diff --git a/articles/MultiEWCE.html b/articles/MultiEWCE.html index 6c424b5..33580d5 100644 --- a/articles/MultiEWCE.html +++ b/articles/MultiEWCE.html @@ -89,7 +89,7 @@


-Vignette updated: Nov-04-2023
+Vignette updated: Nov-07-2023

Source: vignettes/MultiEWCE.Rmd @@ -160,8 +160,11 @@

Loading Phenotype

etc…

Now we will get a dataset like this from the HPO.

-gene_data <- HPOExplorer::load_phenotype_to_genes()
-knitr::kable(head(gene_data))
+gene_data <- HPOExplorer::load_phenotype_to_genes() +
## Reading cached RDS file: phenotype_to_genes.txt
+
## + Version: v2023-10-09
+
+knitr::kable(head(gene_data))
@@ -223,7 +226,7 @@

Loading Phenotype

Setting up input arguments for the gen_results function

-
+
 

 
Visualise the results
@@ -328,7 +331,7 @@ 
Visualise the resultsJust as an example, we will create a plot showing the number of
 significant enrichments per phenotype in the all_results data.frame. We
 will use q <= 0.05 as the significance threshold.

-
+
 library(ggplot2)
 library(data.table)
 #### Aggregate results ####
@@ -340,7 +343,7 @@ 
Visualise the results    geom_col() +
     labs(x="Phenotype",y="Enrichments (n)") + 
     theme_bw() 

-
+
 methods::show(plot1)

 

 

@@ -357,7 +360,7 @@ 
merge_results
+
 
## 1 results files found.

 

@@ -366,14 +369,14 @@ 
get_gene_list
+
 phenotypes <- c("Scoliosis")
 gene_set <- HPOExplorer::get_gene_lists(phenotypes = phenotypes,
                                         phenotype_to_genes = gene_data)

 
## Translating all phenotypes to HPO IDs.

 
## ℹ All local files already up-to-date!

 
## + Returning a vector of phenotypes (same order as input).

-
+
 cat(paste(length(unique(gene_set$gene_symbol)),
           "genes associated with",shQuote(phenotypes),":",
           paste(unique(gene_set$gene_symbol)[seq(5)],collapse = ", ")))

@@ -384,7 +387,7 @@ 
get_unfinished_list_names
 
This function is used to find which gene lists you have not yet
 analysed

-
+
 all_phenotypes <- unique(gene_data$hpo_name)
 unfinished <- MultiEWCE::get_unfinished_list_names(list_names = all_phenotypes,
                                                    save_dir_tmp = save_dir_tmp)
@@ -400,27 +403,30 @@ 
Run disease-level enrichment testsSo far, we’ve iterated over gene list grouped by phenotypes. But we
 can also do this at the level of diseases (which are composed of
 combinations of phenotypes).

-
-gene_data <- HPOExplorer::load_phenotype_to_genes("genes_to_phenotype.txt")
-#### Filter only to those with >=4 genes ####
+
+gene_data <- HPOExplorer::load_phenotype_to_genes("genes_to_phenotype.txt")

+
## Reading cached RDS file: genes_to_phenotype.txt

+
## + Version: v2023-10-09

+
+#### Filter only to those with >=4 genes ####
 gene_counts <- gene_data[,list(genes=length(unique(gene_symbol))),
                          by="disease_id"][genes>=4]
 list_names <- unique(gene_counts$disease_id)[seq(5)]

-
+
 all_results <- MultiEWCE::gen_results(ctd = ctd,
                                       gene_data = gene_data,
                                       list_name_column = "disease_id",
                                       list_names = list_names,
                                       annotLevel = 1,
                                       reps = 10)

-
## Results already exist at: /tmp/RtmpHXsbJK/gen_results.rds Use `force_new=TRUE` to overwrite.

+
## Results already exist at: /tmp/RtmpnaSTmh/gen_results.rds Use `force_new=TRUE` to overwrite.

 

 

 
Full analysis
 

 
Run the following code the replicate the main analysis in the study
 described here.

