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llrs-rochegithub-actions[bot]m7praverissimo
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Replace table by plot on tm_missing_data (#922)
# Pull Request <!--- Replace `#nnn` with your issue link for reference. --> Fixes #495 Replaces the table by a plot on "By Variables Levels" tab. The colors match those in the other plots of the module. It also required to add a "new" dependency, formatters, which is a dependency of tern, rlistings, rtable. I added it on Suggests. There is an extra commit to update the lintr names ```r data <- within(teal_data(), { ADSL <- rADSL ADRS <- rADRS }) join_keys(data) <- default_cdisc_join_keys[names(data)] init( data = data, modules = modules(tm_missing_data()) ) |> runApp() ``` --------- Signed-off-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com> Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
1 parent 8a94c04 commit 2bc2641

16 files changed

+249
-146
lines changed

‎.lintr‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,5 +2,6 @@ linters: linters_with_defaults(
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line_length_linter = line_length_linter(120),
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object_usage_linter = NULL,
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object_name_linter = object_name_linter(styles = c("snake_case", "symbols"), regexes = c(ANL = "^ANL_?[0-9A-Z_]*$", ADaM = "^r?AD[A-Z]{2,3}_?[0-9]*$")),
5-
indentation_linter = NULL
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indentation_linter = NULL,
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pipe_consistency_linter = NULL
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)

‎R/tm_a_pca.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -435,7 +435,7 @@ srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, deco
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teal.reporter::teal_card(obj),
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teal.reporter::teal_card("## Module's output(s)")
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)
438-
teal.code::eval_code(obj, 'library("ggplot2");library("dplyr");library("tidyr")') # nolint: quotes
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teal.code::eval_code(obj, "library(ggplot2);library(dplyr);library(tidyr)")
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})
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anl_merged_q <- reactive({
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req(anl_merged_input())

‎R/tm_a_regression.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -461,7 +461,7 @@ srv_a_regression <- function(id,
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teal.reporter::teal_card(obj),
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teal.reporter::teal_card("## Module's output(s)")
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)
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teal.code::eval_code(obj, 'library("ggplot2");library("dplyr")') # nolint: quotes
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teal.code::eval_code(obj, "library(ggplot2);library(dplyr)")
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})
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anl_merged_q <- reactive({

‎R/tm_data_table.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -309,7 +309,7 @@ srv_data_table <- function(id,
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teal::validate_has_data(df, min_nrow = 1L, msg = paste("data", dataname, "is empty"))
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qenv <- teal.code::eval_code(
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data(),
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'library("dplyr");library("DT")' # nolint: quotes.
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"library(dplyr);library(DT)"
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)
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teal.code::eval_code(
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qenv,

‎R/tm_g_association.R‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -151,8 +151,8 @@ tm_g_association <- function(label = "Association",
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show_association = TRUE,
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plot_height = c(600, 400, 5000),
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plot_width = NULL,
154-
distribution_theme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"), # nolint: line_length.
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association_theme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"), # nolint: line_length.
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distribution_theme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"), # nolint line_length_linter.
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association_theme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"), # nolint line_length_linter.
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pre_output = NULL,
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post_output = NULL,
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ggplot2_args = teal.widgets::ggplot2_args(),
@@ -345,7 +345,7 @@ srv_tm_g_association <- function(id,
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teal.reporter::teal_card(obj),
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teal.reporter::teal_card("## Module's output(s)")
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)
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teal.code::eval_code(obj, 'library("ggplot2");library("dplyr")') # nolint: quotes
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teal.code::eval_code(obj, "library(ggplot2);library(dplyr)")
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})
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anl_merged_q <- reactive({
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req(anl_merged_input())

‎R/tm_g_bivariate.R‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -558,9 +558,9 @@ srv_g_bivariate <- function(id,
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teal.reporter::teal_card(obj),
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teal.reporter::teal_card("## Module's output(s)")
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)
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obj %>%
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teal.code::eval_code('library("ggplot2");library("dplyr")') %>%
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teal.code::eval_code(as.expression(anl_merged_input()$expr)) # don't mix char with expr in single eval_code
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obj |>
562+
teal.code::eval_code("library(ggplot2);library(dplyr)") |>
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teal.code::eval_code(as.expression(anl_merged_input()$expr))
564564
})
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merged <- list(

