R/plot-statistics-interactive.R
In kueckelj/confuns: Convenience Functions
Defines functions
plot_categorical_statistics_shiny
plot_descriptive_statistics_shiny
moduleCategoricalStatisticsPlotServer
moduleCategoricalStatisticsPlotUI
moduleDescriptiveStatisticsPlotServer
moduleDescriptiveStatisticsPlotUI
plot_statistics_interactive
Documented in
plot_categorical_statistics_shiny
plot_descriptive_statistics_shiny
plot_statistics_interactive
#' @title Opens interactive application
#'
#' @inherit df params
#'
#' @export
plot_statistics_interactive <- function(df, n.across.subset = 10){
shiny::runApp(
shiny::shinyApp(
ui = function(){
shinydashboard::dashboardPage(
header = shinydashboard::dashboardHeader(title = "Descriptive Statistics"),
sidebar = shinydashboard::dashboardSidebar(
collapsed = TRUE,
shinydashboard::sidebarMenu(
shinydashboard::menuItem(
text = "Descriptive Statistisc",
tabName = "descr_statistics",
selected = TRUE
)
)
),
body = shinydashboard::dashboardBody(
shinybusy::add_busy_spinner(spin = "cube-grid", margins = c(0, 10), color = "red"),
shinydashboard::tabItems(
shinydashboard::tabItem(tabName = "descr_statistics",
shiny::fluidRow(
moduleDescriptiveStatisticsPlotUI(id = "descr_stat"),
moduleCategoricalStatisticsPlotUI(id = "categ_stat")
)
)
)
)
)
},
server = function(input, output, session){
# shiny helper
shinyhelper::observe_helpers()
moduleDescriptiveStatisticsPlotServer(id = "descr_stat",
df = df,
n.across.subset = n.across.subset)
moduleCategoricalStatisticsPlotServer(id = "categ_stat",
df = df,
n.across.subset = n.across.subset)
}
)
)
}
# Modules -----------------------------------------------------------------
# descriptive
moduleDescriptiveStatisticsPlotUI <- function(id, module_width = 6, module_headline = "Descriptive Statistics"){
ns <- shiny::NS(id)
shiny::tagList(
shiny::column(width = module_width,
shiny::wellPanel(
shiny::fluidRow(
shiny::column(width = 12,
shiny::h4(shiny::strong(module_headline)),
shiny::plotOutput(outputId = ns("module_plot")),
html_breaks(1),
plot_and_save(ns = ns),
html_breaks(1),
shiny::fluidRow(
hs(4,shiny::uiOutput(outputId = ns("change_order")))
),
html_breaks(2),
shiny::fluidRow(
hs(4,shiny::uiOutput(outputId = ns("across"))),
hs(4,shiny::uiOutput(outputId = ns("across.subset"))),
hs(4,shiny::uiOutput(outputId = ns("variables"))),
),
shiny::fluidRow(
hs(4,shiny::uiOutput(outputId = ns("plot.type"))),
hs(4,shiny::uiOutput(outputId = ns("clrp")))
),
shiny::uiOutput(outputId = ns("point_add_on")),
shiny::uiOutput(outputId = ns("statistics"))
)
)
)
)
)
}
moduleDescriptiveStatisticsPlotServer <- function(id, df, n.across.subset = 10){
shiny::moduleServer(
id = id,
module = function(input, output, session){
# Reactive values ---------------------------------------------------------
input_df <- shiny::reactive({ df })
# -----
# Render UIs --------------------------------------------------------------
output$variables <- shiny::renderUI({
ns <- session$ns
num_variables <-
dplyr::select_if(input_df(), .predicate = base::is.numeric) %>%
base::colnames()
include_variables_picker_input(ns = ns,
id = "variables",
choices = num_variables,
selected = num_variables[1])
})
output$across <- shiny::renderUI({
ns <- session$ns
across_groups <-
across_options(df, n.across.subset = n.across.subset)
shiny::req(across_groups)
across_picker_input(ns = ns, choices = across_groups)
})
output$across.subset <- shiny::renderUI({
ns <- session$ns
shiny::req(input$across)
across_subset_options <-
across_subset_options(df = input_df(), across = input$across)
across_subset_picker_input(ns = ns,
id = "across.subset",
choices = across_subset_options,
selected = across_subset_options)
})
output$clrp <- shiny::renderUI({
ns <- session$ns
colorpanel_picker_input(ns = ns, id = "clrp")
})
output$change_order <- shiny::renderUI({
ns <- session$ns
shiny::req(input$across.subset)
change_order_input(ns = ns, items = input$across.subset)
})
output$plot.type <- shiny::renderUI({
ns <- session$ns
shinyWidgets::pickerInput(inputId = ns("plot.type"),
label = "Plottype:",
choices = pretty_plottypes,
selected = "boxplot",
multiple = FALSE)
})
# --- Point add on
output$point_add_on <- shiny::renderUI({
ns <- session$ns
shiny::req(input$plot.type %in% testable_plottypes)
across_groups <-
across_options(df, n.across.subset = n.across.subset)
shiny::tagList(
shiny::fluidRow(
hs(2,
shinyWidgets::radioGroupButtons(
inputId = ns("display.points"),
label = "Display Points:",
choices = c("Yes" = "yes", "No" = "no"),
selected = "no"
)
),
hs(2,
shinyWidgets::pickerInput(
inputId = ns("shape.to"),
label = "Shape to:",
choices = c("None" = "none", across_groups),
selected = "none")
),
hs(2, color_picker_input(ns = ns, id = "pt.color")),
hs(3, slider_input_alpha(ns = ns, id = "pt.alpha")),
hs(3, slider_input_size(ns = ns, id = "pt.size")),
)
)
})
# --- Statistical part
output$statistics <- shiny::renderUI({
ns <- session$ns
shiny::validate(
shiny::need(
expr = input$plot.type %in% testable_plottypes,
message = "Choose Box- or Violinplot to perform statistical tests."