-
+
 gene_data <- HPOExplorer::load_phenotype_to_genes()
 gene_data[,n_gene:=length(unique(gene_symbol)),by="hpo_id"]
 gene_data <- gene_data[n_gene>=4,]
@@ -435,10 +441,10 @@ 
Full analysis
 
Session info
 

-
+
 utils::sessionInfo()

-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-02 r85465)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -460,41 +466,41 @@ 
Session info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] data.table_1.14.8 ggplot2_3.4.4     MultiEWCE_0.1.8   BiocStyle_2.30.0 
+## [1] data.table_1.14.8 ggplot2_3.4.4     MultiEWCE_0.1.8   BiocStyle_2.31.0 
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] later_1.3.1                   bitops_1.0-7                 
-##   [3] ggplotify_0.1.2               GeneOverlap_1.38.0           
+##   [3] ggplotify_0.1.2               GeneOverlap_1.39.0           
 ##   [5] filelock_1.0.2                tibble_3.2.1                 
 ##   [7] ontologyPlot_1.6              ggnetwork_0.5.12             
-##   [9] graph_1.80.0                  httr2_0.2.3                  
-##  [11] lifecycle_1.0.3               rstatix_0.7.2                
-##  [13] HPOExplorer_0.99.12           rprojroot_2.0.3              
-##  [15] lattice_0.21-9                backports_1.4.1              
-##  [17] magrittr_2.0.3                limma_3.58.1                 
+##   [9] graph_1.81.0                  httr2_0.2.3                  
+##  [11] lifecycle_1.0.4               rstatix_0.7.2                
+##  [13] HPOExplorer_0.99.12           rprojroot_2.0.4              
+##  [15] lattice_0.22-5                backports_1.4.1              
+##  [17] magrittr_2.0.3                limma_3.59.1                 
 ##  [19] plotly_4.10.3                 sass_0.4.7                   
 ##  [21] rmarkdown_2.25                jquerylib_0.1.4              
 ##  [23] yaml_2.3.7                    httpuv_1.6.12                
 ##  [25] HGNChelper_0.8.1              DBI_1.1.3                    
 ##  [27] RColorBrewer_1.1-3            lubridate_1.9.3              
-##  [29] abind_1.4-5                   zlibbioc_1.48.0              
-##  [31] GenomicRanges_1.54.1          purrr_1.0.2                  
-##  [33] BiocGenerics_0.48.1           RCurl_1.98-1.13              
+##  [29] abind_1.4-5                   zlibbioc_1.49.0              
+##  [31] GenomicRanges_1.55.1          purrr_1.0.2                  
+##  [33] BiocGenerics_0.49.1           RCurl_1.98-1.13              
 ##  [35] yulab.utils_0.1.0             rappdirs_0.3.3               
-##  [37] GenomeInfoDbData_1.2.11       IRanges_2.36.0               
-##  [39] S4Vectors_0.40.1              gitcreds_0.1.2               
+##  [37] GenomeInfoDbData_1.2.11       IRanges_2.37.0               
+##  [39] S4Vectors_0.41.1              gitcreds_0.1.2               
 ##  [41] tidytree_0.4.5                piggyback_0.1.5              
 ##  [43] pkgdown_2.0.7                 codetools_0.2-19             
-##  [45] DelayedArray_0.28.0           tidyselect_1.2.0             
+##  [45] DelayedArray_0.29.0           tidyselect_1.2.0             
 ##  [47] aplot_0.2.2                   farver_2.1.1                 
-##  [49] matrixStats_1.0.0             stats4_4.3.1                 
-##  [51] BiocFileCache_2.10.1          jsonlite_1.8.7               
+##  [49] matrixStats_1.1.0             stats4_4.4.0                 
+##  [51] BiocFileCache_2.11.1          jsonlite_1.8.7               
 ##  [53] ellipsis_0.3.2                systemfonts_1.0.5            
-##  [55] paintmap_1.0                  tools_4.3.1                  
-##  [57] treeio_1.26.0                 ragg_1.2.6                   
+##  [55] paintmap_1.0                  tools_4.4.0                  
+##  [57] treeio_1.27.0                 ragg_1.2.6                   
 ##  [59] Rcpp_1.0.11                   glue_1.6.2                   
-##  [61] SparseArray_1.2.0             xfun_0.41                    
-##  [63] MatrixGenerics_1.14.0         GenomeInfoDb_1.38.0          
+##  [61] SparseArray_1.3.0             xfun_0.41                    
+##  [63] MatrixGenerics_1.15.0         GenomeInfoDb_1.39.0          
 ##  [65] RNOmni_1.0.1.2                dplyr_1.1.3                  
 ##  [67] withr_2.5.2                   BiocManager_1.30.22          
 ##  [69] fastmap_1.1.1                 fansi_1.0.5                  
@@ -505,45 +511,45 @@ 
