Updated README and vignettes

csbg · Jun 11, 2024 · b5574d2 · b5574d2
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diff --git a/R/create_limma_report.R b/R/create_limma_report.R
@@ -52,58 +52,62 @@ create_limma_report <- function(run_limma_splines_result,
   }
   ###
 
-
-  plots <- c(plots, list("Average Difference Conditions"))
-  plots_sizes <- c(plots_sizes, 999)
-
-  header_info <- list(header_name = "Average Difference Conditions")
-  section_headers_info <- c(section_headers_info, list(header_info))
-
-  for (i in seq_along(avrg_diff_conditions)) {
-    element_name <- names(avrg_diff_conditions)[i]
-    top_table <- avrg_diff_conditions[[i]]
+  # length == 0 when there was just one level or no interaction effect
+  if (length(avrg_diff_conditions) > 0) {
 
-    comparison <- remove_prefix(element_name, "avrg_diff_")
-    title <- paste("P-Value Histogram:", comparison)
+    plots <- c(plots, list("Average Difference Conditions"))
+    plots_sizes <- c(plots_sizes, 999)
 
-    p_value_hist <- create_p_value_histogram(top_table = top_table,
-                                             adj_pthresh = adj_pthresh,
-                                             title = title)
+    header_info <- list(header_name = "Average Difference Conditions")
+    section_headers_info <- c(section_headers_info, list(header_info))
 
-    compared_levels <- stringr::str_split(comparison, "_vs_")[[1]]
-
-    volcano_plot <- create_volcano_plot(top_table = top_table,
-                                        adj_pthresh = adj_pthresh,
-                                        compared_levels)
-
-    plots <- c(plots, list(p_value_hist), list(volcano_plot))
-    plots_sizes <- c(plots_sizes, 1, 1.5)
+    for (i in seq_along(avrg_diff_conditions)) {
+      element_name <- names(avrg_diff_conditions)[i]
+      top_table <- avrg_diff_conditions[[i]]
+
+      comparison <- remove_prefix(element_name, "avrg_diff_")
+      title <- paste("P-Value Histogram:", comparison)
+
+      p_value_hist <- create_p_value_histogram(top_table = top_table,
+                                               adj_pthresh = adj_pthresh,
+                                               title = title)
+
+      compared_levels <- stringr::str_split(comparison, "_vs_")[[1]]
+
+      volcano_plot <- create_volcano_plot(top_table = top_table,
+                                          adj_pthresh = adj_pthresh,
+                                          compared_levels)
+
+      plots <- c(plots, list(p_value_hist), list(volcano_plot))
+      plots_sizes <- c(plots_sizes, 1, 1.5)
+    }
   }
-  ###
-
-
-  plots <- c(plots, list("Interaction of Condition and Time"))
-  plots_sizes <- c(plots_sizes, 999)
-
-  header_info <- list(header_name = "Interaction of Condition and Time")
-  section_headers_info <- c(section_headers_info, list(header_info))
+
+  # length == 0 when there was just one level or no interaction effect
+  if (length(interaction_condition_time) > 0) {
 
-  for (i in seq_along(interaction_condition_time)) {
-    element_name <- names(interaction_condition_time)[i]
-    title <- paste(element_name, ": Adj. p-value vs. F-statistic")
-    top_table <- interaction_condition_time[[i]]
-
-    comparison <- remove_prefix(element_name, "time_interaction_")
-    title <- paste("P-Value Histogram:", comparison)
+    plots <- c(plots, list("Interaction of Condition and Time"))
+    plots_sizes <- c(plots_sizes, 999)
 
-    p_value_hist <- create_p_value_histogram(top_table = top_table,
-                                             adj_pthresh = adj_pthresh,
-                                             title = title)
+    header_info <- list(header_name = "Interaction of Condition and Time")
+    section_headers_info <- c(section_headers_info, list(header_info))
 
