resolved merge conflicts, greatly updated README file, made final Doc…

…kerfile for Docker image of package
csbg · Jun 11, 2024 · 9ce0430 · 9ce0430
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diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,12 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Rauter"
+  given-names: "Thomas"
+  orcid: "https://orcid.org/0000-0000-0000-0000"
+title: "SplineOmics: A Tool for Time-Series Omics Data Analysis"
+version: 0.1.0
+doi: 10.5281/zenodo.1234567
+date-released: 2024-06-11
+url: "https://github.com/csbg/SplineOmics"
+
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,12 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 export(cluster_hits)
+export(create_gsea_report)
 export(download_enrichr_databases)
 export(explore_data)
 export(extract_data)
-export(limma_hyperparams_screen)
-export(run_gsea)
 export(run_limma_splines)
+export(screen_limma_hyperparams)
 importFrom(ComplexHeatmap,Heatmap)
 importFrom(ComplexHeatmap,draw)
 importFrom(ComplexHeatmap,ht_opt)

diff --git a/R/run_gsea.R → R/create_gsea_report.R b/R/run_gsea.R → R/create_gsea_report.R
@@ -1,4 +1,4 @@
-# This function uses the function run_gsea to run 
+# This function uses the function create_gsea_report to run 
 
 
 
@@ -29,22 +29,22 @@
 #' 
 #' @export
 #' 
-run_gsea <- function(levels_clustered_hits,
-                     genes,
-                     databases,
-                     report_info,
-                     params = NA,
-                     plot_titles = NA,
-                     background = NULL,
-                     report_dir = here::here()) {
+create_gsea_report <- function(levels_clustered_hits,
+                               genes,
+                               databases,
+                               report_info,
+                               params = NA,
+                               plot_titles = NA,
+                               background = NULL,
+                               report_dir = here::here()) {
 
   # Check report_info and report_dir
   args <- lapply(as.list(match.call()[-1]), eval, parent.frame())
   input_control <- InputControl$new(args)
   input_control$auto_validate()
 
   # Control the test not covered by the InputControl class
-  control_inputs_gsea_report(levels_clustered_hits = levels_clustered_hits,
+  control_inputs_create_gsea_report(levels_clustered_hits = levels_clustered_hits,
                              genes = genes,
                              databases = databases,
                              params = params,
@@ -81,8 +81,8 @@ run_gsea <- function(levels_clustered_hits,
                        plots_sizes = plots_sizes, 
                        report_info = report_info,
                        level_headers_info = level_headers_info,
-                       report_type = "gsea_report",
-                       filename = "gsea_report",
+                       report_type = "create_gsea_report",
+                       filename = "create_gsea_report",
                        report_dir = report_dir)
 
   return(plots)
@@ -108,7 +108,7 @@ run_gsea <- function(levels_clustered_hits,
 #' matching `levels_clustered_hits`.
 #' @param background A character vector of background genes or NULL.
 #'
-control_inputs_gsea_report <- function(levels_clustered_hits,
+control_inputs_create_gsea_report <- function(levels_clustered_hits,
                                        genes,
                                        databases,
                                        params,
@@ -149,13 +149,13 @@ control_inputs_gsea_report <- function(levels_clustered_hits,
 #' @description
 #' This function manages the GSEA analysis for a specific level. It extracts
 #' genes associated with the clustered hits, removes rows with `NA` values,
-#' and runs the GSEA analysis using the `run_gsea` function.
+#' and runs the GSEA analysis using the `create_gsea_report` function.
 #'
 #' @param clustered_hits A dataframe containing the clustered hits for a 
 #' specific level. It must include a column named `feature` to extract genes.
 #' @param level_name A character string representing the name of the level.
 #'
-#' @return The result of the `run_gsea` function, which typically includes 
+#' @return The result of the `create_gsea_report` function, which typically includes 
 #' various plots and enrichment results.
 #'
 manage_gsea_level <- function(clustered_hits,
@@ -167,7 +167,7 @@ manage_gsea_level <- function(clustered_hits,
 
   message(paste("\n\n Running clusterProfiler for the level:", level_name))
 
