pkgdown

.Rbuildignore

@@ -3,3 +3,6 @@
 ^LICENSE\.md$
 ^doc$
 ^Meta$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.Rhistory

@@ -1,75 +1,3 @@
-sctSpecies = "human",
-cores = 1,
-MergeResults = TRUE) {
-# remove gene lists that do not have enough valid genes (>= 4)
-list_names <- get_valid_gene_lists(ctd,
-list_names = list_names,
-gene_data = gene_data,
-list_name_column = list_name_column,
-gene_column = gene_column)
-# Create results directory and remove finished gene lists
-if (!file.exists(results_dir)) {
-dir.create(results_dir)
-}
-if (!overwrite_past_analysis) {
-list_names <- get_unfinished_list_names(list_names,results_dir)
-}
-# Run analysis
-ewce_para(list_names = list_names,
-gene_data = phenotype_to_genes,
-list_name_column = "Phenotype",
-gene_column = "Gene",
-results_directory = results_dir,
-ctd_file = ctd,
-background_genes = background,
-bootstrap_reps = reps,
-annotation_Level= annotLevel,
-genes_Species = genelistSpecies,
-ctd_Species = sctSpecies,
-cores = cores)
-# Combine results into a single dataframe
-if (MergeResults) {
-results_final <- merge_results(results_dir = results_dir,
-list_name_column = list_name_column)
-saveRDS(results_final,paste0("results_",Sys.time(),"_",Sys.Date()))
-return(results_final)
-}
-}
-# TEST IT
-test_results <-  gen_results(ctd = ctd,
-gene_data = phenotype_to_genes,
-list_names = Phenotypes,
-background_genes = background,
-list_name_column = "Phenotype",
-gene_column = "Gene",
-results_dir = "results/",
-overwrite_past_analysis = FALSE,
-reps = 10,
-annotLevel = 1,
-genelistSpecies = "human",
-sctSpecies = "human",
-cores = 1,
-MergeResults = TRUE)
-#' Is not analysed?
-#'
-#' Takes a gene list name and checks the output results directory to see if that
-#' gene list has been analysed yet. The ewce_para function outputs the results
-#' for each gene list in to the results directory with name format list_name.rds
-#' @param list_name The name of a gene list e.g. "Phenotypic abnormality"
-#' @param results_dir The path to results directory (with "/" at the end)
-#' @return True or false <bool>
-#' @export
-is_not_analysed <- function(list_name,results_dir) {
-file_path <- paste0(results_dir,list_name,".rds")
-if (file.exists(file_path)){
-return (FALSE)
-} else {
-return (TRUE)
-}
-}
-# TEST IT
-test_results <-  gen_results(ctd = ctd,
-gene_data = phenotype_to_genes,
 list_names = Phenotypes,
 background_genes = background,
 list_name_column = "Phenotype",
@@ -510,3 +438,75 @@ load("data/CTD_DescartesHuman.rda")
 load("tests/testthat/data/CTD_DescartesHuman.rda")
 devtools::test()
 devtools::test()
+phenotype_to_genes = load_phenotype_to_genes("data/phenotype_to_genes.txt")
+library(HPOExplorer)
+phenotype_to_genes = load_phenotype_to_genes("data/phenotype_to_genes.txt")
+phenotype_to_genes = load_phenotype_to_genes("tests/testhat/data/phenotype_to_genes.txt")
+phenotype_to_genes = load_phenotype_to_genes("tests/testthat/data/phenotype_to_genes.txt")
+devtools::load_all()
+?ewce_para
+load("tests/testthat/data/CTD_DescartesHuman.rda")
+Phenos1 = unique(phenotype_to_genes$Phenotype)[1:5]
+Phenos2 = unique(phenotype_to_genes$Phenotype)[1:10]
+results1 <- ewce_para(Phenos1,
+phenotype_to_genes,
+list_name_column = "Phenotype",
+gene_column ="Gene",
+results_directory = "results",
+ctd_file = ctd,
+background_genes = unique(phenotype_to_genes$Gene),
+bootstrap_reps = 10,
+annotation_Level = 1,
+genes_Species = "human",
+ctd_Species = "human",
+cores = 1)
+mkdir("results")
+file.create("results")
+dir.create("results")
+file.create("results")
+dir.create("results")
+results1 <- ewce_para(Phenos1,
+phenotype_to_genes,
+list_name_column = "Phenotype",
+gene_column ="Gene",
+results_directory = "results",
+ctd_file = ctd,
+background_genes = unique(phenotype_to_genes$Gene),
+bootstrap_reps = 10,
+annotation_Level = 1,
+genes_Species = "human",
+ctd_Species = "human",
+cores = 1)
+dir.create(tests/testthat/data/results)
+dir.create("tests/testthat/data/results")
+devtools::test()
+devtools::test()
+devtools::test()
+devtools::test()
+devtools::test()
+devtools::test()
+devtools::test()
+resultsdir = "data/results"
+for (f in list.files(paste0("tests/testthat/",resultsdir))) {
+file.remove(paste0("tests/testthat/",resultsdir,f))
+}
+for (f in list.files(paste0("tests/testthat/",resultsdir))) {
+file.remove(paste0("tests/testthat/",resultsdir,"/",f))
+}
+roxygen2::roxygenise()
+?gen_results
+devtools::test()
+devtools::test()
+devtools::test()
+devtools::test()
+dir.create("testing/test")
+dir.create("testing")
+file.remove("testing")
+dir.remove("testing")
+remove.file("testing")
+file.remove("testing")
+dir.remove("testing")
+devtools::test()
+devtools::check()
+devtools::test()
+devtools::check()

.gitignore

@@ -3,3 +3,4 @@ inst/doc
 /doc/
 /Meta/
 tests/testthat/data/
+

_pkgdown.yml

@@ -0,0 +1,5 @@
+url: ~
+
+template:
+  params:
+    bootswatch: cerulean