Session info##  [79] gtools_3.9.4                  RSQLite_2.3.3                
 ##  [81] utf8_1.2.4                    tidyr_1.3.0                  
 ##  [83] generics_0.1.3                httr_1.4.7                   
-##  [85] htmlwidgets_1.6.2             S4Arrays_1.2.0               
+##  [85] htmlwidgets_1.6.2             S4Arrays_1.3.0               
 ##  [87] ontologyIndex_2.11            pkgconfig_2.0.3              
 ##  [89] gtable_0.3.4                  blob_1.2.4                   
-##  [91] SingleCellExperiment_1.24.0   XVector_0.42.0               
+##  [91] SingleCellExperiment_1.25.0   XVector_0.43.0               
 ##  [93] htmltools_0.5.7               carData_3.0-5                
 ##  [95] bookdown_0.36                 scales_1.2.1                 
-##  [97] Biobase_2.62.0                png_0.1-8                    
+##  [97] Biobase_2.63.0                png_0.1-8                    
 ##  [99] ggfun_0.1.3                   knitr_1.45                   
 ## [101] reshape2_1.4.4                coda_0.19-4                  
 ## [103] statnet.common_4.9.0          nlme_3.1-163                 
 ## [105] curl_5.1.0                    cachem_1.0.8                 
-## [107] stringr_1.5.0                 BiocVersion_3.18.0           
-## [109] KernSmooth_2.23-22            parallel_4.3.1               
-## [111] AnnotationDbi_1.64.1          desc_1.4.2                   
-## [113] pillar_1.9.0                  grid_4.3.1                   
+## [107] stringr_1.5.0                 BiocVersion_3.19.1           
+## [109] KernSmooth_2.23-22            parallel_4.4.0               
+## [111] AnnotationDbi_1.65.2          desc_1.4.2                   
+## [113] pillar_1.9.0                  grid_4.4.0                   
 ## [115] vctrs_0.6.4                   gplots_3.1.3                 
 ## [117] promises_1.2.1                ggpubr_0.6.0                 
 ## [119] car_3.1-2                     dbplyr_2.4.0                 
-## [121] xtable_1.8-4                  Rgraphviz_2.46.0             
-## [123] evaluate_0.23                 orthogene_1.8.0              
-## [125] cli_3.6.1                     compiler_4.3.1               
+## [121] xtable_1.8-4                  Rgraphviz_2.47.0             
+## [123] evaluate_0.23                 orthogene_1.9.0              
+## [125] cli_3.6.1                     compiler_4.4.0               
 ## [127] rlang_1.1.2                   crayon_1.5.2                 
 ## [129] grr_0.9.5                     ggsignif_0.6.4               
 ## [131] labeling_0.4.3                gprofiler2_0.2.2             
 ## [133] EWCE_1.11.2                   plyr_1.8.9                   
 ## [135] fs_1.6.3                      stringi_1.7.12               
-## [137] BiocParallel_1.36.0           viridisLite_0.4.2            
-## [139] ewceData_1.10.0               network_1.18.1               
+## [137] BiocParallel_1.37.0           viridisLite_0.4.2            
+## [139] ewceData_1.11.0               network_1.18.1               
 ## [141] babelgene_22.9                munsell_0.5.0                
-## [143] Biostrings_2.70.1             gh_1.4.0                     
+## [143] Biostrings_2.71.1             gh_1.4.0                     
 ## [145] lazyeval_0.2.2                homologene_1.4.68.19.3.27    
-## [147] Matrix_1.6-1.1                ExperimentHub_2.10.0         
+## [147] Matrix_1.6-1.1                ExperimentHub_2.11.0         
 ## [149] patchwork_1.1.3               bit64_4.0.5                  
-## [151] KEGGREST_1.42.0               statmod_1.5.0                
+## [151] KEGGREST_1.43.0               statmod_1.5.0                
 ## [153] shiny_1.7.5.1                 highr_0.10                   
-## [155] SummarizedExperiment_1.32.0   interactiveDisplayBase_1.40.0
-## [157] AnnotationHub_3.10.0          broom_1.0.5                  
+## [155] SummarizedExperiment_1.33.0   interactiveDisplayBase_1.41.0
+## [157] AnnotationHub_3.11.0          broom_1.0.5                  
 ## [159] memoise_2.0.1                 bslib_0.5.1                  
-## [161] ggtree_3.10.0                 bit_4.0.5                    
+## [161] ggtree_3.11.0                 bit_4.0.5                    
 ## [163] ape_5.7-1

