adding term definitions.
@@ -752,23 +752,23 @@ Examples
phenos2 <- add_pheno_frequency(phenos = phenos)
#> Annotating phenotype frequencies.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Adding genes and disease IDs.
phenos <- example_phenos()
phenos2 <- add_prevalence(phenos = phenos)
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Adding genes and disease IDs.
#> Mapping disease_id --> mondo_id
#> Loading cached ontology: /github/home/.cache/R/KGExplorer/mondo.rds
#> 11 / 7,359 (0.15%) mondo_id missing.
#> 11 / 7,359 (0.15%) mondo_name missing.
-#> 2,699 / 7,359 (36.68%) mondo_def missing.
+#> 2,695 / 7,359 (36.62%) mondo_def missing.
#> Mapping disease_id --> mondo_id
#> Loading cached ontology: /github/home/.cache/R/KGExplorer/mondo.rds
#> 25 / 6,089 (0.41%) mondo_id missing.
#> 25 / 6,089 (0.41%) mondo_name missing.
-#> 1,078 / 6,089 (17.7%) mondo_def missing.
+#> 1,077 / 6,089 (17.69%) mondo_def missing.
#> Prevalence added for 0 / 7,359 disease_id IDs (0%)
#> Prevalence added for 0 / 10 hpo_id IDs (0%)
#> Prevalence added for 0 / 6,824 mondo_id IDs (0%)
@@ -776,7 +776,7 @@ Examples
phenos2 <- add_severity(phenos = phenos)
#> Annotating phenos with modifiers
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Adding genes and disease IDs.
phenos <- example_phenos()
phenos2 <- add_tier(phenos = phenos)
diff --git a/reference/add_disease.html b/reference/add_disease.html
index 70cc14d..10c22a9 100644
--- a/reference/add_disease.html
+++ b/reference/add_disease.html
@@ -127,7 +127,7 @@ Examples
phenos <- example_phenos()
phenos2 <- add_disease(phenos = phenos)
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Adding genes and disease IDs.
Functions
Examples
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Extracting data for 24 descendents.
#> Computing gene counts.
#> Adding term definitions.
diff --git a/reference/get_gene_lists.html b/reference/get_gene_lists.html
index ec28a59..7717fca 100644
--- a/reference/get_gene_lists.html
+++ b/reference/get_gene_lists.html
@@ -119,7 +119,7 @@ Examples
gene_lists <- get_gene_lists(phenotypes = phenotypes)
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
top_phenos <- get_top_phenos()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
#> Assigning severity classes.
diff --git a/reference/gpt_annot_check.html b/reference/gpt_annot_check.html
index 4a01fd7..534d038 100644
--- a/reference/gpt_annot_check.html
+++ b/reference/gpt_annot_check.html
@@ -118,7 +118,7 @@ Examples
checks <- gpt_annot_check()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
#> Querying HPO for matching terms.
diff --git a/reference/gpt_annot_class.html b/reference/gpt_annot_class.html
index 35cda73..0d141ae 100644
--- a/reference/gpt_annot_class.html
+++ b/reference/gpt_annot_class.html
@@ -115,7 +115,7 @@ Examples
res_coded <- gpt_annot_codify()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
res_class <- gpt_annot_class(res_coded)
diff --git a/reference/gpt_annot_codify.html b/reference/gpt_annot_codify.html
index 0493650..798beb5 100644
--- a/reference/gpt_annot_codify.html
+++ b/reference/gpt_annot_codify.html
@@ -119,7 +119,7 @@ Examples
res_coded <- gpt_annot_codify()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
Examples
res_coded <- gpt_annot_codify()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
annot_melt <- gpt_annot_melt(res_coded)
diff --git a/reference/gpt_annot_plot.html b/reference/gpt_annot_plot.html
index 1260dcd..0e2bf1a 100644
--- a/reference/gpt_annot_plot.html
+++ b/reference/gpt_annot_plot.html
@@ -124,7 +124,7 @@ Examples
plots <- gpt_annot_plot()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
#> Adding level-2 ancestor to each HPO ID.
diff --git a/reference/gpt_annot_plot_branches.html b/reference/gpt_annot_plot_branches.html
index b7358c0..da2b176 100644
--- a/reference/gpt_annot_plot_branches.html
+++ b/reference/gpt_annot_plot_branches.html
@@ -124,7 +124,7 @@ Examples
out <- gpt_annot_plot_branches()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
#> Adding level-2 ancestor to each HPO ID.
