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tm_g_gh_density_distribution_plot.R
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tm_g_gh_density_distribution_plot.R
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#' Density Distribution Plot
#'
#' This teal module renders the UI and calls the functions that create a density distribution plot
#' and an accompanying summary table.
#'
#' @param label menu item label of the module in the teal app.
#' @param trt_group \code{\link[teal.transform]{choices_selected}} object with available choices and pre-selected option
#' for variable names representing treatment group e.g. `ARM`.
#' @param color_manual vector of colors applied to treatment values.
#' @param color_comb name or hex value for combined treatment color.
#' @param plot_height controls plot height.
#' @param plot_width optional, controls plot width.
#' @param font_size font size control for title, `x-axis` label, `y-axis` label and legend.
#' @param line_size plot line thickness.
#' @param hline_arb numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.
#' @param hline_arb_color a character vector of at most length of \code{hline_arb}.
#' naming the color for the arbitrary horizontal lines.
#' @param hline_arb_label a character vector of at most length of \code{hline_arb}.
#' naming the label for the arbitrary horizontal lines.
#' @param facet_ncol numeric value indicating number of facets per row.
#' @param comb_line display combined treatment line toggle.
#' @param rotate_xlab 45 degree rotation of `x-axis` values.
#'
#' @inheritParams teal.widgets::standard_layout
#' @inheritParams tm_g_gh_scatterplot
#'
#'
#' @author Nick Paszty (npaszty) [email protected]
#' @author Balazs Toth (tothb2) [email protected]
#'
#' @details None
#'
#' @export
#'
#' @examples
#'
#' # Example using ADaM structure analysis dataset.
#'
#' library(dplyr)
#'
#' # original ARM value = dose value
#' arm_mapping <- list(
#' "A: Drug X" = "150mg QD",
#' "B: Placebo" = "Placebo",
#' "C: Combination" = "Combination"
#' )
#' ADSL <- goshawk::rADSL
#' ADLB <- goshawk::rADLB
#' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
#' ADLB <- ADLB %>%
#' dplyr::mutate(
#' AVISITCD = dplyr::case_when(
#' AVISIT == "SCREENING" ~ "SCR",
#' AVISIT == "BASELINE" ~ "BL",
#' grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
#' TRUE ~ as.character(NA)
#' ),
#' AVISITCDN = dplyr::case_when(
#' AVISITCD == "SCR" ~ -2,
#' AVISITCD == "BL" ~ 0,
#' grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
#' TRUE ~ as.numeric(NA)
#' ),
#' AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
#' TRTORD = dplyr::case_when(
#' ARMCD == "ARM C" ~ 1,
#' ARMCD == "ARM B" ~ 2,
#' ARMCD == "ARM A" ~ 3
#' ),
#' ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
#' ARM = factor(ARM) %>% reorder(TRTORD),
#' ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
#' ACTARM = factor(ACTARM) %>% reorder(TRTORD)
#' )
#'
#' attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
#' attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
#'
#' app <- teal::init(
#' data = teal.data::cdisc_data(
#' teal.data::cdisc_dataset("ADSL", ADSL, code = "ADSL <- goshawk::rADSL"),
#' teal.data::cdisc_dataset(
#' "ADLB",
#' ADLB,
#' code = "ADLB <- goshawk::rADLB
#' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
#' ADLB <- ADLB %>%
#' dplyr::mutate(AVISITCD = dplyr::case_when(
#' AVISIT == 'SCREENING' ~ 'SCR',
#' AVISIT == 'BASELINE' ~ 'BL',
#' grepl('WEEK', AVISIT) ~
#' paste('W', stringr::str_extract(AVISIT, '(?<=(WEEK ))[0-9]+')),
#' TRUE ~ as.character(NA)),
#' AVISITCDN = dplyr::case_when(
#' AVISITCD == 'SCR' ~ -2,
#' AVISITCD == 'BL' ~ 0,
#' grepl('W', AVISITCD) ~ as.numeric(gsub('[^0-9]*', '', AVISITCD)),
#' TRUE ~ as.numeric(NA)),
#' AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
#' TRTORD = dplyr::case_when(
#' ARMCD == 'ARM C' ~ 1,
#' ARMCD == 'ARM B' ~ 2,
#' ARMCD == 'ARM A' ~ 3),
#' ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
#' ARM = factor(ARM) %>% reorder(TRTORD),
#' ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
#' ACTARM = factor(ACTARM) %>% reorder(TRTORD))
#' attr(ADLB[['ARM']], 'label') <- var_labels[['ARM']]
#' attr(ADLB[['ACTARM']], 'label') <- var_labels[['ACTARM']]",
#' vars = list(arm_mapping = arm_mapping)
#' ),
#' check = TRUE
#' ),
#' modules = teal::modules(
#' teal.goshawk::tm_g_gh_density_distribution_plot(
#' label = "Density Distribution Plot",
#' dataname = "ADLB",