)
)
shiny::validate(
shiny::need(
expr = base::length(input$across.subset) > 1,
message = "At least two groups are needed to perform statistical tests."
)
)
shiny::validate(
shiny::need(
expr = base::length(input$variables) == 1,
message = "Exactly one variable is needed to perform statistical tests."
)
)
shiny::tagList(
shiny::fluidRow(
hs(width = 8,
shinyWidgets::radioGroupButtons(
inputId = ns("test_options_pairwise"),
label = "Pairwise Test:",
choices = pretty_stattests_pairwise,
selected = "none",
justified = TRUE)
),
hs(width = 4,
shinyWidgets::pickerInput(
inputId = ns("ref.group"),
label = "Reference Group:",
choices = input$across.subset,
multiple = FALSE)
)
),
shiny::fluidRow(
hs(width = 8,
shinyWidgets::radioGroupButtons(
inputId = ns("test_options_groupwise"),
label = "Groupwise Test:",
choices = pretty_stattests_groupwise,
selected = "none",
justified = TRUE)
)
)
)
})
# ---
# -----
# Reactive expressions ----------------------------------------------------
#!!! awkward solution to the problem that input$change_order_order changes it's class somehow
across_subset_ordered <- shiny::reactive({
hlpr_order_input(input$change_order_order)
})
module_plot <- shiny::eventReactive(input$update_plot, {
plot_descriptive_statistics_shiny(
df = input_df(),
variables = input$variables,
across = input$across,
across.subset = across_subset_ordered(),
test.pairwise = input$test_options_pairwise,
test.groupwise = input$test_options_groupwise,
clrp = input$clrp,
display.points = base::ifelse(input$display.points == "yes", TRUE, FALSE),
pt.size = input$pt.size,
pt.alpha = (1 - input$pt.alpha),
pt.color = input$pt.color,
shape.to = input$shape.to,
n.obs = 100,
ref.group = input$ref.group,
plot.type = input$plot.type,
give_feedback = list(in.shiny = TRUE),
verbose = FALSE
)
})
# -----
# Plot outputs ------------------------------------------------------------
output$module_plot <- shiny::renderPlot({
shiny::req(module_plot())
module_plot()
})
output$save_as_pdf <- shiny::downloadHandler(
filename = function(){
base::paste("name", ".pdf", sep = "")
},
content = function(file){
grDevices::pdf(file)
plot(module_plot())
grDevices::dev.off()
},
contentType = "application/pdf"
)
}
)
}
# categorical
moduleCategoricalStatisticsPlotUI <- function(id, module_width = 6, module_headline = "Categorical Statistics"){
ns <- shiny::NS(id)
shiny::tagList(
shiny::column(width = module_width,
shiny::wellPanel(
shiny::fluidRow(
shiny::column(width = 12,
shiny::h4(shiny::strong(module_headline)),
shiny::plotOutput(outputId = ns("module_plot")),
html_breaks(1),
plot_and_save(ns = ns),
html_breaks(1),
shiny::fluidRow(
hs(12,shiny::uiOutput(outputId = ns("change_order")))
),
html_breaks(2),
shiny::fluidRow(
hs(4,shiny::uiOutput(outputId = ns("across"))),
hs(4,shiny::uiOutput(outputId = ns("across.subset"))),
hs(4,shiny::uiOutput(outputId = ns("categorical_variables")))
),
shiny::fluidRow(
hs(4, shiny::uiOutput(outputId = ns("bar_position"))),
hs(4, shiny::uiOutput(outputId = ns("clrp")))
)
)
)
)
)
)
}
moduleCategoricalStatisticsPlotServer <- function(id, df, n.across.subset){
shiny::moduleServer(
id = id,
module = function(input, output, session){
# Reactive values ---------------------------------------------------------
input_df <- shiny::reactive({ df })
# -----
# Render UIs --------------------------------------------------------------
output$across <- shiny::renderUI({
ns <- session$ns
across_choices<-
across_options(df = input_df(), n.across.subset = n.across.subset)
shiny::req(across_choices)
across_picker_input(ns = ns,
choices = across_choices,
selected = across_choices[1])
})
output$across.subset <- shiny::renderUI({
ns <- session$ns
shiny::req(input$across)
across_subset_options <-
across_subset_options(df = input_df(), across = input$across)
across_subset_picker_input(ns = ns,
id = "across.subset",
choices = across_subset_options,
selected = across_subset_options)
})
output$bar_position <- shiny::renderUI({
ns <- session$ns
bar_position_picker_input(ns = ns)
})
output$categorical_variables <- shiny::renderUI({
ns <- session$ns
ctg_variables <-
across_options(df = input_df(), n.across.subset = n.across.subset)
ctg_variables <-
purrr::keep(.x = ctg_variables, .p = ~ !.x %in% input$across)
include_variables_picker_input(ns = ns,
id = "categorical_variables",
choices = ctg_variables,
selected = ctg_variables[1])
})
output$change_order <- shiny::renderUI({
ns <- session$ns
shiny::req(input$across.subset)
change_order_input(ns = ns, items = input$across.subset)
})
output$clrp <- shiny::renderUI({
ns <- session$ns
colorpanel_picker_input(ns = ns, id = "clrp")
})
# -----
# Reactive expressions ----------------------------------------------------
across_subset_ordered <- shiny::reactive({
hlpr_order_input(input$change_order_order)
})
module_plot <- shiny::eventReactive(input$update_plot, {
checkpoint(evaluate = base::length(input$categorical_variables) != 0,
case_false = "no_features_selected")
plot_categorical_statistics_shiny(
df = input_df(),
variables = input$categorical_variables,
across = input$across,
across.subset = across_subset_ordered(),
clrp = input$clrp,
position = input$bar_position
)
})
# -----
# Plot outputs ------------------------------------------------------------
output$module_plot <- shiny::renderPlot({
shiny::req(module_plot())
module_plot()
})
output$save_as_pdf <- shiny::downloadHandler(
filename = function(){
base::paste("name", ".pdf", sep = "")
},
content = function(file){
grDevices::pdf(file)
plot(module_plot())
grDevices::dev.off()
},
contentType = "application/pdf"
)
}
)
}
# Plotting functions ------------------------------------------------------
#' @title Plot descriptive statistics
#'
#' @description Old but working plotting function for shiny application.
