1441 Introduce transformators parameter in modules #826
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m7pr
changed the title
…sengineering/teal.modules.general into 1441_transformators@main
…y documented in teal_module
Merge branch '1441_transformators@main' of https://github.com/insightsengineering/teal.modules.general into 1441_transformators@main # Conflicts: # man/tm_a_pca.Rd # man/tm_a_regression.Rd # man/tm_g_association.Rd # man/tm_g_bivariate.Rd # man/tm_g_distribution.Rd # man/tm_g_response.Rd # man/tm_g_scatterplot.Rd # man/tm_g_scatterplotmatrix.Rd # man/tm_missing_data.Rd # man/tm_outliers.Rd # man/tm_t_crosstable.Rd
Unit Tests Summary 1 files 22 suites 13m 14s ⏱️ Results for commit 1764c3e. ♻️ This comment has been updated with latest results. |
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Additional test case details
Results for commit de74d65 ♻️ This comment has been updated with latest results. |
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There are 15 modules:
ls -1 *.R | grep "tm_*"
tm_a_pca.Ro
tm_a_regression.R
tm_data_table.R
tm_file_viewer.R
tm_front_page.R
tm_g_association.R
tm_g_bivariate.R
tm_g_distribution.R
tm_g_response.R
tm_g_scatterplot.R
tm_g_scatterplotmatrix.R
tm_missing_data.R
tm_outliers.R
tm_t_crosstable.R
tm_variable_browser.RMinus the three mentioned as not implemented: tm_data_table, tm_file_viewer and tm_front_page, this leaves tm_variable_browser as not implemented and not commented on. But as it doesn't have decorators I guess it falls on the same list.
About the difference between the defaults on transformators and decorators, I think it makes sense to have the same default. The suggested idea could work well with minimal changes.
@llrs-roche I was thinking about changing defaults for What are your thoughts on this @gogonzo ? Should we unify |
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My 2 cents: On one hand I like that these two arguments doing similar things have similar arguments default that differentiate from the others. On the other hand I would prefer to have NULL as default, but list seems like a good indicator that more than one can be provided 👍 |
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Thanks for backing up the discussion. I'll proceed with changing |
Example with no decorators and no transformators# general data example
data <- teal_data()
data <- within(data, {
require(nestcolor)
USArrests <- USArrests
})
app <- init(
data = data,
modules = modules(
tm_a_pca(
"PCA",
dat = data_extract_spec(
dataname = "USArrests",
select = select_spec(
choices = variable_choices(
data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
),
selected = c("Murder", "Assault"),
multiple = TRUE
),
filter = NULL
)
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}Example with decorators and no transformatorsfootnote_dec <- teal_transform_module(
label = "Footnote",
ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = "I am a good decorator"),
server = function(id, data) {
moduleServer(id, function(input, output, session) {
logger::log_info("🟢 Footnote called to action!", namespace = "teal.modules.general")
reactive(
within(
data(),
{
footnote_str <- footnote
plot <- plot + ggplot2::labs(caption = footnote_str)
},
footnote = input$footnote
)
)
})
}
)
title_plot <- teal_transform_module(
server = make_teal_transform_server(
expression(
logger::log_info("🔴 Title being called to action!", namespace = "teal.modules.general"),
plot <- plot + ggplot2::ggtitle("A title to the plot")
)
)
)
# CDISC data example
data <- teal_data()
data <- within(data, {
require(nestcolor)
ADSL <- rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
app <- init(
data = data,
modules = modules(
tm_g_response(
label = "Response Plots",
decorators = list(footnote_dec, title_plot),
response = data_extract_spec(
dataname = "ADSL",
select = select_spec(
label = "Select variable:",
choices = variable_choices(data[["ADSL"]], c("BMRKR2", "COUNTRY")),
selected = "BMRKR2",
multiple = FALSE,
fixed = FALSE
)
),
x = data_extract_spec(
dataname = "ADSL",
select = select_spec(
label = "Select variable:",
choices = variable_choices(data[["ADSL"]], c("SEX", "RACE")),
selected = "RACE",
multiple = FALSE,
fixed = FALSE
)
)
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
Example with no decorators and with transformators# general data example
data <- teal_data()
data <- within(data, {
require(nestcolor)
CO2 <- data.frame(CO2)
})
head_transformator <-
teal_transform_module(
label = "Custom transformator for CO2",
ui = function(id) {
ns <- NS(id)
tags$div(
numericInput(ns("n_rows"), "Number of rows to subset", value = 6, min = 1, max = 150, step = 1)
)
},
server = function(id, data) {
moduleServer(id, function(input, output, session) {
reactive({
within(data(),
{
CO2 <- head(CO2, num_rows)
},
num_rows = input$n_rows
)
})
})
}
)
app <- init(
data = data,
modules = tm_g_bivariate(
transformators = list(head_transformator),
x = data_extract_spec(
dataname = "CO2",
select = select_spec(
label = "Select variable:",
choices = variable_choices(data[["CO2"]]),
selected = "conc",
fixed = FALSE
)
),
y = data_extract_spec(
dataname = "CO2",
select = select_spec(
label = "Select variable:",
choices = variable_choices(data[["CO2"]]),
selected = "uptake",
multiple = FALSE,
fixed = FALSE
)
),
row_facet = data_extract_spec(
dataname = "CO2",
select = select_spec(