 

 

diff --git a/articles/MultiEWCE_files/figure-html/display-1.png b/articles/MultiEWCE_files/figure-html/display-1.png
index ddf0aea..828b0ae 100644
Binary files a/articles/MultiEWCE_files/figure-html/display-1.png and b/articles/MultiEWCE_files/figure-html/display-1.png differ
diff --git a/articles/docker.html b/articles/docker.html
index 232ede5..7341726 100644
--- a/articles/docker.html
+++ b/articles/docker.html
@@ -89,7 +89,7 @@ 

             
             

 

-Vignette updated: Nov-04-2023

+Vignette updated: Nov-07-2023

 

       
       Source: vignettes/docker.Rmd
@@ -165,8 +165,8 @@ 
Session Info
 utils::sessionInfo()

-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-02 r85465)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -188,39 +188,39 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] MultiEWCE_0.1.8  BiocStyle_2.30.0
+## [1] MultiEWCE_0.1.8  BiocStyle_2.31.0
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] later_1.3.1                   bitops_1.0-7                 
-##   [3] ggplotify_0.1.2               GeneOverlap_1.38.0           
+##   [3] ggplotify_0.1.2               GeneOverlap_1.39.0           
 ##   [5] filelock_1.0.2                tibble_3.2.1                 
 ##   [7] ontologyPlot_1.6              ggnetwork_0.5.12             
-##   [9] graph_1.80.0                  lifecycle_1.0.3              
+##   [9] graph_1.81.0                  lifecycle_1.0.4              
 ##  [11] rstatix_0.7.2                 HPOExplorer_0.99.12          
-##  [13] rprojroot_2.0.3               lattice_0.21-9               
+##  [13] rprojroot_2.0.4               lattice_0.22-5               
 ##  [15] backports_1.4.1               magrittr_2.0.3               
-##  [17] limma_3.58.1                  plotly_4.10.3                
+##  [17] limma_3.59.1                  plotly_4.10.3                
 ##  [19] sass_0.4.7                    rmarkdown_2.25               
 ##  [21] jquerylib_0.1.4               yaml_2.3.7                   
 ##  [23] httpuv_1.6.12                 HGNChelper_0.8.1             
 ##  [25] DBI_1.1.3                     RColorBrewer_1.1-3           
-##  [27] abind_1.4-5                   zlibbioc_1.48.0              
-##  [29] GenomicRanges_1.54.1          purrr_1.0.2                  
-##  [31] BiocGenerics_0.48.1           RCurl_1.98-1.13              
+##  [27] abind_1.4-5                   zlibbioc_1.49.0              
+##  [29] GenomicRanges_1.55.1          purrr_1.0.2                  
+##  [31] BiocGenerics_0.49.1           RCurl_1.98-1.13              
 ##  [33] yulab.utils_0.1.0             rappdirs_0.3.3               
-##  [35] GenomeInfoDbData_1.2.11       IRanges_2.36.0               
-##  [37] S4Vectors_0.40.1              tidytree_0.4.5               
+##  [35] GenomeInfoDbData_1.2.11       IRanges_2.37.0               
+##  [37] S4Vectors_0.41.1              tidytree_0.4.5               
 ##  [39] piggyback_0.1.5               pkgdown_2.0.7                
-##  [41] DelayedArray_0.28.0           tidyselect_1.2.0             
-##  [43] aplot_0.2.2                   matrixStats_1.0.0            
-##  [45] stats4_4.3.1                  BiocFileCache_2.10.1         
+##  [41] DelayedArray_0.29.0           tidyselect_1.2.0             
+##  [43] aplot_0.2.2                   matrixStats_1.1.0            
+##  [45] stats4_4.4.0                  BiocFileCache_2.11.1         
 ##  [47] jsonlite_1.8.7                ellipsis_0.3.2               
 ##  [49] systemfonts_1.0.5             paintmap_1.0                 
-##  [51] tools_4.3.1                   treeio_1.26.0                
+##  [51] tools_4.4.0                   treeio_1.27.0                
 ##  [53] ragg_1.2.6                    Rcpp_1.0.11                  
-##  [55] glue_1.6.2                    SparseArray_1.2.0            
-##  [57] xfun_0.41                     MatrixGenerics_1.14.0        
-##  [59] GenomeInfoDb_1.38.0           RNOmni_1.0.1.2               
+##  [55] glue_1.6.2                    SparseArray_1.3.0            
+##  [57] xfun_0.41                     MatrixGenerics_1.15.0        
+##  [59] GenomeInfoDb_1.39.0           RNOmni_1.0.1.2               
