updated testing and passing checks

MoseleyBioinformaticsLab · Oct 30, 2024 · 9e757df · 9e757df
1 parent f60bc7c
commit 9e757df
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Showing 86 changed files with 96 additions and 343 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -4,11 +4,6 @@
 ^\.Rproj\.user$
 ^\.travis\.yml$
 ^\.push_gh_pages\.sh$
-tests.R
-test_data_gen.R
-test_data.RData
-test_table_data.rds
-test_combine_filter.rda
 ^\.github\workflows\.yml$
 ^\.github$
 ^executable_related$
@@ -27,3 +22,4 @@ test_combine_filter.rda
 ^doc$
 ^docs$
 ^_pkgdown\.yml$
+^examples_test_data$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: categoryCompare2
-Version: 0.100.25
+Version: 0.100.26
 Title: Meta-Analysis of High-Throughput Experiments Using Feature
         Annotations
 Authors@R: c(
@@ -18,7 +18,7 @@ Depends: R (>= 3.5.0)
 Suggests: knitr, markdown, estrogen, org.Hs.eg.db, hgu95av2.db, limma,
         affy, genefilter, testthat (>= 3.0.0), visNetwork, Cairo,
         DiagrammeR, KEGGREST, docopt (>= 0.7.0), RCy3, hgu95av2cdf,
-        rmarkdown, fgsea
+        rmarkdown, fgsea, data.table, withr
 Imports: Biobase, methods, AnnotationDbi, colorspace, graph, igraph,
         jsonlite, base64enc, dplyr, purrr, rlang, GO.db, stats
 LazyLoad: yes

diff --git a/R/gsea.R b/R/gsea.R
@@ -18,6 +18,7 @@ setClass("gsea_features",
 #' @param min_features the minimum number of features for an annotation (default = 15)
 #' @param max_features the maximum number of features for an annotation (default = 500)
 #' @param return_type  what type of object should be returned? ("cc2" or "fgsea")
+#' @param ... other `fgsea` options
 #' 
 #' @details The runtime is dependent on the maximum size of the provided annotation,
 #'   so the authors of `fgsea` recommend a maximum size of 500. In addition, to calculate
@@ -82,6 +83,9 @@ gsea_feature_enrichment = function(gsea_features,
 #' @return data.table
 enriched_to_fgsea = function(in_enriched)
 {
+  if (!requireNamespace("data.table", quietly = TRUE)) {
+    stop("data.table must be installed!")
+  }
   ranks = in_enriched@ranks
   results = data.table::as.data.table(in_enriched@statistics@statistic_data)
   rename_list = c(pval = "p", padj = "padjust", log2err = "log2err", ES = "es", NES = "nes", size = "size", leadingEdge = "leading_edge")

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/command_line_interface.html b/docs/articles/command_line_interface.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/v2_guide.html b/docs/articles/v2_guide.html
diff --git a/docs/articles/v2_visnetwork_guide.html b/docs/articles/v2_visnetwork_guide.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   command_line_interface: command_line_interface.html
   v2_guide: v2_guide.html
   v2_visnetwork_guide: v2_visnetwork_guide.html
-last_built: 2024-10-30T17:56Z
+last_built: 2024-10-30T18:58Z
 urls:
   reference: https://moseleybioinformaticslab.github.io/categoryCompare2/reference
   article: https://moseleybioinformaticslab.github.io/categoryCompare2/articles
diff --git a/docs/reference/add_data_to_graph.html b/docs/reference/add_data_to_graph.html
diff --git a/docs/reference/add_tooltip.html b/docs/reference/add_tooltip.html
diff --git a/docs/reference/annotation.html b/docs/reference/annotation.html
diff --git a/docs/reference/annotation_2_json.html b/docs/reference/annotation_2_json.html
diff --git a/docs/reference/annotation_combinations.html b/docs/reference/annotation_combinations.html
diff --git a/docs/reference/annotation_gene_table.html b/docs/reference/annotation_gene_table.html
diff --git a/docs/reference/assign_colors.html b/docs/reference/assign_colors.html
diff --git a/docs/reference/assign_communities.html b/docs/reference/assign_communities.html
diff --git a/docs/reference/binomial_basic.html b/docs/reference/binomial_basic.html
diff --git a/docs/reference/binomial_feature_enrichment.html b/docs/reference/binomial_feature_enrichment.html
diff --git a/docs/reference/binomial_features-class.html b/docs/reference/binomial_features-class.html
diff --git a/docs/reference/binomial_result-class.html b/docs/reference/binomial_result-class.html
diff --git a/docs/reference/categoryCompare2.html b/docs/reference/categoryCompare2.html
diff --git a/docs/reference/cc_graph.html b/docs/reference/cc_graph.html
diff --git a/docs/reference/combine_annotation_features.html b/docs/reference/combine_annotation_features.html
diff --git a/docs/reference/combine_annotations.html b/docs/reference/combine_annotations.html
diff --git a/docs/reference/combine_enrichments.html b/docs/reference/combine_enrichments.html
diff --git a/docs/reference/combine_text.html b/docs/reference/combine_text.html
diff --git a/docs/reference/combined_coefficient.html b/docs/reference/combined_coefficient.html
diff --git a/docs/reference/combined_enrichment.html b/docs/reference/combined_enrichment.html
diff --git a/docs/reference/combined_significant_calls.html b/docs/reference/combined_significant_calls.html