#'
#' @param variables Character vector. The names of the numeric variables of interest.
#' @inherit check_across_subset params
#' @param plot.type Character value. One of \emph{'histogram', 'ridgeplot', 'boxplot',
#' 'violinplot'} or \emph{'density'} to visualize the value distribution of those
#' variables specified via the \code{variables} argument.
#'
#' If set to \emph{'boxplot'} or \emph{'violinplot'} and only one variable is
#' specified statistical test can be performed.
#'
#' @param binwidth Numeric value. Only relevant if \code{plot_type} is set to \emph{'histogram'}.
#' @param display.points Logical. If set to TRUE the value distribution of \code{n.cells} is additionally
#' displayed by points.
#' @param n.obs Numeric value.
#' @param shape.to Character value. Denotes the discrete variable to which the shape of the
#' points are mapped. (Ignored if \code{display.points} is set to FALSE.)
#' @param test.pairwise Character value. One of \emph{'none', 't.test', 'wilcox.test'}.
#' @param test.groupwise Character value. One of \emph{'none', 'anova', 'kruskal.test'}.
#' @param ref.group Character value. Denotes the reference group for the statistical tests. Must
#' be one value of the variable specified in \code{across}.
#' @inherit colors params
#' @param ... Additional arguments given to \code{ggplot2::facet_wrap()}.
#' @inherit verbose params
#'
plot_descriptive_statistics_shiny <- function(df,
variables = "all",
across,
across.subset = NULL,
plot.type = "boxplot",
binwidth,
test.pairwise = "none",
test.groupwise = "none",
display.points = FALSE,
pt.size = 1.2,
pt.alpha = 0.8,
pt.color = "black",
n.obs = 100,
shape.to = "none",
ref.group,
clrp = "milo",
... ,
verbose = TRUE){
make_available(..., verbose = verbose)
# 1. Control --------------------------------------------------------------
df <- dplyr::ungroup(x = df)
if(!plot.type %in% c("histogram", "density", "ridgeplot", "boxplot", "violinplot")){
base::stop("Argument 'plot.type' needs to be one of 'histogram', 'density', 'ridgeplot', 'boxplot', 'violinplot'.")
}
if(plot.type %in% c("violinplot", "ridgeplot", "boxplot")){
max_length = 10
} else {
max_length = 25
}
is_value(clrp, "character", "clrp")
# check across input
is_value(across, "character", "across")
check_data_frame(
df = df,
var.class = list(c("character", "factor")) %>% magrittr::set_names(across),
ref = "df"
)
# check variable input
confuns::is_vec(variables, "character", "variables")
if(base::all(variables == "all")){
if(base::isTRUE(verbose)){base::message("Argument 'variables' set to 'all'. Extracting all valid, numeric variables.")}
variables <- base::colnames(dplyr::select_if(.tbl = df, .predicate = base::is.numeric))
} else {
check_list <-
purrr::map(variables, function(i){c("numeric", "integer")}) %>%
magrittr::set_names(value = variables)
confuns::check_data_frame(
df = df,
var.class = check_list,
ref = "df"
)
if(base::isTRUE(verbose)){"All specified variables found."}
}
# prevent naming issues
if(base::any(c("variables", "values") %in% c(variables, across))){
call_flexibly(fn = "give_feedback",
fn.ns = "",
default = list(msg = "Arguments 'across' and 'variables' must not contain/be equal to 'variables' and/or 'values'.",
type = "error",
fdb.fn = "stop"),
v.fail = base::stop("See error-message above.")
)
}
df <- check_across_subset(df = df, across = across, across.subset = across.subset)
# -----
# 2. Data extraction ------------------------------------------------------
df <-
tidyr::pivot_longer(
data = df,
cols = dplyr::all_of(x = variables),
names_to = "variables",
values_to = "values"
)
reverse <- FALSE
# -----
# 3. Display add on -------------------------------------------------------
# ggplot main
if(plot.type %in% c("density","histogram")){
ggplot_main <-
ggplot2::ggplot(data = df, mapping = ggplot2::aes(x = values))
} else if(plot.type == "ridgeplot"){
ggplot_main <-
ggplot2::ggplot(data = df, mapping = ggplot2::aes(x = values, y = .data[[across]]))
} else if(plot.type %in% c("violinplot", "boxplot")){
ggplot_main <-
ggplot2::ggplot(data = df, mapping = ggplot2::aes(x = .data[[across]], y = values))
}
# ggplot geom
if(plot.type == "histogram"){
display_add_on <-
list(
ggplot2::geom_histogram(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", binwidth = binwidth,
data = df),
ggplot2::labs(y = NULL)
)
} else if(plot.type == "density"){
display_add_on <-
list(
ggplot2::geom_density(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", data = df,alpha = 0.825),
ggplot2::labs(y = "Density")
)
} else if(plot.type == "ridgeplot"){
reverse <- TRUE
display_add_on <-
list(
ggridges::geom_density_ridges(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", data = df, alpha = 0.825),
ggplot2::labs(y = across, x = NULL)
)
} else if(plot.type == "violinplot"){
display_add_on <-
list(
ggplot2::geom_violin(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", data = df),
ggplot2::labs(y = NULL, x = across)
)
} else if(plot.type == "boxplot"){
display_add_on <-
list(
ggplot2::geom_boxplot(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", data = df),
ggplot2::labs(y = NULL, x = across)
)
}
# -----
# 4. Statistic add on -----------------------------------------------------
max_value <- base::max(df[["values"]], na.rm = TRUE)
labels_y <- NULL
n_variables <- dplyr::n_distinct(df[["variables"]])
# --- pairwise statistics
if(n_variables == 1 & plot.type %in% testable_plottypes){
if(test.pairwise %in% c("t.test", "wilcox.test")){
comparison_list <-
ggpubr_comparison_list(ref.group = ref.group, groups = base::levels(df[[across]]))
labels_y <- ggpubr_y_labels(lst = comparison_list, max.value = max_value)
pairwise_add_on <- list(
ggpubr::stat_compare_means(
method = test.pairwise,
comparisons = comparison_list,
label.y = labels_y,
data = df
)
)
} else if(test.pairwise == "none") {
if(base::isTRUE(verbose)){base::message("Skip pairwise testing.")}
pairwise_add_on <- list()
} else if(base::is.character(test.pairwise)){
base::warning("Invalid input for argument 'test.pairwise'.")