#' param_var = "PARAMCD",
#' param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
#' xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
#' trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
#' color_manual = c(
#' "150mg QD" = "#000000",
#' "Placebo" = "#3498DB",
#' "Combination" = "#E74C3C"
#' ),
#' color_comb = "#39ff14",
#' comb_line = TRUE,
#' plot_height = c(500, 200, 2000),
#' font_size = c(12, 8, 20),
#' line_size = c(1, .25, 3),
#' hline_arb = c(.02, .05),
#' hline_arb_color = c("red", "black"),
#' hline_arb_label = c("Horizontal Line A", "Horizontal Line B")
#' )
#' )
#' )
#' if (interactive()) {
#' shinyApp(app$ui, app$server)
#' }
tm_g_gh_density_distribution_plot <- function(label, # nolint
dataname,
param_var,
param,
xaxis_var,
trt_group,
color_manual = NULL,
color_comb = NULL,
plot_height = c(500, 200, 2000),
plot_width = NULL,
font_size = c(12, 8, 20),
line_size = c(1, .25, 3),
hline_arb = numeric(0),
hline_arb_color = "red",
hline_arb_label = "Horizontal line",
facet_ncol = 2L,
comb_line = TRUE,
rotate_xlab = FALSE,
pre_output = NULL,
post_output = NULL) {
logger::log_info("Initializing tm_g_gh_density_distribution_plot")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(param_var)
checkmate::assert_class(param, "choices_selected")
checkmate::assert_class(xaxis_var, "choices_selected")
checkmate::assert_class(trt_group, "choices_selected")
checkmate::assert_numeric(font_size, len = 3)
checkmate::assert_numeric(line_size, len = 3)
checkmate::assert_int(facet_ncol)
checkmate::assert_flag(comb_line)
checkmate::assert_flag(rotate_xlab)
validate_line_arb_arg(hline_arb, hline_arb_color, hline_arb_label)
checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)
checkmate::assert_numeric(
plot_width[1],
lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
)
args <- as.list(environment())
module(
label = label,
datanames = dataname,
server = srv_g_density_distribution_plot,
server_args = list(
dataname = dataname,
param_var = param_var,
param = param,
trt_group = trt_group,
color_manual = color_manual,
color_comb = color_comb,
plot_height = plot_height,
plot_width = plot_width
),
ui = ui_g_density_distribution_plot,
ui_args = args
)
}
ui_g_density_distribution_plot <- function(id, ...) {
ns <- NS(id)
a <- list(...)
teal.widgets::standard_layout(
output = div(
fluidRow(
teal.widgets::plot_with_settings_ui(id = ns("plot"))
),
fluidRow(column(
width = 12,
br(), hr(),
h4("Descriptive Statistics"),
DT::dataTableOutput(ns("table_ui"))
))
),
encoding = div(
### Reporter
teal.reporter::simple_reporter_ui(ns("simple_reporter")),
###
templ_ui_dataname(a$dataname),
teal.widgets::optionalSelectInput(
ns("trt_group"),
label = "Select Treatment Variable",
choices = a$trt_group$choices,
selected = a$trt_group$selected,
multiple = FALSE
),
templ_ui_params_vars(
ns,
xparam_choices = a$param$choices, xparam_selected = a$param$selected, xparam_label = "Select a Biomarker",
xchoices = a$xaxis_var$choices, xselected = a$xaxis_var$selected
),
templ_ui_constraint(ns, label = "Data Constraint"),
ui_arbitrary_lines(id = ns("hline_arb"), a$hline_arb, a$hline_arb_label, a$hline_arb_color),
teal.widgets::panel_group(
teal.widgets::panel_item(
title = "Plot Aesthetic Settings",
toggle_slider_ui(
ns("xrange_scale"),
label = "X-Axis Range Zoom",
min = -1000000,
max = 1000000,
value = c(-1000000, 1000000)
),
toggle_slider_ui(
ns("yrange_scale"),
label = "Y-Axis Range Zoom",
min = -1000000,
max = 1000000,
value = c(-1000000, 1000000)
),
numericInput(ns("facet_ncol"), "Number of Plots Per Row:", a$facet_ncol, min = 1),
checkboxInput(ns("comb_line"), "Display Combined line", a$comb_line),
checkboxInput(ns("rug_plot"), "Include rug plot", value = FALSE),
checkboxInput(ns("rotate_xlab"), "Rotate X-axis Label", a$rotate_xlab)
),
teal.widgets::panel_item(
title = "Plot settings",
teal.widgets::optionalSliderInputValMinMax(ns("font_size"), "Font Size", a$font_size, ticks = FALSE),
teal.widgets::optionalSliderInputValMinMax(
ns("line_size"),
"Line Size",
value_min_max = a$line_size,
step = .25,
ticks = FALSE
)
)
)
),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
),
pre_output = a$pre_output,
post_output = a$post_output
)
}
srv_g_density_distribution_plot <- function(id, # nolint
data,
reporter,
filter_panel_api,
dataname,
param_var,
param,
trt_group,
color_manual,
color_comb,
plot_height,
plot_width) {
with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
checkmate::assert_class(data, "tdata")