-    plots <- c(plots, list(p_value_hist))
-    plots_sizes <- c(plots_sizes, 1)
+    for (i in seq_along(interaction_condition_time)) {
+      element_name <- names(interaction_condition_time)[i]
+      title <- paste(element_name, ": Adj. p-value vs. F-statistic")
+      top_table <- interaction_condition_time[[i]]
+
+      comparison <- remove_prefix(element_name, "time_interaction_")
+      title <- paste("P-Value Histogram:", comparison)
+
+      p_value_hist <- create_p_value_histogram(top_table = top_table,
+                                               adj_pthresh = adj_pthresh,
+                                               title = title)
+
+      plots <- c(plots, list(p_value_hist))
+      plots_sizes <- c(plots_sizes, 1)
+    }
   }
-  ###
 
   all_top_tables <- c(time_effect,
                       avrg_diff_conditions,
@@ -269,10 +273,10 @@ shorten_names <- function(name,
 #' \code{\link{plot2base64}}, \code{\link{create_progress_bar}}
 #' 
 build_create_limma_report <- function(header_section, 
-                               plots, 
-                               plots_sizes, 
-                               level_headers_info,
-                               output_file_path = here::here()) {  
+                                      plots, 
+                                      plots_sizes, 
+                                      level_headers_info,
+                                      output_file_path = here::here()) {  
 
   html_content <- paste(header_section, "<!--TOC-->", sep = "\n")
 
@@ -319,13 +323,7 @@ build_create_limma_report <- function(header_section,
         next
       } 
     }
-
-    # Process each plot
-    # plot <- plots[[index]]
-    # plot_size <- plots_sizes[[index]]
-    # img_tag <- plot2base64(plot, plot_size)
-    # html_content <- paste(html_content, img_tag, sep="\n")
-
+
     html_content <- process_plots(plots = plots,
                                   plots_sizes = plots_sizes,
                                   index = index,
@@ -349,6 +347,5 @@ build_create_limma_report <- function(header_section,
     dir.create(dir_path, recursive = TRUE)
   }
 
-  # Write the HTML content to file
   writeLines(html_content, output_file_path)
 }
diff --git a/R/screen_limma_hyperparams.R b/R/screen_limma_hyperparams.R
@@ -60,7 +60,7 @@ screen_limma_hyperparams <- function(datas,
                                      adj_pthresholds = c(0.05),
                                      meta_batch_column = NA,  # batch-effect
                                      meta_batch2_column = NA,
-                                     time_unit = "m",    # For the plot labels
+                                     time_unit = "min",    # For the plot labels
                                      padjust_method = "BH") {
 
   modes <- c()
@@ -104,7 +104,6 @@ screen_limma_hyperparams <- function(datas,
                               spline_test_configs = spline_test_configs,
                               meta_batch_column = meta_batch_column,
                               meta_batch2_column = meta_batch2_column,
-                              # designs,
                               time_unit = time_unit)
 
   timestamp <- format(Sys.time(), "%d_%m_%Y-%H_%M_%S")
@@ -225,7 +224,6 @@ plot_limma_combos_results <- function(top_tables_combos,
                                       spline_test_configs,
                                       meta_batch_column,
                                       meta_batch2_column,
-                                      # designs,
                                       time_unit = time_unit) {
 
   names_extracted <- stringr::str_extract(names(top_tables_combos),
@@ -246,9 +244,7 @@ plot_limma_combos_results <- function(top_tables_combos,
                                    format = "[:bar] :percent")
   pb$tick(0)
 
-  time_unit_labels <- c("s" = "[sec]", "m" = "[min]", "h" = "[hours]", 
-                        "d" = "[days]")
-  time_unit_label <- time_unit_labels[time_unit]
+  time_unit_label <- paste0("[", time_unit, "]")
 
   if (!is.na(meta_batch_column)) {
 

diff --git a/R/utils_input_validation.R b/R/utils_input_validation.R
@@ -790,7 +790,8 @@ InputControl <- R6::R6Class("InputControl",
       if (!is.character(time_unit) ||
            length(time_unit) != 1 ||
            nchar(time_unit) > 15) {
-        stop(paste0("time_unit must be a single character with < 16 letters"),
+        stop(paste0("time_unit must be a single character vector with", 
+                    "< 16 letters"),
              call. = FALSE)
       }
     },

diff --git a/README.Rmd b/README.Rmd
@@ -13,7 +13,7 @@ knitr::opts_chunk$set(
 
 # SplineOmics <img src="man/figures/hex_logo.png" style="float: right; width: 150px; margin-left: 300px; vertical-align: middle;"/>
 