-  result <- run_gsea_level(clustered_genes = clustered_hits,
+  result <- create_gsea_report_level(clustered_genes = clustered_hits,
                            databases = databases,
                            params = clusterProfiler_params,
                            plot_title = level_name)
@@ -246,7 +246,7 @@ process_result <- function(level_result,
 #' processing individual plots. The TOC is inserted into the HTML content, 
 #' which is then finalized and written to the specified output file.
 #' 
-build_gsea_report <- function(header_section,
+build_create_gsea_report <- function(header_section,
                               plots,
                               plots_sizes,
                               level_headers_info,
@@ -541,7 +541,7 @@ check_params <- function(params) {
 #'
 #' @importFrom clusterProfiler enricher
 #'
-run_gsea_level <- function(clustered_genes,
+create_gsea_report_level <- function(clustered_genes,
                            databases,
                            params = NA,
                            plot_title = "",
@@ -726,7 +726,7 @@ generate_section_content <- function(section_info,
   base64_df <- sprintf('<a href="%s" download="count2small_results.xlsx">
                     <button>Download count2small_results.xlsx</button></a>', 
                        encode_df_to_base64(section_info$raw_enrich_results,
-                                           "gsea_report"))
+                                           "create_gsea_report"))
 
   html_content <- paste(html_content, 
                         section_header, 

diff --git a/R/limma_report.R → R/create_limma_report.R b/R/limma_report.R → R/create_limma_report.R
@@ -1,17 +1,17 @@
-# The function limma_report() takes the top_tables of the three different 
+# The function create_limma_report() takes the top_tables of the three different 
 # categories (within level time diff, between level average diff, and 
 # between level average and time diff) and makes histogram and vulcano plots 
 # and places them into a nice HTML report.
 
 
 
-# Exported function: limma_report() --------------------------------------------
+# Exported function: create_limma_report() --------------------------------------------
 
 
-limma_report <- function(run_limma_splines_result,
-                         report_info,
-                         adj_pthresh = 0.05,
-                         report_dir = here::here()) {
+create_limma_report <- function(run_limma_splines_result,
+                                report_info,
+                                adj_pthresh = 0.05,
+                                report_dir = here::here()) {
 
   # Control the function arguments
   args <- lapply(as.list(match.call()[-1]), eval, parent.frame())
@@ -120,8 +120,8 @@ limma_report <- function(run_limma_splines_result,
                        report_info,
                        data = all_top_tables,
                        level_headers_info = section_headers_info,
-                       report_type = "limma_report",
-                       filename = "limma_report",
+                       report_type = "create_limma_report",
+                       filename = "create_limma_report",
                        report_dir = report_dir)
 
   return(plots)
@@ -268,7 +268,7 @@ shorten_names <- function(name,
 #' @seealso
 #' \code{\link{plot2base64}}, \code{\link{create_progress_bar}}
 #' 
-build_limma_report <- function(header_section, 
+build_create_limma_report <- function(header_section, 
                                plots, 
                                plots_sizes, 
                                level_headers_info,

diff --git a/R/limma_hyperparams_screen.R → R/screen_limma_hyperparams.R b/R/limma_hyperparams_screen.R → R/screen_limma_hyperparams.R
@@ -1,6 +1,6 @@
-#' limma_hyperparams_screen.R contains the exported package function 
-#' limma_hyperparams_screen  and all the functions that make up the 
-#' functionality of limma_hyperparams_screen. limma_hyperparams_screen runs the 
+#' screen_limma_hyperparams.R contains the exported package function 
+#' screen_limma_hyperparams  and all the functions that make up the 
+#' functionality of screen_limma_hyperparams. screen_limma_hyperparams runs the 
 #' other package function, run_limma_splines, for a time series omics dataset,
 #' for different hyperparameters. Such are for example degree of freedom of the
 #' spline, type of spline, limma design formula, and different versions of the 
@@ -9,7 +9,7 @@
 #' and structured manner. Therefore, this function streamlines that process.
 