moduleServer(id, function(input, output, session) {
anl_q_output <- constr_anl_q(
session, input, data, dataname,
param_id = "xaxis_param", param_var = param_var, trt_group = input$trt_group, min_rows = 2
)
anl_q <- anl_q_output()$value
# update sliders for axes taking constraints into account
xrange_slider <- toggle_slider_server("xrange_scale")
yrange_slider <- toggle_slider_server("yrange_scale")
keep_range_slider_updated(session, input, xrange_slider$update_state, "xaxis_var", "xaxis_param", anl_q)
keep_range_slider_updated(
session,
input,
yrange_slider$update_state,
"xaxis_var",
"xaxis_param",
anl_q,
is_density = TRUE
)
keep_data_const_opts_updated(session, input, anl_q, "xaxis_param")
horizontal_line <- srv_arbitrary_lines("hline_arb")
iv_r <- reactive({
iv <- shinyvalidate::InputValidator$new()
iv$add_rule("xaxis_param", shinyvalidate::sv_required("Please select a biomarker"))
iv$add_rule("trt_group", shinyvalidate::sv_required("Please select a treatment variable"))
iv$add_rule("xaxis_var", shinyvalidate::sv_required("Please select an X-Axis variable"))
iv$add_rule("facet_ncol", plots_per_row_validate_rules())
iv$add_validator(horizontal_line()$iv_r())
iv$add_validator(anl_q_output()$iv_r())
iv$enable()
iv
})
create_plot <- reactive({
teal::validate_inputs(iv_r())
req(anl_q())
# nolint start
param <- input$xaxis_param
xaxis_var <- input$xaxis_var
xlim <- xrange_slider$state()$value
ylim <- yrange_slider$state()$value
font_size <- input$font_size
line_size <- input$line_size
hline_arb <- horizontal_line()$line_arb
hline_arb_label <- horizontal_line()$line_arb_label
hline_arb_color <- horizontal_line()$line_arb_color
facet_ncol <- input$facet_ncol
comb_line <- input$comb_line
rug_plot <- input$rug_plot
rotate_xlab <- input$rotate_xlab
trt_group <- input$trt_group
# nolint end
teal.code::eval_code(
object = anl_q()$qenv,
code = bquote({
p <- goshawk::g_density_distribution_plot(
data = ANL,
param_var = .(param_var),
param = .(param),
xaxis_var = .(xaxis_var),
trt_group = .(trt_group),
xlim = .(xlim),
ylim = .(ylim),
color_manual = .(color_manual),
color_comb = .(color_comb),
font_size = .(font_size),
line_size = .(line_size),
facet_ncol = .(facet_ncol),
comb_line = .(comb_line),
hline_arb = .(hline_arb),
hline_arb_label = .(hline_arb_label),
hline_arb_color = .(hline_arb_color),
rug_plot = .(rug_plot)
)
})
)
})
create_table <- reactive({
req(iv_r()$is_valid())
req(anl_q())
param <- input$xaxis_param
xaxis_var <- input$xaxis_var
font_size <- input$font_size
trt_group <- input$trt_group
teal.code::eval_code(
object = anl_q()$qenv,
code = bquote(
tbl <- goshawk::t_summarytable(
data = ANL,
trt_group = .(trt_group),
param_var = .(param_var),
param = .(param),
xaxis_var = .(xaxis_var),
font_size = .(font_size)
)
)
)
})
plot_r <- reactive({
create_plot()[["p"]]
})
plot_data <- teal.widgets::plot_with_settings_srv(
id = "plot",
plot_r = plot_r,
height = plot_height,
width = plot_width,
)
output$table_ui <- DT::renderDataTable({
req(create_table())
tbl <- create_table()[["tbl"]]
numeric_cols <- names(dplyr::select_if(tbl, is.numeric))
DT::datatable(tbl, rownames = FALSE, options = list(scrollX = TRUE)) %>%
DT::formatRound(numeric_cols, 2)
})
joined_qenvs <- reactive({
req(create_plot(), create_table())
teal.code::join(create_plot(), create_table())
})
teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(joined_qenvs())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(joined_qenvs())))
)
teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(
teal.code::get_code(joined_qenvs())
),
title = "Show R Code for Density Distribution Plot"
)
### REPORTER
if (with_reporter) {
card_fun <- function(comment, label) {
card <- report_card_template_goshawk(
title = "Density Distribution Plot",
label = label,
with_filter = with_filter,
filter_panel_api = filter_panel_api,
constraint_list = list(
constraint_var = input$constraint_var,
constraint_range_min = input$constraint_range_min,
constraint_range_max = input$constraint_range_max
)
)
card$append_text("Plot", "header3")
card$append_plot(plot_r(), dim = plot_data$dim())
card$append_text("Descriptive Statistics", "header3")
card$append_table(
create_table()[["tbl"]] %>% dplyr::mutate_if(is.numeric, round, 2)
)
if (!comment == "") {
card$append_text("Comment", "header3")
card$append_text(comment)
}
card$append_src(
paste(
teal.code::get_code(
teal.code::join(create_plot(), create_table())
),
collapse = "\n"
)
)
card
}
teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
}
###
})
}