}
# --- groupwise statistic
if(test.groupwise %in% c("anova", "kruskal.test")){
if(base::is.null(labels_y)){
label_y <- max_value*1.1
} else if(base::is.numeric(labels_y)){
label_y <- base::max(labels_y, na.rm = TRUE)*1.1
}
groupwise_add_on <- list(
ggpubr::stat_compare_means(
method = test.groupwise,
label.y = label_y,
data = df
)
)
} else if(test.groupwise == "none"){
if(base::isTRUE(verbose)){base::message("Skip groupwise testing.")}
groupwise_add_on <- list()
} else {
base::warning("Invalid input for argument 'test.groupwise'.")
groupwise_add_on <- list()
}
} else {
pairwise_add_on <- list()
groupwise_add_on <- list()
# base::warning("set up confuns warnings")
}
# -----
# 5. Jitter add on -------------------------------------------------------
if(base::isTRUE(display.points) & plot.type %in% testable_plottypes){
jitter_data <-
dplyr::group_by(.data = df, !!rlang::sym(across)) %>%
dplyr::slice_sample(n = n.obs)
if(shape.to != "none"){
jitter_add_on <-
ggplot2::geom_jitter(
data = jitter_data, size = pt.size, alpha = pt.alpha,
color = pt.color, mapping = ggplot2::aes(shape = .data[[shape.to]])
)
} else {
jitter_add_on <-
ggplot2::geom_jitter(
data = jitter_data, size = pt.size, alpha = pt.alpha,
color = pt.color, height = 0.25, width = 0.25
)
}
} else {
jitter_add_on <- list()
}
# -----
# 6. Plotting -------------------------------------------------------------
facet_add_on <-
call_flexibly(fn = "facet_wrap",
fn.ns = "ggplot2",
default = list(facets = stats::as.formula(. ~ variables),
scales = "free"),
v.fail = ggplot2::facet_wrap(facets = . ~ variables, scales = "free"))
ggplot_main +
display_add_on +
facet_add_on +
confuns::scale_color_add_on(aes = "fill", variable = "discrete",
clrp = clrp, guide = ggplot2::guide_legend(reverse = reverse)) +
ggplot2::theme_classic() +
ggplot2::theme(
axis.text.y = ggplot2::element_text(color = "black"),
axis.text.x = ggplot2::element_text(color = "black"),
strip.text.y = ggplot2::element_text(angle = 0, face = "italic", size = 14),
strip.placement = "outside",
strip.background = ggplot2::element_rect(color = "white", fill = "white"),
panel.spacing.y = ggplot2::unit(10, "pt")
) +
ggplot2::labs(x = NULL) +
pairwise_add_on +
groupwise_add_on +
jitter_add_on
}
#' Title
#'
#'
#' @return
#' @export
#'
plot_categorical_statistics_shiny <- function(df,
variables,
across,
across.subset = NULL,
clrp = "milo",
position = "fill",
...){
# 1. Control --------------------------------------------------------------
# ----
# 2. Additional checks and data extraction -----------------------------------
plot_df <-
tidyr::pivot_longer(data = df,
cols = dplyr::all_of(variables),
names_to = "variables",
values_to = "values")
plot_df <-
check_across_subset(df = plot_df, across = across, across.subset = across.subset)
if(base::is.character(across)){
all_variables <- c(variables, across)
facet_add_on <-
ggplot2::facet_wrap(facets = . ~ variables, scales = "free_x", ...)
fill <- across
theme_add_on <- list()
} else {
all_variables <- variables
facet_add_on <-
ggplot2::facet_wrap(facets = . ~ variables, scales = "free_x", ...)
if(base::length(all_variables) > 1){
fill = "variables"
} else {
fill = "values"
}
theme_add_on <- list(ggplot2::theme(legend.position = "none"))
if(position == "fill" & base::length(all_variables) > 1){
position <- "stack"
base::warning("Argument 'across' is NULL. Using 'stack' for argument 'position'.")
}
}
if(position == "fill"){
scale_y_add_on <-
list(
ggplot2::scale_y_continuous(labels = c(25, 50, 75, 100), breaks = c(0.25, 0.5, 0.75, 1)),
ggplot2::labs(y = "Percentage")
)
} else {
scale_y_add_on <- ggplot2::labs(y = "Count")
}
# ----
ggplot2::ggplot(data = plot_df) +
ggplot2::geom_bar(position = position, color = "black",
mapping = ggplot2::aes(x = values, fill = .data[[fill]])) +
facet_add_on +
confuns::scale_color_add_on(aes = "fill", variable = "discrete", clrp = clrp) +
ggplot2::theme_classic() +
theme_add_on +
ggplot2::theme(strip.background = ggplot2::element_blank()) +
ggplot2::labs(x = "Groups / Clusters") +
scale_y_add_on
}
kueckelj/confuns documentation built on June 28, 2024, 9:19 a.m.