label = "Select variable:",
choices = variable_choices(data[["CO2"]]),
selected = "Type",
fixed = FALSE
)
),
col_facet = data_extract_spec(
dataname = "CO2",
select = select_spec(
label = "Select variable:",
choices = variable_choices(data[["CO2"]]),
selected = "Treatment",
fixed = FALSE
)
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}Example with with decorators and with transformatorshead_transformator <-
teal_transform_module(
label = "Custom transformator for CO2",
ui = function(id) {
ns <- NS(id)
tags$div(
numericInput(ns("n_rows"), "Number of rows to subset", value = 6, min = 1, max = 150, step = 1)
)
},
server = function(id, data) {
moduleServer(id, function(input, output, session) {
reactive({
within(data(),
{
CO2 <- head(CO2, num_rows)
},
num_rows = input$n_rows
)
})
})
}
)
plot_grob_decorator <- function(default_footnote = "I am a good decorator", .var_to_replace = "plot") {
teal_transform_module(
label = "Caption (grob)",
ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = default_footnote),
server = function(id, data) {
moduleServer(id, function(input, output, session) {
logger::log_info("🟠 plot_grob with default: {default_footnote}!", namespace = "teal.modules.general")
reactive({
req(data(), input$footnote)
logger::log_info("changing the footnote {default_footnote}", namespace = "teal.modules.general")
teal.code::eval_code(data(), substitute(
{
footnote_grob <- grid::textGrob(footnote, x = 0, hjust = 0, gp = grid::gpar(fontsize = 10, fontface = "italic", col = "gray50"))
# Arrange the plot and footnote
.var_to_replace <- gridExtra::arrangeGrob(
.var_to_replace,
footnote_grob,
ncol = 1,
heights = grid::unit.c(grid::unit(1, "npc") - grid::unit(1, "lines"), grid::unit(1, "lines"))
)
},
env = list(
footnote = input$footnote,
.var_to_replace = as.name(.var_to_replace)
)))
})
})
}
)
}
# general data example
data <- teal_data()
data <- within(data, {
require(nestcolor)
CO2 <- CO2
factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L))))
CO2[factors] <- lapply(CO2[factors], as.character)
})
app <- init(
data = data,
modules = modules(
tm_g_association(
ref = data_extract_spec(
dataname = "CO2",
select = select_spec(
label = "Select variable:",
choices = variable_choices(data[["CO2"]], c("Plant", "Type", "Treatment")),
selected = "Plant",
fixed = FALSE
)
),
vars = data_extract_spec(
dataname = "CO2",
select = select_spec(
label = "Select variables:",
choices = variable_choices(data[["CO2"]], c("Plant", "Type", "Treatment")),
selected = "Treatment",
multiple = TRUE,
fixed = FALSE
)
),
transformators = list(head_transformator),
decorators = list(plot_grob_decorator("I am a good grob (association)"))
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
Example with with decorators and with transformators AND DECORATORS IS NAMEDhead_transformator <-
teal_transform_module(
label = "Custom transformator for CO2",
ui = function(id) {
ns <- NS(id)
tags$div(
numericInput(ns("n_rows"), "Number of rows to subset", value = 6, min = 1, max = 150, step = 1)
)
},
server = function(id, data) {
moduleServer(id, function(input, output, session) {
reactive({
within(data(),
{
CO2 <- head(CO2, num_rows)
},
num_rows = input$n_rows
)
})
})
}
)
plot_grob_decorator <- function(default_footnote = "I am a good decorator", .var_to_replace = "plot") {
teal_transform_module(
label = "Caption (grob)",
ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = default_footnote),
server = function(id, data) {
moduleServer(id, function(input, output, session) {
logger::log_info("🟠 plot_grob with default: {default_footnote}!", namespace = "teal.modules.general")
reactive({
req(data(), input$footnote)
logger::log_info("changing the footnote {default_footnote}", namespace = "teal.modules.general")
teal.code::eval_code(data(), substitute(
{
footnote_grob <- grid::textGrob(footnote, x = 0, hjust = 0, gp = grid::gpar(fontsize = 10, fontface = "italic", col = "gray50"))
# Arrange the plot and footnote
.var_to_replace <- gridExtra::arrangeGrob(
.var_to_replace,
footnote_grob,
ncol = 1,
heights = grid::unit.c(grid::unit(1, "npc") - grid::unit(1, "lines"), grid::unit(1, "lines"))
)
},
env = list(
footnote = input$footnote,
.var_to_replace = as.name(.var_to_replace)
)))
})
})
}
)
}
# general data example
data <- teal_data()
data <- within(data, {
require(nestcolor)
CO2 <- CO2
factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L))))
CO2[factors] <- lapply(CO2[factors], as.character)
})
app <- init(
data = data,
modules = modules(
tm_g_association(
ref = data_extract_spec(
dataname = "CO2",
select = select_spec(
label = "Select variable:",
choices = variable_choices(data[["CO2"]], c("Plant", "Type", "Treatment")),
selected = "Plant",
fixed = FALSE
)
),
vars = data_extract_spec(
dataname = "CO2",
select = select_spec(
label = "Select variables:",
choices = variable_choices(data[["CO2"]], c("Plant", "Type", "Treatment")),
selected = "Treatment",
multiple = TRUE,
fixed = FALSE
)
),
transformators = list(head_transformator),
decorators = list(plot = plot_grob_decorator("I am a good grob (association)"))
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
|
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@llrs-roche would you mind revisiting PR? |
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All the other changes since my previous feedback look good. I left a minor comment to help users.