-![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg) ![Maintained? Yes](https://img.shields.io/badge/Maintained%3F-yes-brightgreen.svg)
+![Version](https://img.shields.io/badge/version-0.1.0-blue) ![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg) ![Maintained? Yes](https://img.shields.io/badge/Maintained%3F-yes-brightgreen.svg) ![R CMD Check](https://img.shields.io/badge/R%20CMD%20check-passed-brightgreen) [![Docker](https://img.shields.io/badge/docker-pull-blue)](https://ghcr.io/thomas-rauter/splineomics:0.1.0)
 
 The R package `SplineOmics` gets the significant features (hits) of time-series omics data by using splines and limma for hypothesis testing and clusters the hits based on the spline shape, showing all results in HTML reports.
 
@@ -28,8 +28,10 @@ The R package `SplineOmics` gets the significant features (hits) of time-series
 -   [📦 Dependencies](#-dependencies)
 -   [❓ Getting Help](#-getting-help)
 -   [🤝 Contributing](#-contributing)
+-   [💬 Feedback](#-feedback)
 -   [📜 License](#-license)
 -   [🎓 Citation](#-citation)
+-   [🌟 Contributors](#-contributors)
 
 ## 📘 Introduction {#introduction}
 
@@ -153,7 +155,7 @@ docker run -it -d \
     -v $(pwd)/output:/home/rstudio/output \
     -p 8888:8787 \
     -e PASSWORD=password \
-    --name splineomics_container \
+    --name splineomics \
     thomasrauter/splineomics:0.1.0
 ```
 
@@ -162,13 +164,13 @@ Once the container is running, open a web browser and navigate to <http://localh
 Stop the container:
 
 ``` sh
-docker stop splineomics_container
+docker stop splineomics
 ```
 
 Start the container again:
 