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Defines functions plot_categorical_statistics_shiny plot_descriptive_statistics_shiny moduleCategoricalStatisticsPlotServer moduleCategoricalStatisticsPlotUI moduleDescriptiveStatisticsPlotServer moduleDescriptiveStatisticsPlotUI plot_statistics_interactive
Documented in plot_categorical_statistics_shiny plot_descriptive_statistics_shiny plot_statistics_interactive
#' @title Opens interactive application
#'
#' @inherit df params
#'
#' @export
plot_statistics_interactive <- function(df, n.across.subset = 10){
shiny::runApp(
shiny::shinyApp(
ui = function(){
shinydashboard::dashboardPage(
header = shinydashboard::dashboardHeader(title = "Descriptive Statistics"),
sidebar = shinydashboard::dashboardSidebar(
collapsed = TRUE,
shinydashboard::sidebarMenu(
shinydashboard::menuItem(
text = "Descriptive Statistisc",
tabName = "descr_statistics",
selected = TRUE
)
)
),
body = shinydashboard::dashboardBody(
shinybusy::add_busy_spinner(spin = "cube-grid", margins = c(0, 10), color = "red"),
shinydashboard::tabItems(
shinydashboard::tabItem(tabName = "descr_statistics",
shiny::fluidRow(
moduleDescriptiveStatisticsPlotUI(id = "descr_stat"),
moduleCategoricalStatisticsPlotUI(id = "categ_stat")
)
)
)
)
)
},
server = function(input, output, session){
# shiny helper
shinyhelper::observe_helpers()
moduleDescriptiveStatisticsPlotServer(id = "descr_stat",
df = df,
n.across.subset = n.across.subset)
moduleCategoricalStatisticsPlotServer(id = "categ_stat",
df = df,
n.across.subset = n.across.subset)
}
)
)
}
# Modules -----------------------------------------------------------------
# descriptive
moduleDescriptiveStatisticsPlotUI <- function(id, module_width = 6, module_headline = "Descriptive Statistics"){
ns <- shiny::NS(id)
shiny::tagList(
shiny::column(width = module_width,
shiny::wellPanel(
shiny::fluidRow(
shiny::column(width = 12,
shiny::h4(shiny::strong(module_headline)),
shiny::plotOutput(outputId = ns("module_plot")),
html_breaks(1),
plot_and_save(ns = ns),
html_breaks(1),
shiny::fluidRow(
hs(4,shiny::uiOutput(outputId = ns("change_order")))
),
html_breaks(2),
shiny::fluidRow(
hs(4,shiny::uiOutput(outputId = ns("across"))),
hs(4,shiny::uiOutput(outputId = ns("across.subset"))),
hs(4,shiny::uiOutput(outputId = ns("variables"))),
),
shiny::fluidRow(
hs(4,shiny::uiOutput(outputId = ns("plot.type"))),
hs(4,shiny::uiOutput(outputId = ns("clrp")))
),
shiny::uiOutput(outputId = ns("point_add_on")),
shiny::uiOutput(outputId = ns("statistics"))
)
)
)
)
)
}
moduleDescriptiveStatisticsPlotServer <- function(id, df, n.across.subset = 10){
shiny::moduleServer(
id = id,
module = function(input, output, session){
# Reactive values ---------------------------------------------------------
input_df <- shiny::reactive({ df })
# -----
# Render UIs --------------------------------------------------------------
output$variables <- shiny::renderUI({
ns <- session$ns
num_variables <-
dplyr::select_if(input_df(), .predicate = base::is.numeric) %>%
base::colnames()
include_variables_picker_input(ns = ns,
id = "variables",
choices = num_variables,
selected = num_variables[1])
})
output$across <- shiny::renderUI({
ns <- session$ns
across_groups <-
across_options(df, n.across.subset = n.across.subset)
shiny::req(across_groups)
across_picker_input(ns = ns, choices = across_groups)
})
output$across.subset <- shiny::renderUI({
ns <- session$ns
shiny::req(input$across)
across_subset_options <-
across_subset_options(df = input_df(), across = input$across)
across_subset_picker_input(ns = ns,
id = "across.subset",
choices = across_subset_options,
selected = across_subset_options)
})
output$clrp <- shiny::renderUI({
ns <- session$ns
colorpanel_picker_input(ns = ns, id = "clrp")
})
output$change_order <- shiny::renderUI({
ns <- session$ns
shiny::req(input$across.subset)
change_order_input(ns = ns, items = input$across.subset)
})
output$plot.type <- shiny::renderUI({
ns <- session$ns
shinyWidgets::pickerInput(inputId = ns("plot.type"),
label = "Plottype:",
choices = pretty_plottypes,
selected = "boxplot",
multiple = FALSE)
})
# --- Point add on
output$point_add_on <- shiny::renderUI({
ns <- session$ns
shiny::req(input$plot.type %in% testable_plottypes)
across_groups <-
across_options(df, n.across.subset = n.across.subset)
shiny::tagList(
shiny::fluidRow(
hs(2,
shinyWidgets::radioGroupButtons(
inputId = ns("display.points"),
label = "Display Points:",
choices = c("Yes" = "yes", "No" = "no"),
selected = "no"
)
),
hs(2,
shinyWidgets::pickerInput(
inputId = ns("shape.to"),
label = "Shape to:",
choices = c("None" = "none", across_groups),
selected = "none")
),
hs(2, color_picker_input(ns = ns, id = "pt.color")),
hs(3, slider_input_alpha(ns = ns, id = "pt.alpha")),
hs(3, slider_input_size(ns = ns, id = "pt.size")),
)
)
})
# --- Statistical part
output$statistics <- shiny::renderUI({
ns <- session$ns
shiny::validate(
shiny::need(
expr = input$plot.type %in% testable_plottypes,
message = "Choose Box- or Violinplot to perform statistical tests."
