R/example_data.R

In CRI-iAtlas/iatlas.modules: iAatlas Modules

utils::globalVariables("iris")

# Example Iris Data ----------------------------------------------------------

example_iris_data <- function(.feature = NULL, .feature_class = NULL){
  tbl <- iris %>%
    dplyr::as_tibble() %>%
    dplyr::rename("group_name" = "Species") %>%
    dplyr::mutate(
      "sample_name" = as.character(1:dplyr::n())
    ) %>%
    tidyr::pivot_longer(
      !c("group_name", "sample_name"),
      names_to = "feature_name",
      values_to = "feature_value"
    ) %>%
    dplyr::inner_join(
      dplyr::tribble(
        ~feature_name,  ~feature_class,
        "Sepal.Length", "Length",
        "Sepal.Width",  "Width",
        "Petal.Length", "Length",
        "Petal.Width",  "Width",
      ),
      by = "feature_name"
    )


  if(!is.null(.feature)){
    tbl <- dplyr::filter(tbl, .data$feature_name == .feature)
  }

  if(!is.null(.feature_class)){
    tbl <- dplyr::filter(tbl, .data$feature_class == .feature_class)
  }

  dplyr::select(
    tbl,
    "sample_name",
    "feature_name",
    "group_name",
    "feature_value"
  )
}

example_iris_data_one_dataset <- function(.feature = NULL, .feature_class = NULL){
  example_iris_data(.feature, .feature_class) %>%
    dplyr::mutate("dataset_name" = "Iris")
}

example_iris_data_two_datasets <- function(.feature = NULL, .feature_class = NULL){
  example_iris_data(.feature, .feature_class) %>%
    dplyr::mutate("dataset_name" = dplyr::if_else(
      as.integer(.data$sample_name) %% 2 == 0,
      "Iris2",
      "Iris1"
    ))
}

example_iris_data_missing_column <- function(.feature = NULL, .feature_class = NULL){
  dplyr::select(example_iris_data_one_dataset(), -"sample_name")
}

example_heatmap_iris_data <- function(){
  dplyr::inner_join(

    example_iris_data_one_dataset() %>%
      dplyr::mutate(
        "feature_display" = stringr::str_replace(.data$feature_name, "\\.", " ")
      ) %>%
      dplyr::select(-"feature_name"),

    example_iris_data() %>%
      dplyr::mutate(
        "response_display" = stringr::str_replace(.data$feature_name, "\\.", " ")
      ) %>%
      dplyr::filter(.data$response_display == "Sepal Width") %>%
      dplyr::select("sample_name", "response_display", "response_value" ="feature_value"),

    by = "sample_name"
  )
}

example_iris_data_feature_data <- function(){
  dplyr::tribble(
    ~feature_name,  ~feature_display, ~Class1,  ~Class2, ~feature_order,
    "Sepal.Length", "Sepal Length",   "Length", "Sepal", 1,
    "Sepal.Width",  "Sepal Width",    "Width",  "Sepal", 2,
    "Petal.Length", "Petal Length",   "Length", "Petal", 3,
    "Petal.Width",  "Petal Width",    "Width",  "Petal", 4
  )
}

example_iris_data_features_1_class <- function(){
  example_iris_data_feature_data() %>%
    dplyr::select(
      "feature_name",
      "feature_display",
      "feature_class" = "Class1",
      "feature_order"
    )
}

example_iris_data_feature_data_no_class <- function(){
  example_iris_data_feature_data() %>%
    dplyr::select("feature_name", "feature_display")
}

example_distributions_iris_data_feature_data_2_classes <- function(){
  example_iris_data_feature_data() %>%
    dplyr::select(-"feature_order")
}

example_distributions_iris_data_feature_data_1_class <- function(){
  example_iris_data_feature_data() %>%
    dplyr::select(-c("feature_order", "Class2"))
}

example_distributions_iris_data_feature_data_missing_column <- function(){
  example_iris_data_feature_data() %>%
    dplyr::select("feature_name", "Class1")
}

example_distributions_iris_data_feature_data_duplicated_feature <- function(){
  example_distributions_iris_data_feature_data_1_class() %>%
    tibble::add_row(
      "feature_name" = "Sepal.Length",
      "feature_display" = "Sepal Width",
      "Class1" = "Length"
    )
}

example_iris_data_groups <- function(){
  dplyr::tribble(
    ~group_name,  ~group_display, ~group_color, ~group_description,
    "setosa",     "Setosa",       "#FF0000",    "Iris Species: Setosa",
    "versicolor", "Versicolor",   "#0000FF",    "Iris Species: Versicolor",
    "virginica",  "Virginica",    "#FFFF00",    "Iris Species: Virginica",
  )
}

example_iris_data_groups2 <- function(){
  dplyr::tribble(
    ~group_name,  ~group_display,
    "setosa",     "Setosa",
    "versicolor", "Versicolor",
    "virginica",  "Virginica",
  )
}

example_iris_data_groups_missing_column <- function(){
  dplyr::tribble(
    ~group_name,  ~group_display, ~group_color, ~group_description,
    "setosa",     "Setosa",       "#FF0000",    "Iris Species: Setosa",
    "versicolor", "Versicolor",   "#0000FF",    "Iris Species: Versicolor",
    "virginica",  "Virginica",    "#FFFF00",    "Iris Species: Virginica",
  )
}

example_scatterplot_iris_data_4_features <- function(){
  tbl <- iris %>%
    dplyr::as_tibble() %>%
    dplyr::mutate("sample_name" = as.character(1:dplyr::n())) %>%
    dplyr::rename("group_display" = "Species")
}

example_scatterplot_iris_data_3_features <- function(){
  tbl <- example_scatterplot_iris_data_4_features() %>%
    dplyr::select("sample_name", "group_display", "Sepal.Length", "Sepal.Width", "Petal.Length")
}

example_scatterplot_iris_data_2_features <- function(){
  tbl <- example_scatterplot_iris_data_4_features() %>%
    dplyr::select("sample_name", "group_display", "Sepal.Length", "Sepal.Width")
}