 ``` sh
-docker start splineomics_container
+docker start splineomics
 ```
 
 ### Inspect Docker container installations
@@ -245,6 +247,16 @@ Please adhere to our [Code of Conduct](CODE_OF_CONDUCT.md) in all your interacti
 
 Thank you for considering contributing to `SplineOmics`. Your efforts are what make the open-source community a fantastic place to learn, inspire, and create.
 
+## 💬 Feedback
+
+We appreciate your feedback! Besides raising issues, you can provide feedback in the following ways:
+
+-   **Direct Email**: Send your feedback directly to [Thomas Rauter](mailto:thomas.rauter@plus.ac.at).
+
+-   **Anonymous Feedback**: Use [this Google Form](https://forms.gle/jocMXSxLf3GrGBdT9) to provide anonymous feedback by answering questions.
+
+Your feedback helps us improve the project and address any issues you may encounter.
+
 ## 📜 License {#license}
 
 This package is licensed under the MIT License: [LICENSE](./LICENSE)
@@ -256,3 +268,10 @@ This package is licensed under the MIT License: [LICENSE](./LICENSE)
 The `SplineOmics` package is currently not published in a peer-reviewed scientific journal or similar outlet. However, if this package helped you in your work, consider citing this GitHub repository.
 
 Also, if you like the package, consider giving the GitHub repository a star. Your support helps us in the continued development and improvement of `SplineOmics`. Thank you for using our package!
+
+## 🌟 Contributors
+
+-   [Thomas-Rauter](https://github.com/Thomas-Rauter) - 🚀 Wrote the package, developed the approach together with VSchaepertoens under guidance from nfortelny.
+-   [nfortelny](https://github.com/nfortelny) - 🧠 Principal Investigator, provided guidance and support
+-   [skafdasschaf](https://github.com/skafdasschaf) - 🔧 Helped reviewing code, delivered improvement suggestions
+-   [VSchaepertoens](https://github.com/VSchaepertoens) - ✨ Developed parts of the functions and the overall approach together with Thomas-Rauter
diff --git a/README.md b/README.md
@@ -1,9 +1,12 @@
 
 # SplineOmics <img src="man/figures/hex_logo.png" style="float: right; width: 150px; margin-left: 300px; vertical-align: middle;"/>
 
-![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)
-![Maintained?
-Yes](https://img.shields.io/badge/Maintained%3F-yes-brightgreen.svg)
+![Version](https://img.shields.io/badge/version-0.1.0-blue) ![License:
+MIT](https://img.shields.io/badge/License-MIT-yellow.svg) ![Maintained?
+Yes](https://img.shields.io/badge/Maintained%3F-yes-brightgreen.svg) ![R
+CMD
+Check](https://img.shields.io/badge/R%20CMD%20check-passed-brightgreen)
+[![Docker](https://img.shields.io/badge/docker-pull-blue)](https://ghcr.io/thomas-rauter/splineomics:0.1.0)
 
 The R package `SplineOmics` gets the significant features (hits) of
 time-series omics data by using splines and limma for hypothesis testing
@@ -21,8 +24,10 @@ HTML reports.
 - [📦 Dependencies](#-dependencies)
 - [❓ Getting Help](#-getting-help)
 - [🤝 Contributing](#-contributing)
+- [💬 Feedback](#-feedback)
 - [📜 License](#-license)
 - [🎓 Citation](#-citation)
+- [🌟 Contributors](#-contributors)
 
 ## 📘 Introduction
 
@@ -188,7 +193,7 @@ docker run -it -d \
     -v $(pwd)/output:/home/rstudio/output \
     -p 8888:8787 \
     -e PASSWORD=password \
-    --name splineomics_container \
+    --name splineomics \
     thomasrauter/splineomics:0.1.0
 ```
 
@@ -201,13 +206,13 @@ the `SplineOmics` package is installed.
 Stop the container:
 
 ``` sh
-docker stop splineomics_container
+docker stop splineomics
 ```
 
 Start the container again:
 
 ``` sh
-docker start splineomics_container
+docker start splineomics
 ```
 
 ### Inspect Docker container installations
@@ -325,6 +330,21 @@ Thank you for considering contributing to `SplineOmics`. Your efforts
 are what make the open-source community a fantastic place to learn,
 inspire, and create.
 
+## 💬 Feedback
+
+We appreciate your feedback! Besides raising issues, you can provide
+feedback in the following ways:
+
+- **Direct Email**: Send your feedback directly to [Thomas
+  Rauter](mailto:thomas.rauter@plus.ac.at).
+
+- **Anonymous Feedback**: Use [this Google
+  Form](https://forms.gle/jocMXSxLf3GrGBdT9) to provide anonymous
+  feedback by answering questions.
+
+Your feedback helps us improve the project and address any issues you
+may encounter.
+
 ## 📜 License
 
 This package is licensed under the MIT License: [LICENSE](./LICENSE)
@@ -340,3 +360,16 @@ you in your work, consider citing this GitHub repository.
 Also, if you like the package, consider giving the GitHub repository a
 star. Your support helps us in the continued development and improvement
 of `SplineOmics`. Thank you for using our package!
+
+## 🌟 Contributors
+
+- [Thomas-Rauter](https://github.com/Thomas-Rauter) - 🚀 Wrote the
+  package, developed the approach together with VSchaepertoens under
+  guidance from nfortelny.
+- [nfortelny](https://github.com/nfortelny) - 🧠 Principal Investigator,
+  provided guidance and support
+- [skafdasschaf](https://github.com/skafdasschaf) - 🔧 Helped reviewing
+  code, delivered improvement suggestions
+- [VSchaepertoens](https://github.com/VSchaepertoens) - ✨ Developed
+  parts of the functions and the overall approach together with
+  Thomas-Rauter