)
)
shiny::validate(
shiny::need(
expr = base::length(input$across.subset) > 1,
message = "At least two groups are needed to perform statistical tests."
)
)
shiny::validate(
shiny::need(
expr = base::length(input$variables) == 1,
message = "Exactly one variable is needed to perform statistical tests."
)
)
shiny::tagList(
shiny::fluidRow(
hs(width = 8,
shinyWidgets::radioGroupButtons(
inputId = ns("test_options_pairwise"),
label = "Pairwise Test:",
choices = pretty_stattests_pairwise,
selected = "none",
justified = TRUE)
),
hs(width = 4,
shinyWidgets::pickerInput(
inputId = ns("ref.group"),
label = "Reference Group:",
choices = input$across.subset,
multiple = FALSE)
)
),
shiny::fluidRow(
hs(width = 8,
shinyWidgets::radioGroupButtons(
inputId = ns("test_options_groupwise"),
label = "Groupwise Test:",
choices = pretty_stattests_groupwise,
selected = "none",
justified = TRUE)
)
)
)
})
# ---
# -----
# Reactive expressions ----------------------------------------------------
#!!! awkward solution to the problem that input$change_order_order changes it's class somehow
across_subset_ordered <- shiny::reactive({
hlpr_order_input(input$change_order_order)
})
module_plot <- shiny::eventReactive(input$update_plot, {
plot_descriptive_statistics_shiny(
df = input_df(),
variables = input$variables,
across = input$across,
across.subset = across_subset_ordered(),
test.pairwise = input$test_options_pairwise,
test.groupwise = input$test_options_groupwise,
clrp = input$clrp,
display.points = base::ifelse(input$display.points == "yes", TRUE, FALSE),
pt.size = input$pt.size,
pt.alpha = (1 - input$pt.alpha),
pt.color = input$pt.color,
shape.to = input$shape.to,
n.obs = 100,
ref.group = input$ref.group,
plot.type = input$plot.type,
give_feedback = list(in.shiny = TRUE),
verbose = FALSE
)
})
# -----
# Plot outputs ------------------------------------------------------------
output$module_plot <- shiny::renderPlot({
shiny::req(module_plot())
module_plot()
})
output$save_as_pdf <- shiny::downloadHandler(
filename = function(){
base::paste("name", ".pdf", sep = "")
},
content = function(file){
grDevices::pdf(file)
plot(module_plot())
grDevices::dev.off()
},
contentType = "application/pdf"
)
}
)
}
# categorical
moduleCategoricalStatisticsPlotUI <- function(id, module_width = 6, module_headline = "Categorical Statistics"){
ns <- shiny::NS(id)
shiny::tagList(
shiny::column(width = module_width,
shiny::wellPanel(
shiny::fluidRow(
shiny::column(width = 12,
shiny::h4(shiny::strong(module_headline)),
shiny::plotOutput(outputId = ns("module_plot")),
html_breaks(1),
plot_and_save(ns = ns),
html_breaks(1),
shiny::fluidRow(
hs(12,shiny::uiOutput(outputId = ns("change_order")))
),
html_breaks(2),
shiny::fluidRow(
hs(4,shiny::uiOutput(outputId = ns("across"))),
hs(4,shiny::uiOutput(outputId = ns("across.subset"))),
hs(4,shiny::uiOutput(outputId = ns("categorical_variables")))
),
shiny::fluidRow(
hs(4, shiny::uiOutput(outputId = ns("bar_position"))),
hs(4, shiny::uiOutput(outputId = ns("clrp")))
)
)
)
)
)
)
}
moduleCategoricalStatisticsPlotServer <- function(id, df, n.across.subset){
shiny::moduleServer(
id = id,
module = function(input, output, session){
# Reactive values ---------------------------------------------------------
input_df <- shiny::reactive({ df })
# -----
# Render UIs --------------------------------------------------------------
output$across <- shiny::renderUI({
ns <- session$ns
across_choices<-
across_options(df = input_df(), n.across.subset = n.across.subset)
shiny::req(across_choices)
across_picker_input(ns = ns,
choices = across_choices,
selected = across_choices[1])
})
output$across.subset <- shiny::renderUI({
ns <- session$ns
shiny::req(input$across)
across_subset_options <-
across_subset_options(df = input_df(), across = input$across)
across_subset_picker_input(ns = ns,
id = "across.subset",
choices = across_subset_options,
selected = across_subset_options)
})
output$bar_position <- shiny::renderUI({
ns <- session$ns
bar_position_picker_input(ns = ns)
})
output$categorical_variables <- shiny::renderUI({
ns <- session$ns
ctg_variables <-
across_options(df = input_df(), n.across.subset = n.across.subset)
ctg_variables <-
purrr::keep(.x = ctg_variables, .p = ~ !.x %in% input$across)
include_variables_picker_input(ns = ns,
id = "categorical_variables",
choices = ctg_variables,
selected = ctg_variables[1])
})
output$change_order <- shiny::renderUI({
ns <- session$ns
shiny::req(input$across.subset)
change_order_input(ns = ns, items = input$across.subset)
})
output$clrp <- shiny::renderUI({
ns <- session$ns
colorpanel_picker_input(ns = ns, id = "clrp")
})
# -----
# Reactive expressions ----------------------------------------------------
across_subset_ordered <- shiny::reactive({
hlpr_order_input(input$change_order_order)
})
module_plot <- shiny::eventReactive(input$update_plot, {
checkpoint(evaluate = base::length(input$categorical_variables) != 0,
case_false = "no_features_selected")
plot_categorical_statistics_shiny(
df = input_df(),
variables = input$categorical_variables,
across = input$across,
across.subset = across_subset_ordered(),
clrp = input$clrp,
position = input$bar_position
)
})
# -----
# Plot outputs ------------------------------------------------------------
output$module_plot <- shiny::renderPlot({
shiny::req(module_plot())
module_plot()
})
output$save_as_pdf <- shiny::downloadHandler(
filename = function(){
base::paste("name", ".pdf", sep = "")
},
content = function(file){
grDevices::pdf(file)
plot(module_plot())
grDevices::dev.off()
},
contentType = "application/pdf"
)
}
)
}
# Plotting functions ------------------------------------------------------
#' @title Plot descriptive statistics
#'
#' @description Old but working plotting function for shiny application.
