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introduce decorators for tm_missing_data #809

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introduce decorators for tm_missing_data #809

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cca4193
this is not there yet!
m7pr Nov 22, 2024
ad975fd
Merge branch '1187_decorate_output@main' into tm_missing_data_module@…
m7pr Nov 22, 2024
8f0687b
chore: rename ui/srv_teal_transform_data to ui/srv_transform_teal_data
averissimo Nov 22, 2024
e5f7864
Merge branch '1187_decorate_output@main' into tm_missing_data_module@…
averissimo Nov 22, 2024
2c3c297
fix: move all decoration to 1 chunk and fix problems
averissimo Nov 22, 2024
5a27da7
Merge branch '1187_decorate_output@main' into tm_missing_data_module@…
m7pr Nov 22, 2024
314e06c
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m7pr Nov 25, 2024
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184 changes: 127 additions & 57 deletions R/tm_missing_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,18 @@
#'
#' @inherit shared_params return
#'
#' @section Decorating `tm_missing_data`:
#'
#' This module generates the following objects, which can be modified in place using decorators:
#' - `summary_plot_top` (`ggplot2`)
#' - `summary_plot_bottom` (`ggplot2`)
#' - `combination_plot_top` (`ggplot2`)
#' - `combination_plot_bottom` (`ggplot2`)
#' - `table` ([DT::datatable()])
#'
#' For additional details and examples of decorators, refer to the vignette
#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
#'
#' @examplesShinylive
#' library(teal.modules.general)
#' interactive <- function() TRUE
Expand Down Expand Up @@ -87,7 +99,8 @@ tm_missing_data <- function(label = "Missing data",
"Combinations Main" = teal.widgets::ggplot2_args(labs = list(title = NULL))
),
pre_output = NULL,
post_output = NULL) {
post_output = NULL,
decorators = NULL) {
message("Initializing tm_missing_data")

# Requires Suggested packages
Expand Down Expand Up @@ -121,14 +134,19 @@ tm_missing_data <- function(label = "Missing data",

checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
checkmate::assert_list(decorators, "teal_transform_module", null.ok = TRUE)
# End of assertions

ans <- module(
label,
server = srv_page_missing_data,
server_args = list(
parent_dataname = parent_dataname, plot_height = plot_height,
plot_width = plot_width, ggplot2_args = ggplot2_args, ggtheme = ggtheme
parent_dataname = parent_dataname,
plot_height = plot_height,
plot_width = plot_width,
ggplot2_args = ggplot2_args,
ggtheme = ggtheme,
decorators = decorators
),
ui = ui_page_missing_data,
datanames = "all",
Expand Down Expand Up @@ -165,7 +183,7 @@ ui_page_missing_data <- function(id, pre_output = NULL, post_output = NULL) {

# Server function for the missing data module (all datasets)
srv_page_missing_data <- function(id, data, reporter, filter_panel_api, parent_dataname,
plot_height, plot_width, ggplot2_args, ggtheme) {
plot_height, plot_width, ggplot2_args, ggtheme, decorators) {
with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
moduleServer(id, function(input, output, session) {
Expand Down Expand Up @@ -215,7 +233,8 @@ srv_page_missing_data <- function(id, data, reporter, filter_panel_api, parent_d
id = ns(x),
summary_per_patient = if_subject_plot,
ggtheme = ggtheme,
datanames = datanames
datanames = datanames,
decorators = decorators
)
)
}
Expand Down Expand Up @@ -248,7 +267,8 @@ srv_page_missing_data <- function(id, data, reporter, filter_panel_api, parent_d
parent_dataname = parent_dataname,
plot_height = plot_height,
plot_width = plot_width,
ggplot2_args = ggplot2_args
ggplot2_args = ggplot2_args,
decorators = decorators
)
}
)
Expand Down Expand Up @@ -326,7 +346,7 @@ ui_missing_data <- function(id, by_subject_plot = FALSE) {
}

# UI encoding for the missing data module (all datasets)
encoding_missing_data <- function(id, summary_per_patient = FALSE, ggtheme, datanames) {
encoding_missing_data <- function(id, summary_per_patient = FALSE, ggtheme, datanames, decorators) {
ns <- NS(id)

tagList(
Expand Down Expand Up @@ -401,6 +421,7 @@ encoding_missing_data <- function(id, summary_per_patient = FALSE, ggtheme, data
)
)
),
ui_transform_teal_data(ns("decorator"), transformators = decorators),
teal.widgets::panel_item(
title = "Plot settings",
selectInput(
Expand All @@ -416,7 +437,7 @@ encoding_missing_data <- function(id, summary_per_patient = FALSE, ggtheme, data