 ##  [61] dplyr_1.1.3                   BiocManager_1.30.22          
 ##  [63] fastmap_1.1.1                 fansi_1.0.5                  
 ##  [65] caTools_1.18.2                digest_0.6.33                
@@ -230,43 +230,43 @@ 
Session Info##  [73] RSQLite_2.3.3                 utf8_1.2.4                   
 ##  [75] tidyr_1.3.0                   generics_0.1.3               
 ##  [77] data.table_1.14.8             httr_1.4.7                   
-##  [79] htmlwidgets_1.6.2             S4Arrays_1.2.0               
+##  [79] htmlwidgets_1.6.2             S4Arrays_1.3.0               
 ##  [81] ontologyIndex_2.11            pkgconfig_2.0.3              
 ##  [83] gtable_0.3.4                  blob_1.2.4                   
-##  [85] SingleCellExperiment_1.24.0   XVector_0.42.0               
+##  [85] SingleCellExperiment_1.25.0   XVector_0.43.0               
 ##  [87] htmltools_0.5.7               carData_3.0-5                
 ##  [89] bookdown_0.36                 scales_1.2.1                 
-##  [91] Biobase_2.62.0                png_0.1-8                    
+##  [91] Biobase_2.63.0                png_0.1-8                    
 ##  [93] ggfun_0.1.3                   knitr_1.45                   
 ##  [95] reshape2_1.4.4                coda_0.19-4                  
 ##  [97] statnet.common_4.9.0          nlme_3.1-163                 
 ##  [99] curl_5.1.0                    cachem_1.0.8                 
-## [101] stringr_1.5.0                 BiocVersion_3.18.0           
-## [103] KernSmooth_2.23-22            parallel_4.3.1               
-## [105] AnnotationDbi_1.64.1          desc_1.4.2                   
-## [107] pillar_1.9.0                  grid_4.3.1                   
+## [101] stringr_1.5.0                 BiocVersion_3.19.1           
+## [103] KernSmooth_2.23-22            parallel_4.4.0               
+## [105] AnnotationDbi_1.65.2          desc_1.4.2                   
+## [107] pillar_1.9.0                  grid_4.4.0                   
 ## [109] vctrs_0.6.4                   gplots_3.1.3                 
 ## [111] promises_1.2.1                ggpubr_0.6.0                 
 ## [113] car_3.1-2                     dbplyr_2.4.0                 
-## [115] xtable_1.8-4                  Rgraphviz_2.46.0             
-## [117] evaluate_0.23                 orthogene_1.8.0              
-## [119] cli_3.6.1                     compiler_4.3.1               
+## [115] xtable_1.8-4                  Rgraphviz_2.47.0             
+## [117] evaluate_0.23                 orthogene_1.9.0              
+## [119] cli_3.6.1                     compiler_4.4.0               
 ## [121] rlang_1.1.2                   crayon_1.5.2                 
 ## [123] grr_0.9.5                     ggsignif_0.6.4               
 ## [125] gprofiler2_0.2.2              EWCE_1.11.2                  
 ## [127] plyr_1.8.9                    fs_1.6.3                     
 ## [129] stringi_1.7.12                viridisLite_0.4.2            
-## [131] ewceData_1.10.0               network_1.18.1               
+## [131] ewceData_1.11.0               network_1.18.1               
 ## [133] babelgene_22.9                munsell_0.5.0                
-## [135] Biostrings_2.70.1             lazyeval_0.2.2               
+## [135] Biostrings_2.71.1             lazyeval_0.2.2               
 ## [137] homologene_1.4.68.19.3.27     Matrix_1.6-1.1               
-## [139] ExperimentHub_2.10.0          patchwork_1.1.3              
+## [139] ExperimentHub_2.11.0          patchwork_1.1.3              
 ## [141] bit64_4.0.5                   ggplot2_3.4.4                
-## [143] KEGGREST_1.42.0               statmod_1.5.0                
-## [145] shiny_1.7.5.1                 SummarizedExperiment_1.32.0  
-## [147] interactiveDisplayBase_1.40.0 AnnotationHub_3.10.0         
+## [143] KEGGREST_1.43.0               statmod_1.5.0                
+## [145] shiny_1.7.5.1                 SummarizedExperiment_1.33.0  
+## [147] interactiveDisplayBase_1.41.0 AnnotationHub_3.11.0         
 ## [149] broom_1.0.5                   memoise_2.0.1                
-## [151] bslib_0.5.1                   ggtree_3.10.0                
+## [151] bslib_0.5.1                   ggtree_3.11.0                
 ## [153] bit_4.0.5                     ape_5.7-1