#'
#' @param variables Character vector. The names of the numeric variables of interest.
#' @inherit check_across_subset params
#' @param plot.type Character value. One of \emph{'histogram', 'ridgeplot', 'boxplot',
#' 'violinplot'} or \emph{'density'} to visualize the value distribution of those
#' variables specified via the \code{variables} argument.
#'
#' If set to \emph{'boxplot'} or \emph{'violinplot'} and only one variable is
#' specified statistical test can be performed.
#'
#' @param binwidth Numeric value. Only relevant if \code{plot_type} is set to \emph{'histogram'}.
#' @param display.points Logical. If set to TRUE the value distribution of \code{n.cells} is additionally
#' displayed by points.
#' @param n.obs Numeric value.
#' @param shape.to Character value. Denotes the discrete variable to which the shape of the
#' points are mapped. (Ignored if \code{display.points} is set to FALSE.)
#' @param test.pairwise Character value. One of \emph{'none', 't.test', 'wilcox.test'}.
#' @param test.groupwise Character value. One of \emph{'none', 'anova', 'kruskal.test'}.
#' @param ref.group Character value. Denotes the reference group for the statistical tests. Must
#' be one value of the variable specified in \code{across}.
#' @inherit colors params
#' @param ... Additional arguments given to \code{ggplot2::facet_wrap()}.
#' @inherit verbose params
#'
plot_descriptive_statistics_shiny <- function(df,
variables = "all",
across,
across.subset = NULL,
plot.type = "boxplot",
binwidth,
test.pairwise = "none",
test.groupwise = "none",
display.points = FALSE,
pt.size = 1.2,
pt.alpha = 0.8,
pt.color = "black",
n.obs = 100,
shape.to = "none",
ref.group,
clrp = "milo",
... ,
verbose = TRUE){
make_available(..., verbose = verbose)
# 1. Control --------------------------------------------------------------
df <- dplyr::ungroup(x = df)
if(!plot.type %in% c("histogram", "density", "ridgeplot", "boxplot", "violinplot")){
base::stop("Argument 'plot.type' needs to be one of 'histogram', 'density', 'ridgeplot', 'boxplot', 'violinplot'.")
}
if(plot.type %in% c("violinplot", "ridgeplot", "boxplot")){
max_length = 10
} else {
max_length = 25
}
is_value(clrp, "character", "clrp")
# check across input
is_value(across, "character", "across")
check_data_frame(
df = df,
var.class = list(c("character", "factor")) %>% magrittr::set_names(across),
ref = "df"
)
# check variable input
confuns::is_vec(variables, "character", "variables")
if(base::all(variables == "all")){
if(base::isTRUE(verbose)){base::message("Argument 'variables' set to 'all'. Extracting all valid, numeric variables.")}
variables <- base::colnames(dplyr::select_if(.tbl = df, .predicate = base::is.numeric))
} else {
check_list <-
purrr::map(variables, function(i){c("numeric", "integer")}) %>%
magrittr::set_names(value = variables)
confuns::check_data_frame(
df = df,
var.class = check_list,
ref = "df"
)
if(base::isTRUE(verbose)){"All specified variables found."}
}
# prevent naming issues
if(base::any(c("variables", "values") %in% c(variables, across))){
call_flexibly(fn = "give_feedback",
fn.ns = "",
default = list(msg = "Arguments 'across' and 'variables' must not contain/be equal to 'variables' and/or 'values'.",
type = "error",
fdb.fn = "stop"),
v.fail = base::stop("See error-message above.")
)
}
df <- check_across_subset(df = df, across = across, across.subset = across.subset)
# -----
# 2. Data extraction ------------------------------------------------------
df <-
tidyr::pivot_longer(
data = df,
cols = dplyr::all_of(x = variables),
names_to = "variables",
values_to = "values"
)
reverse <- FALSE
# -----
# 3. Display add on -------------------------------------------------------
# ggplot main
if(plot.type %in% c("density","histogram")){
ggplot_main <-
ggplot2::ggplot(data = df, mapping = ggplot2::aes(x = values))
} else if(plot.type == "ridgeplot"){
ggplot_main <-
ggplot2::ggplot(data = df, mapping = ggplot2::aes(x = values, y = .data[[across]]))
} else if(plot.type %in% c("violinplot", "boxplot")){
ggplot_main <-
ggplot2::ggplot(data = df, mapping = ggplot2::aes(x = .data[[across]], y = values))
}
# ggplot geom
if(plot.type == "histogram"){
display_add_on <-
list(
ggplot2::geom_histogram(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", binwidth = binwidth,
data = df),
ggplot2::labs(y = NULL)
)
} else if(plot.type == "density"){
display_add_on <-
list(
ggplot2::geom_density(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", data = df,alpha = 0.825),
ggplot2::labs(y = "Density")
)
} else if(plot.type == "ridgeplot"){
reverse <- TRUE
display_add_on <-
list(
ggridges::geom_density_ridges(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", data = df, alpha = 0.825),
ggplot2::labs(y = across, x = NULL)
)
} else if(plot.type == "violinplot"){
display_add_on <-
list(
ggplot2::geom_violin(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", data = df),
ggplot2::labs(y = NULL, x = across)
)
} else if(plot.type == "boxplot"){
display_add_on <-
list(
ggplot2::geom_boxplot(mapping = ggplot2::aes(fill = !!rlang::sym(across)),
color = "black", data = df),
ggplot2::labs(y = NULL, x = across)
)
}
# -----
# 4. Statistic add on -----------------------------------------------------
max_value <- base::max(df[["values"]], na.rm = TRUE)
labels_y <- NULL
n_variables <- dplyr::n_distinct(df[["variables"]])
# --- pairwise statistics
if(n_variables == 1 & plot.type %in% testable_plottypes){
if(test.pairwise %in% c("t.test", "wilcox.test")){
comparison_list <-
ggpubr_comparison_list(ref.group = ref.group, groups = base::levels(df[[across]]))
labels_y <- ggpubr_y_labels(lst = comparison_list, max.value = max_value)
pairwise_add_on <- list(
ggpubr::stat_compare_means(
method = test.pairwise,
comparisons = comparison_list,
label.y = labels_y,
data = df
)
)
} else if(test.pairwise == "none") {
if(base::isTRUE(verbose)){base::message("Skip pairwise testing.")}
pairwise_add_on <- list()
} else if(base::is.character(test.pairwise)){
base::warning("Invalid input for argument 'test.pairwise'.")