diff --git a/reference/gpt_annot_read.html b/reference/gpt_annot_read.html
index 229f1b1..dbbd13c 100644
--- a/reference/gpt_annot_read.html
+++ b/reference/gpt_annot_read.html
@@ -144,7 +144,7 @@ Examples
gpt_annot <- gpt_annot_read()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
Examples
X <- hpo_to_matrix(terms = phenos$hpo_id)
#> Constructing HPO gene x phenotype matrix.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Annotating gene-disease associations with Evidence Score
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for:
-#> - 10514 diseases
-#> - 5171 genes
-#> + Version: 2025-01-25
+#> - 10630 diseases
+#> - 5300 genes
+#> + Version: 2025-02-16
Value
Examples
phenotype_to_genes <- load_phenotype_to_genes()
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
Functions
Examples
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Extracting data for 24 descendents.
#> Computing gene counts.
#> Adding term definitions.
@@ -402,7 +402,7 @@ Examples
#> Removing isolated nodes.
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Extracting data for 24 descendents.
#> Computing gene counts.
#> Adding term definitions.
@@ -425,7 +425,7 @@ Examples
#> Converting graph to ggnetwork.
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Extracting data for 24 descendents.
#> Computing gene counts.
#> Adding term definitions.
@@ -444,7 +444,7 @@ Examples
#> Creating ggnetwork plot.
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Extracting data for 24 descendents.
#> Computing gene counts.
#> Adding term definitions.
@@ -457,7 +457,7 @@ Examples
terms <- get_hpo()@terms[seq(100)]
tiers <- make_tiers(terms = terms)
#> Reading cached RDS file: phenotype.hpoa
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> keyword_set=Tier1: Found 0 terms matching category.
#> keyword_set=Tier2: Found 0 terms matching category.
#> keyword_set=Tier3: Found 0 terms matching category.
diff --git a/reference/map_disease.html b/reference/map_disease.html
index bd7bc12..73d2a93 100644
--- a/reference/map_disease.html
+++ b/reference/map_disease.html
@@ -128,7 +128,7 @@ Arguments
Examples
dat <- HPOExplorer::load_phenotype_to_genes()
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
out <- map_disease(dat = dat, workers=1)
#> Adding disease_name and disease_description.
Value
Examples
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Extracting data for 24 descendents.
#> Computing gene counts.
#> Adding term definitions.
@@ -163,7 +163,7 @@ Examples
grl <- phenos_to_granges(phenos = phenos)
#> Converting phenos to GRangesList.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Adding genes and disease IDs.
#> Loading required namespace: ensembldb
#> Gathering metadata for 2513 unique genes.
diff --git a/reference/plot_evidence-1.png b/reference/plot_evidence-1.png
index 5d60d1a..8e3b60b 100644
Binary files a/reference/plot_evidence-1.png and b/reference/plot_evidence-1.png differ
diff --git a/reference/plot_evidence.html b/reference/plot_evidence.html
index 5c25a50..3998846 100644
--- a/reference/plot_evidence.html
+++ b/reference/plot_evidence.html
@@ -116,32 +116,32 @@ Examples
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for:
-#> - 10514 diseases
-#> - 5171 genes
-#> + Version: 2025-01-25
+#> - 10630 diseases
+#> - 5300 genes
+#> + Version: 2025-02-16
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for:
-#> - 10514 diseases
-#> - 5171 genes
-#> + Version: 2025-01-25
+#> - 10630 diseases
+#> - 5300 genes
+#> + Version: 2025-02-16
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> Annotating gene-disease associations with Evidence Score
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for:
-#> - 10514 diseases
-#> - 5171 genes
-#> + Version: 2025-01-25
+#> - 10630 diseases
+#> - 5300 genes
+#> + Version: 2025-02-16
#> 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: 2025-01-25
+#> - 10630 diseases
+#> - 5300 genes
+#> + Version: 2025-02-16
#> `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`.
diff --git a/reference/plot_top_phenos.html b/reference/plot_top_phenos.html
index cda612f..ed5bfd7 100644
--- a/reference/plot_top_phenos.html
+++ b/reference/plot_top_phenos.html
@@ -187,7 +187,7 @@ Examples
res_class <- gpt_annot_class()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
-#> + Version: 2025-01-16
+#> + Version: v2025-01-16
#> 384 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,752 phenotypes.
#> Assigning severity classes.