 


 

diff --git a/index.html b/index.html
index ff9a281..e429a5d 100644
--- a/index.html
+++ b/index.html
@@ -95,7 +95,7 @@
 
 

 

-README updated: Nov-04-2023
+README updated: Nov-07-2023
 
 

 
diff --git a/pkgdown.yml b/pkgdown.yml
index a9dc297..11e489c 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   MultiEWCE: MultiEWCE.html
   docker: docker.html
-last_built: 2023-11-04T22:59Z
+last_built: 2023-11-07T16:30Z
 
diff --git a/reference/add_ctd.html b/reference/add_ctd.html
index 1baf59f..9842199 100644
--- a/reference/add_ctd.html
+++ b/reference/add_ctd.html
@@ -145,7 +145,11 @@ 
Arguments

     
Examples

     
results <- load_example_results()
 results2 <- add_ctd(results=results)
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 #> Annotating phenos with Disease
+#> Reading cached RDS file: phenotype.hpoa
+#> + Version: v2023-10-09
 

     

   

diff --git a/reference/correlation_heatmap.html b/reference/correlation_heatmap.html
index 5f219cc..bf4f7cc 100644
--- a/reference/correlation_heatmap.html
+++ b/reference/correlation_heatmap.html
@@ -174,10 +174,15 @@ 
Examples

     
top_targets <- example_targets$top_targets[seq(100),]
 hm <- correlation_heatmap(top_targets = top_targets)
 #> Constructing HPO gene x phenotype matrix.
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 #> Annotating gene-disease associations with Evidence score
 #> Annotating phenos with Disease
+#> Reading cached RDS file: phenotype.hpoa
+#> + Version: v2023-10-09
 #> Gathering data from GenCC.
 #> Importing cached file.
+#> + Version: 2023-11-07
 #> Computing all parwise correlations.
 #> Aggregating results by group_var='hpo_name'/'hpo_id'/'ancestor_name'/'ontLvl'/'onset_top'
 #> Loading required namespace: ComplexHeatmap
diff --git a/reference/ewce_para.html b/reference/ewce_para.html
index 4ce593f..fd433e1 100644
--- a/reference/ewce_para.html
+++ b/reference/ewce_para.html
@@ -173,13 +173,15 @@ 
Value

     

     
Examples

     
gene_data <- HPOExplorer::load_phenotype_to_genes()
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 ctd <- MultiEWCE::load_example_ctd()
-list_names <- unique(gene_data$hpo_name)[seq(3)]
+list_names <- unique(gene_data$hpo_id)[seq(3)]
 res_files <- ewce_para(ctd = ctd,
                        gene_data = gene_data,
                        list_names = list_names,
                        reps = 10)
-#> Error in check_bootstrap_args(sct_data = sct_data, hits = hits, annotLevel = annotLevel,     reps = reps, controlledCT = controlledCT): Must provide a gene list to hits.
+#> Computing gene counts.
 

     

   

diff --git a/reference/ewce_plot.html b/reference/ewce_plot.html
index 5fba70d..84dd09f 100644
--- a/reference/ewce_plot.html
+++ b/reference/ewce_plot.html
@@ -130,7 +130,7 @@ 
Examples

 #> loading from cache
 #> see ?ewceData and browseVignettes('ewceData') for documentation
 #> loading from cache
-#> 1 core(s) assigned as workers (3 reserved).
+#> 1 core(s) assigned as workers (1 reserved).
 #> Generating gene background for mouse x human ==> human
 #> Gathering ortholog reports.
 #> Retrieving all genes using: homologene.
@@ -217,7 +217,7 @@ 
Examples

 #> Computing BH-corrected q-values.
 #> 1 significant cell type enrichment results @ q<0.05 : 
 #>    CellType annotLevel p fold_change sd_from_mean q
-#> 1 microglia          1 0    2.004934     4.030195 0
+#> 1 microglia          1 0    2.064236     4.714929 0
 plt <- MultiEWCE::ewce_plot(total_res = full_results$results)
 

     

diff --git a/reference/frequency_barplot.html b/reference/frequency_barplot.html
index 9bd159d..be5c9e5 100644
--- a/reference/frequency_barplot.html
+++ b/reference/frequency_barplot.html
@@ -109,9 +109,15 @@ 
Examples

 fp_res <- frequency_barplot(results=results)
 #> Annotating phenotype frequencies.
 #> Annotating phenos with Disease
+#> Reading cached RDS file: phenotype.hpoa
+#> + Version: v2023-10-09
 #> Adding level-3 ancestor to each HPO ID.
 #> ℹ All local files already up-to-date!
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 #> Annotating gene frequencies.
+#> Reading cached RDS file: genes_to_phenotype.txt
+#> + Version: v2023-10-09
 #> Adding level-3 ancestor to each HPO ID.
 #> ℹ All local files already up-to-date!
 #> 96.2% of rows are NA.
diff --git a/reference/frequency_histogram-1.png b/reference/frequency_histogram-1.png
index c64647d..452a965 100644
Binary files a/reference/frequency_histogram-1.png and b/reference/frequency_histogram-1.png differ
diff --git a/reference/frequency_histogram.html b/reference/frequency_histogram.html
index 4ebca10..1618437 100644
--- a/reference/frequency_histogram.html
+++ b/reference/frequency_histogram.html
@@ -109,9 +109,15 @@ 
Examples