}
# --- groupwise statistic
if(test.groupwise %in% c("anova", "kruskal.test")){
if(base::is.null(labels_y)){
label_y <- max_value*1.1
} else if(base::is.numeric(labels_y)){
label_y <- base::max(labels_y, na.rm = TRUE)*1.1
}
groupwise_add_on <- list(
ggpubr::stat_compare_means(
method = test.groupwise,
label.y = label_y,
data = df
)
)
} else if(test.groupwise == "none"){
if(base::isTRUE(verbose)){base::message("Skip groupwise testing.")}
groupwise_add_on <- list()
} else {
base::warning("Invalid input for argument 'test.groupwise'.")
groupwise_add_on <- list()
}
} else {
pairwise_add_on <- list()
groupwise_add_on <- list()
# base::warning("set up confuns warnings")
}
# -----
# 5. Jitter add on -------------------------------------------------------
if(base::isTRUE(display.points) & plot.type %in% testable_plottypes){
jitter_data <-
dplyr::group_by(.data = df, !!rlang::sym(across)) %>%
dplyr::slice_sample(n = n.obs)
if(shape.to != "none"){
jitter_add_on <-
ggplot2::geom_jitter(
data = jitter_data, size = pt.size, alpha = pt.alpha,
color = pt.color, mapping = ggplot2::aes(shape = .data[[shape.to]])
)
} else {
jitter_add_on <-
ggplot2::geom_jitter(
data = jitter_data, size = pt.size, alpha = pt.alpha,
color = pt.color, height = 0.25, width = 0.25
)
}
} else {
jitter_add_on <- list()
}
# -----
# 6. Plotting -------------------------------------------------------------
facet_add_on <-
call_flexibly(fn = "facet_wrap",
fn.ns = "ggplot2",
default = list(facets = stats::as.formula(. ~ variables),
scales = "free"),
v.fail = ggplot2::facet_wrap(facets = . ~ variables, scales = "free"))
ggplot_main +
display_add_on +
facet_add_on +
confuns::scale_color_add_on(aes = "fill", variable = "discrete",
clrp = clrp, guide = ggplot2::guide_legend(reverse = reverse)) +
ggplot2::theme_classic() +
ggplot2::theme(
axis.text.y = ggplot2::element_text(color = "black"),
axis.text.x = ggplot2::element_text(color = "black"),
strip.text.y = ggplot2::element_text(angle = 0, face = "italic", size = 14),
strip.placement = "outside",
strip.background = ggplot2::element_rect(color = "white", fill = "white"),
panel.spacing.y = ggplot2::unit(10, "pt")
) +
ggplot2::labs(x = NULL) +
pairwise_add_on +
groupwise_add_on +
jitter_add_on
}
#' Title
#'
#'
#' @return
#' @export
#'
plot_categorical_statistics_shiny <- function(df,
variables,
across,
across.subset = NULL,
clrp = "milo",
position = "fill",
...){
# 1. Control --------------------------------------------------------------
# ----
# 2. Additional checks and data extraction -----------------------------------
plot_df <-
tidyr::pivot_longer(data = df,
cols = dplyr::all_of(variables),
names_to = "variables",
values_to = "values")
plot_df <-
check_across_subset(df = plot_df, across = across, across.subset = across.subset)
if(base::is.character(across)){
all_variables <- c(variables, across)
facet_add_on <-
ggplot2::facet_wrap(facets = . ~ variables, scales = "free_x", ...)
fill <- across
theme_add_on <- list()
} else {
all_variables <- variables
facet_add_on <-
ggplot2::facet_wrap(facets = . ~ variables, scales = "free_x", ...)
if(base::length(all_variables) > 1){
fill = "variables"
} else {
fill = "values"
}
theme_add_on <- list(ggplot2::theme(legend.position = "none"))
if(position == "fill" & base::length(all_variables) > 1){
position <- "stack"
base::warning("Argument 'across' is NULL. Using 'stack' for argument 'position'.")
}
}
if(position == "fill"){
scale_y_add_on <-
list(
ggplot2::scale_y_continuous(labels = c(25, 50, 75, 100), breaks = c(0.25, 0.5, 0.75, 1)),
ggplot2::labs(y = "Percentage")
)
} else {
scale_y_add_on <- ggplot2::labs(y = "Count")
}
# ----
ggplot2::ggplot(data = plot_df) +
ggplot2::geom_bar(position = position, color = "black",
mapping = ggplot2::aes(x = values, fill = .data[[fill]])) +
facet_add_on +
confuns::scale_color_add_on(aes = "fill", variable = "discrete", clrp = clrp) +
ggplot2::theme_classic() +
theme_add_on +
ggplot2::theme(strip.background = ggplot2::element_blank()) +
ggplot2::labs(x = "Groups / Clusters") +
scale_y_add_on
}
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