# Server function for the missing data (single dataset)
srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, parent_dataname,
plot_height, plot_width, ggplot2_args) {
plot_height, plot_width, ggplot2_args, decorators) {
with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
checkmate::assert_class(data, "reactive")
Expand Down Expand Up @@ -718,7 +739,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
qenv <- teal.code::eval_code(
qenv,
substitute(
p1 <- summary_plot_obs %>%
summary_plot_top <- summary_plot_obs %>%
ggplot() +
aes(
x = factor(create_cols_labels(col), levels = x_levels),
Expand Down Expand Up @@ -800,7 +821,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
qenv <- teal.code::eval_code(
qenv,
substitute(
p2 <- summary_plot_patients %>%
summary_plot_bottom <- summary_plot_patients %>%
ggplot() +
aes_(
x = ~ factor(create_cols_labels(col), levels = x_levels),
Expand Down Expand Up @@ -833,34 +854,11 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
ggthemes = parsed_ggplot2_args$ggtheme
)
)
) %>%
teal.code::eval_code(
quote({
g1 <- ggplotGrob(p1)
g2 <- ggplotGrob(p2)
g <- gridExtra::gtable_cbind(g1, g2, size = "first")
g$heights <- grid::unit.pmax(g1$heights, g2$heights)
grid::grid.newpage()
})
)
} else {
qenv <- teal.code::eval_code(
qenv,
quote({
g <- ggplotGrob(p1)
grid::grid.newpage()
})
)
}

teal.code::eval_code(
qenv,
quote(grid::grid.draw(g))
)
qenv
})

summary_plot_r <- reactive(summary_plot_q()[["g"]])

combination_cutoff_q <- reactive({
req(common_code_q())
teal.code::eval_code(
Expand Down Expand Up @@ -976,7 +974,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
qenv,
substitute(
expr = {
p1 <- data_combination_plot_cutoff %>%
combination_plot_top <- data_combination_plot_cutoff %>%
dplyr::select(id, n) %>%
dplyr::distinct() %>%
ggplot(aes(x = id, y = n)) +
Expand All @@ -994,7 +992,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
graph_number_rows <- length(unique(data_combination_plot_cutoff$id))
graph_number_cols <- nrow(data_combination_plot_cutoff) / graph_number_rows

p2 <- data_combination_plot_cutoff %>% ggplot() +
combination_plot_bottom <- data_combination_plot_cutoff %>% ggplot() +
aes(x = create_cols_labels(key), y = id - 0.5, fill = value) +
geom_tile(alpha = 0.85, height = 0.95) +
scale_fill_manual(
Expand All @@ -1008,14 +1006,6 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
labs2 +
ggthemes2 +
themes2

g1 <- ggplotGrob(p1)
g2 <- ggplotGrob(p2)

g <- gridExtra::gtable_rbind(g1, g2, size = "last")
g$heights[7] <- grid::unit(0.2, "null") # rescale to get the bar chart smaller
grid::grid.newpage()
grid::grid.draw(g)
},
env = list(
labs1 = parsed_ggplot2_args1$labs,
Expand All @@ -1029,8 +1019,6 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
)
})

combination_plot_r <- reactive(combination_plot_q()[["g"]])

summary_table_q <- reactive({
req(
input$summary_type == "By Variable Levels", # needed to trigger show r code update on tab change
Expand Down Expand Up @@ -1074,14 +1062,14 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
qenv,
substitute(
expr = {
summary_data <- ANL %>%
table <- ANL %>%
dplyr::mutate(group_var_name := forcats::fct_na_value_to_level(as.factor(group_var_name), "NA")) %>%
dplyr::group_by_at(group_var) %>%
dplyr::filter(group_var_name %in% group_vals)

count_data <- dplyr::summarise(summary_data, n = dplyr::n())
count_data <- dplyr::summarise(table, n = dplyr::n())