Not sure of the implications of the changes on normalize_decorators but I didn't notice any problem with the changes.
I tested adding two decorators with the same name (to see what would happen):
decorators = list(plot = plot_grob_decorator("I am a good grob (association)"),
plot= plot_grob_decorator("I am a good grob 2 (association)"))
The module uses only the first (and doesn't warn about removing the second). I don't think this was covered initially, but maybe it is a good time to consider/add it?
Co-authored-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com>
…#1449) The same changes as in insightsengineering/teal.modules.general#826 We are unifying `decorators` and `transformators` default values for modules
That's funny : ) I think there is a way to extend |
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Hey @llrs-roche @gogonzo this branch now runs tests and checks smoothly and was also covered with few examples of using decorators for one or multiple objects. I will start an issue to cover a situation where a list of decorators has duplicates in names. And another issue to possibly extend tests to cover decorators / transformators case. Other than that, I am merging this PR |
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Checking again and I see this error message on the example with multiple decorators, but it doesn't seem a problem with the decorators machinery, just the decorator function:
But I think it is better to address other problems in separate issues/PR 👍 |
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Yeah @llrs-roche the footnote_dec <- teal_transform_module(
label = "Footnote",
ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = "I am a good decorator"),
server = function(id, data) {
moduleServer(id, function(input, output, session) {
logger::log_info("🟢 Footnote called to action!", namespace = "teal.modules.general")
reactive(
within(
data(),
{
footnote_str <- footnote
histogram_plot <- histogram_plot + ggplot2::labs(caption = footnote_str)
},
footnote = input$footnote
)
)
})
}
)
table_dup_dec <- teal_transform_module(
server = make_teal_transform_server(
expression(
logger::log_info("🔴 Table dup being called to action!", namespace = "teal.modules.general"),
summary_table <- rbind(summary_table, summary_table),
if (exists("test_table")) test_table <- rbind(test_table, test_table, test_table)
)
)
)
# CDISC data example
data <- teal_data()
data <- within(data, {
ADSL <- rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
vars1 <- choices_selected(
variable_choices(data[["ADSL"]], c("ARM", "COUNTRY", "SEX")),
selected = NULL
)
app <- init(
data = data,
modules = modules(
tm_g_distribution(
decorators = list(histogram_plot = list(footnote_dec), summary_table = list(table_dup_dec)),
dist_var = data_extract_spec(
dataname = "ADSL",
select = select_spec(
choices = variable_choices(data[["ADSL"]], c("AGE", "BMRKR1")),
selected = "BMRKR1",
multiple = FALSE,
fixed = FALSE
)
),
strata_var = data_extract_spec(
dataname = "ADSL",
filter = filter_spec(
vars = vars1,
multiple = TRUE
)
),
group_var = data_extract_spec(
dataname = "ADSL",
filter = filter_spec(
vars = vars1,
multiple = TRUE
)
)
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
} |
insightsengineering/teal#1441
Included
transformatorsparameter in modules. This is passed toteal::modulethat does assertions and checks on this parameter.Did not introduce for
tm_data_table,tm_file_viewerandtm_front_pageas we also didn't introducedecoratorsfor those modules. We can always introduce, if there is a user request, but I don't think there will ever be.Lastly, a food for thought: default
decoratorsvalue isNULLwhere defaulttransformatorsvalue islist(). Maybe we can introduce a check, that allowstransformatorsto beNULLon default, and which changesNULLtolist().