 fp_res <- frequency_histogram(results=results)
 #> Annotating phenotype frequencies.
 #> Annotating phenos with Disease
+#> Reading cached RDS file: phenotype.hpoa
+#> + Version: v2023-10-09
 #> Adding level-3 ancestor to each HPO ID.
 #> ℹ All local files already up-to-date!
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 #> Annotating gene frequencies.
+#> Reading cached RDS file: genes_to_phenotype.txt
+#> + Version: v2023-10-09
 #> Adding level-3 ancestor to each HPO ID.
 #> ℹ All local files already up-to-date!
 #> Warning: Ignoring unknown parameters: `binwidth`, `bins`, and `pad`
diff --git a/reference/gen_overlap.html b/reference/gen_overlap.html
index 1a66d97..5d5a9c9 100644
--- a/reference/gen_overlap.html
+++ b/reference/gen_overlap.html
@@ -165,13 +165,20 @@ 
Details

     

     
Examples

     
gene_data <- HPOExplorer::load_phenotype_to_genes()
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 list_names <- unique(gene_data$disease_id)[seq(3)]
 overlap <- gen_overlap(gene_data = gene_data,
                        list_names = list_names)
 #> Splitting data.
-#> 1.13459897041321
 #> 
-#> Saving results ==> /tmp/Rtmp5NzcNQ/gen_overlap.rds
+#> Attaching package: ‘purrr’
+#> The following object is masked from ‘package:base’:
+#> 
+#>     %||%
+#> 1.41372561454773
+#> 
+#> Saving results ==> /tmp/RtmpS5wtsl/gen_overlap.rds
diff --git a/reference/gen_results.html b/reference/gen_results.html index 032dfac..47f0d47 100644 --- a/reference/gen_results.html +++ b/reference/gen_results.html @@ -193,6 +193,8 @@

Details

Examples

gene_data <- HPOExplorer::load_phenotype_to_genes()
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 list_names <- unique(gene_data$hpo_id)[seq(5)]
 ctd <- load_example_ctd()
 all_results <- gen_results(ctd = ctd,
@@ -203,9 +205,9 @@ 
Examples

 #> 2 / 5 gene lists are valid.
 #> Computing gene counts.
 #> Computing gene counts.
-#> Done in: 3.6 seconds.
+#> Done in: 4 seconds.
 #> 
-#> Saving results ==> /tmp/Rtmp5NzcNQ/gen_results.rds
+#> Saving results ==> /tmp/RtmpS5wtsl/gen_results.rds
diff --git a/reference/get_unfinished_list_names.html b/reference/get_unfinished_list_names.html index 4caeb43..97c76e5 100644 --- a/reference/get_unfinished_list_names.html +++ b/reference/get_unfinished_list_names.html @@ -98,6 +98,8 @@

Value

Examples

gene_data <- HPOExplorer::load_phenotype_to_genes()
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 list_names <- unique(gene_data$hpo_name)[seq(3)]
 save_dir_tmp <- file.path(tempdir(),"results")
 ctd <- load_example_ctd()
diff --git a/reference/ggnetwork_plot_full.html b/reference/ggnetwork_plot_full.html
index e6622ef..18fcb15 100644
--- a/reference/ggnetwork_plot_full.html
+++ b/reference/ggnetwork_plot_full.html
@@ -177,6 +177,8 @@ 
Examples

 #> 2,719 associations remain after filtering.
 #> Aggregating results by group_var='hpo_name'
 #> Adding HPO IDs.
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 #> Translating all phenotypes to HPO IDs.
 #> ℹ All local files already up-to-date!
 #> + Returning a vector of phenotypes (same order as input).
diff --git a/reference/merge_results.html b/reference/merge_results.html
index da44aa1..5fe81e6 100644
--- a/reference/merge_results.html
+++ b/reference/merge_results.html
@@ -101,6 +101,8 @@ 
Value

     

     
Examples

     
gene_data <- HPOExplorer::load_phenotype_to_genes()
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 ctd <- MultiEWCE::load_example_ctd()
 list_names <- unique(gene_data$hpo_name)[seq(3)]
 res_files <- ewce_para(ctd = ctd,
diff --git a/reference/plot_ont_lvl.html b/reference/plot_ont_lvl.html
index 76ac3c3..c5cf229 100644
--- a/reference/plot_ont_lvl.html
+++ b/reference/plot_ont_lvl.html
@@ -101,6 +101,8 @@ 
Value

     

     
Examples

     
plts <- plot_ont_lvl()
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 #> Getting absolute ontology level for 10,969 HPO IDs.
 #> ℹ All local files already up-to-date!
 

diff --git a/reference/prioritise_targets.html b/reference/prioritise_targets.html
index 2825ac1..349f8df 100644
--- a/reference/prioritise_targets.html
+++ b/reference/prioritise_targets.html
@@ -425,6 +425,8 @@ 
Examples