summary_data <- dplyr::summarise_all(summary_data, summ_fn) %>%
table <- dplyr::summarise_all(table, summ_fn) %>%
dplyr::mutate(group_var_name := paste0(group_var, ":", group_var_name, "(N=", count_data$n, ")")) %>%
tidyr::pivot_longer(!dplyr::all_of(group_var), names_to = "Variable", values_to = "out") %>%
tidyr::pivot_wider(names_from = group_var, values_from = "out") %>%
Expand All @@ -1108,11 +1096,9 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
)
}

teal.code::eval_code(qenv, quote(summary_data))
within(qenv, quote(table <- DT::datatable(summary_data)))
})

summary_table_r <- reactive(summary_table_q()[["summary_data"]])

by_subject_plot_q <- reactive({
# needed to trigger show r code update on tab change
req(input$summary_type == "Grouped by Subject", common_code_q())
Expand Down Expand Up @@ -1188,7 +1174,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
teal.code::eval_code(
substitute(
expr = {
g <- ggplot(summary_plot_patients, aes(
plot <- ggplot(summary_plot_patients, aes(
x = factor(id, levels = order_subjects),
y = factor(col, levels = ordered_columns[["column"]]),
fill = isna
Expand All @@ -1209,7 +1195,6 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
labs +
ggthemes +
themes
print(g)
},
env = list(
labs = parsed_ggplot2_args$labs,
Expand All @@ -1220,7 +1205,92 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
)
})

by_subject_plot_r <- reactive(by_subject_plot_q()[["g"]])
# Start decoration of objects

# summary_plot_q
decorated_summary_plot_q_no_print <- srv_transform_teal_data(
id = "decorator",
data = summary_plot_q,
transformators = decorators
)
decorated_summary_plot_q <- reactive({
expr <- if (isTRUE(input$if_patients_plot)) {
quote({
g1 <- ggplotGrob(summary_plot_top)
g2 <- ggplotGrob(summary_plot_bottom)
plot <- gridExtra::gtable_cbind(g1, g2, size = "first")
plot$heights <- grid::unit.pmax(g1$heights, g2$heights)
})
} else {
quote({
g1 <- ggplotGrob(summary_plot_top)
plot <- g1
})
}
decorated_summary_plot_q_no_print() %>%
eval_code(expr) %>%
within({
grid::grid.newpage()
grid::grid.draw(plot)
})
})

# combination_plot_q
decorated_combination_plot_q_no_print <- srv_transform_teal_data(
id = "decorator",
data = combination_plot_q,
transformators = decorators
)
decorated_combination_plot_q <- reactive({
within(
decorated_combination_plot_q_no_print(),
{
g1 <- ggplotGrob(combination_plot_top)
g2 <- ggplotGrob(combination_plot_bottom)

plot <- gridExtra::gtable_rbind(g1, g2, size = "last")
plot$heights[7] <- grid::unit(0.2, "null") # rescale to get the bar chart smaller
grid::grid.newpage()
grid::grid.draw(plot)
}
)
})

# summary_table_q
decorated_summary_table_q <- srv_transform_teal_data(
id = "decorator",
data = summary_table_q,
transformators = decorators
)

# by_subject_plot_q
decorated_by_subject_plot_q_no_print <- srv_transform_teal_data(
id = "decorator",
data = by_subject_plot_q,
transformators = decorators
)
decorated_by_subject_plot_q <- reactive(within(decorated_by_subject_plot_q_no_print(), print(plot)))

# Output objects for use in widgets
summary_plot_r <- reactive({
req(summary_plot_q())
decorated_summary_plot_q()[["plot"]]
})

combination_plot_r <- reactive({
req(combination_plot_q())
decorated_combination_plot_q()[["plot"]]
})

summary_table_r <- reactive({
req(summary_table_q())
decorated_summary_table_q()[["table"]]
})

by_subject_plot_r <- reactive({
req(by_subject_plot_q()) # Ensure original errors are displayed
decorated_by_subject_plot_q()[["plot"]]
})

output$levels_table <- DT::renderDataTable(
expr = {
Expand Down Expand Up @@ -1272,7 +1342,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(final_q())),
verbatim_content = reactive(teal.code::get_code(req(final_q()))),
title = "Show R Code for Missing Data"
)

Expand Down Expand Up @@ -1308,7 +1378,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
card$append_text("Comment", "header3")
card$append_text(comment)
}
card$append_src(teal.code::get_code(final_q()))
card$append_src(teal.code::get_code(req(final_q())))
card
}
teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
Expand Down
8 changes: 4 additions & 4 deletions man/tm_a_pca.Rd
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