 
-# Exported function: limma_hyperparams_screen() --------------------------------
+# Exported function: screen_limma_hyperparams() --------------------------------
 
 
 #' Limma Hyperparameters Screening
@@ -49,7 +49,7 @@
 #'
 #' @export
 #'
-limma_hyperparams_screen <- function(datas, 
+screen_limma_hyperparams <- function(datas, 
                                      datas_descr,
                                      metas, 
                                      designs, 
@@ -1016,7 +1016,7 @@ process_combo_pair <- function(combo_pair,
   generate_report_html(plots = plots, 
                        plots_sizes = plots_len, 
                        report_info = report_info,
-                       report_type = "limma_hyperparams_screen",
+                       report_type = "screen_limma_hyperparams",
                        filename = combo_pair_name,
                        timestamp = timestamp,
                        report_dir = report_dir, )

diff --git a/R/utils_report_generation.R b/R/utils_report_generation.R
@@ -22,7 +22,7 @@
 #' @param meta A dataframe, containing metadata that should
 #'             be directly embedded in the HTML report for downloading.
 #' @param report_type A character string specifying the report type 
-#'                    ('limma_hyperparams_screen' or 'cluster_hits').
+#'                    ('screen_limma_hyperparams' or 'cluster_hits').
 #' @param mode A character string specifying the mode 
 #'            ('isolated' or 'integrated').
 #' @param filename A character string specifying the filename for the report.
@@ -60,18 +60,18 @@ generate_report_html <- function(plots,
     } else {
       title <- "explore batch-corrected data"
     }
-  } else if (report_type == "limma_hyperparams_screen") {
+  } else if (report_type == "screen_limma_hyperparams") {
     title <- paste("hyperparams screen |", filename)
-  } else if (report_type == "limma_report") {
+  } else if (report_type == "create_limma_report") {
     title <- "limma report"
   } else if (report_type == "cluster_hits") {                         
     title <- "clustered hits | within level"
-  } else if (report_type == "gsea_report") {                         
+  } else if (report_type == "create_gsea_report") {                         
     title <- "gsea"
 
   } else {
-    stop(paste("report_type must be explore_hits, limma_hyperparams_screen,", 
-               "limma_report, or cluster_hits"),
+    stop(paste("report_type must be explore_hits, screen_limma_hyperparams,", 
+               "create_limma_report, or cluster_hits"),
          call. = FALSE)
   }
 
@@ -103,7 +103,7 @@ generate_report_html <- function(plots,
 
     if (field == "data" && !any(is.na(data)))  {
 
-      if (report_type == "limma_report") {
+      if (report_type == "create_limma_report") {
         base64_df <- sprintf('<a href="%s" download="top_tables.xlsx">
                             <button>Download top_tables.xlsx</button></a>', 
                             encode_df_to_base64(data))
@@ -138,7 +138,7 @@ generate_report_html <- function(plots,
   # Close the table
   header_section <- paste(header_section, "</table>", sep = "\n")
 
-  if (report_type == "gsea_report") {
+  if (report_type == "create_gsea_report") {
     databases_text <- paste(report_info$databases, collapse = ", ")
     header_section <- paste(header_section, 
                             "<p style='font-size: 20px;'>Databases used: ", 
@@ -161,24 +161,24 @@ generate_report_html <- function(plots,
                               plots_sizes = plots_sizes, 
                               output_file_path = output_file_path)
 
-  } else if (report_type == "limma_hyperparams_screen") {
+  } else if (report_type == "screen_limma_hyperparams") {
 
     build_hyperparams_screen_report(header_section = header_section, 
                                     plots = plots, 
                                     plots_sizes = plots_sizes, 
                                     output_file_path = output_file_path)
 
-  } else if (report_type == "limma_report") {
+  } else if (report_type == "create_limma_report") {
 
-    build_limma_report(header_section = header_section,
+    build_create_limma_report(header_section = header_section,
                        plots = plots,
                        plots_sizes = plots_sizes,
                        level_headers_info = level_headers_info,
                        output_file_path = output_file_path)
 
-  } else if (report_type == "gsea_report") {
+  } else if (report_type == "create_gsea_report") {
 
-    build_gsea_report(header_section = header_section,
+    build_create_gsea_report(header_section = header_section,
                       plots = plots,
                       plots_sizes = plots_sizes,
                       level_headers_info = level_headers_info,
@@ -306,7 +306,7 @@ encode_df_to_base64 <- function(df,
     # Convert list of dataframes to Excel with multiple sheets
 
     if (!is.na(report_type)) {
-      if (report_type == "gsea_report") {
+      if (report_type == "create_gsea_report") {
         all_names <- names(df)
         sheet_names <- sapply(all_names, extract_and_combine)
       }