 #> Adding term definitions.
 #> ℹ All local files already up-to-date!
 #> Annotating phenos with Disease
+#> Reading cached RDS file: phenotype.hpoa
+#> + Version: v2023-10-09
 #> Adding disease metadata: Definitions, Preferred.Label
 #> Importing Orphanet metadata.
 #> Importing OMIM metadata.
@@ -516,6 +518,12 @@ 
Examples

 #>  - Diseases: 1 
 #>  - Cell types: 1
 #> Annotating phenos with n_diseases
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
+#> Reading cached RDS file: genes_to_phenotype.txt
+#> + Version: v2023-10-09
+#> Reading cached RDS file: phenotype.hpoa
+#> + Version: v2023-10-09
 #> Prioritised targets: step='pheno_ndiseases_threshold' 
 #>  - Rows: 1 
 #>  - Phenotypes: 1 
@@ -534,6 +542,8 @@ 
Examples

 #>  - Diseases: 1 
 #>  - Cell types: 1
 #> Converting phenos to GRanges.
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 #> Loading required namespace: ensembldb
 #> Gathering metadata for 2 unique genes.
 #> Loading required namespace: EnsDb.Hsapiens.v75
@@ -554,6 +564,7 @@ 
Examples

 #> Annotating gene-disease associations with Evidence score
 #> Gathering data from GenCC.
 #> Importing cached file.
+#> + Version: 2023-11-07
 #> Prioritised targets: step='keep_evidence' 
 #>  - Rows: 2 
 #>  - Phenotypes: 1 
@@ -574,6 +585,8 @@ 
Examples

 #>  - Diseases: 1 
 #>  - Cell types: 1 
 #>  - Genes: 2
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 #> Prioritised targets: step='keep_specificity_quantiles' 
 #>  - Rows: 2 
 #>  - Phenotypes: 1 
@@ -587,6 +600,8 @@ 
Examples

 #>  - Cell types: 1 
 #>  - Genes: 2
 #> Annotating gene frequencies.
+#> Reading cached RDS file: genes_to_phenotype.txt
+#> + Version: v2023-10-09
 #> Prioritised targets: step='gene_frequency_threshold' 
 #>  - Rows: 2 
 #>  - Phenotypes: 1 
diff --git a/reference/prioritise_targets_network.html b/reference/prioritise_targets_network.html
index 6de2d35..3b92bb3 100644
--- a/reference/prioritise_targets_network.html
+++ b/reference/prioritise_targets_network.html
@@ -253,7 +253,7 @@ 
Examples

 #> Loading required namespace: tidygraph
 #> Creating network.
 #> Creating plot.
-#> Saving plot ==> /tmp/Rtmp5NzcNQ/file184038df2cf_prioritise_targets_network.html
+#> Saving plot ==> /tmp/RtmpS5wtsl/file71be7315db93_prioritise_targets_network.html
diff --git a/reference/report_plot.html b/reference/report_plot.html index e934ed3..e2e8cde 100644 --- a/reference/report_plot.html +++ b/reference/report_plot.html @@ -173,6 +173,10 @@

Examples

rep_dt <- example_targets$report gp <- report_plot(rep_dt=rep_dt, results=results) #> report_plot:: Preparing data. +#> Reading cached RDS file: phenotype.hpoa +#> + Version: v2023-10-09 +#> Reading cached RDS file: phenotype_to_genes.txt +#> + Version: v2023-10-09 #> Loading required namespace: rvest #> report_plot:: Preparing plot. #> Warning: The `facets` argument of `facet_grid()` is deprecated as of ggplot2 2.2.0. @@ -180,7 +184,7 @@

Examples

#> ℹ The deprecated feature was likely used in the MultiEWCE package. #> Please report the issue at #> <https://github.com/neurogenomics/MultiEWCE/issues>. -#> Saving plot ==> /tmp/Rtmp5NzcNQ/file184054ea42d_report_plot.pdf +#> Saving plot ==> /tmp/RtmpS5wtsl/file71be24c6958c_report_plot.pdf #> Saving 6.67 x 6.67 in image
diff --git a/reference/ttd_check.html b/reference/ttd_check.html index ccee9e5..0074a24 100644 --- a/reference/ttd_check.html +++ b/reference/ttd_check.html @@ -111,6 +111,8 @@

Arguments

Examples

top_targets <- MultiEWCE::example_targets$top_targets
 top_targets <- HPOExplorer::add_genes(top_targets[q<0.05])
+#> Reading cached RDS file: phenotype_to_genes.txt
+#> + Version: v2023-10-09
 res <- ttd_check(top_targets=top_targets)
 #> Loading required namespace: readxl
 #> Retrieving all organisms available in gprofiler.

hpo_id