‎R/tm_g_distribution.R‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -523,7 +523,7 @@ srv_distribution <- function(id,
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)
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qenv <- reactive(
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teal.code::eval_code(data(), 'library("ggplot2");library("dplyr")') # nolint quotes
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teal.code::eval_code(data(), "library(ggplot2);library(dplyr)")
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)
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anl_merged_q <- reactive({
@@ -663,7 +663,7 @@ srv_distribution <- function(id,
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"Group by variable must be `factor`, `character`, or `integer`"
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)
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)
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qenv <- teal.code::eval_code(qenv, 'library("forcats")') # nolint quotes
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qenv <- teal.code::eval_code(qenv, "library(forcats)")
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qenv <- teal.code::eval_code(
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qenv,
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substitute(
@@ -681,7 +681,7 @@ srv_distribution <- function(id,
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)
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)
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qenv <- teal.code::eval_code(qenv, 'library("forcats")') # nolint quotes
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qenv <- teal.code::eval_code(qenv, "library(forcats)")
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qenv <- teal.code::eval_code(
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qenv,
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substitute(
@@ -891,7 +891,7 @@ srv_distribution <- function(id,
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}
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if (length(t_dist) != 0 && main_type_var == "Density" && length(g_var) == 0 && length(s_var) == 0) {
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qenv <- teal.code::eval_code(qenv, 'library("ggpp")') # nolint quotes
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qenv <- teal.code::eval_code(qenv, "library(ggpp)")
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qenv <- teal.code::eval_code(
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qenv,
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substitute(
@@ -1037,7 +1037,7 @@ srv_distribution <- function(id,
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)
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if (length(t_dist) != 0 && length(g_var) == 0 && length(s_var) == 0) {
1040-
qenv <- teal.code::eval_code(qenv, 'library("ggpp")') # nolint quotes
1040+
qenv <- teal.code::eval_code(qenv, "library(ggpp)")
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qenv <- teal.code::eval_code(
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qenv,
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substitute(
@@ -1233,7 +1233,7 @@ srv_distribution <- function(id,
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qenv <- common_q()
12341234

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if (length(s_var) == 0 && length(g_var) == 0) {
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qenv <- teal.code::eval_code(qenv, 'library("generics")') # nolint quotes
1236+
qenv <- teal.code::eval_code(qenv, "library(generics)")
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qenv <- teal.code::eval_code(
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qenv,
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substitute(
@@ -1247,7 +1247,7 @@ srv_distribution <- function(id,
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)
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)
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} else {
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qenv <- teal.code::eval_code(qenv, 'library("tidyr")') # nolint quotes
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qenv <- teal.code::eval_code(qenv, "library(tidyr)")
12511251
qenv <- teal.code::eval_code(
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qenv,
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substitute(

‎R/tm_g_response.R‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -387,7 +387,7 @@ srv_g_response <- function(id,
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)
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qenv <- reactive(
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teal.code::eval_code(data(), 'library("ggplot2");library("dplyr")') # nolint quotes
390+
teal.code::eval_code(data(), "library(ggplot2);library(dplyr)")
391391
)
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anl_merged_q <- reactive({
@@ -520,7 +520,7 @@ srv_g_response <- function(id,
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resp_cl = resp_cl,
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hjust_value = if (swap_axes) "left" else "middle",
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vjust_value = if (swap_axes) "middle" else -1,
523-
position_anl2_value = if (!freq) quote(position_fill(0.5)) else quote(position_stack(0.5)), # nolint: line_length.
523+
position_anl2_value = if (!freq) quote(position_fill(0.5)) else quote(position_stack(0.5)), # nolint: line_length_linter.
524524
anl3_y = if (!freq) 1.1 else as.name("ns"),
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position_anl3_value = if (!freq) "fill" else "stack"
526526
)

‎R/tm_g_scatterplot.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -587,7 +587,7 @@ srv_g_scatterplot <- function(id,
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teal.reporter::teal_card(obj),
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teal.reporter::teal_card("## Module's output(s)")
589589
)
590-
teal.code::eval_code(data(), 'library("ggplot2");library("dplyr")') # nolint quotes
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teal.code::eval_code(data(), "library(ggplot2);library(dplyr)")
591591
})
592592

593593
anl_merged_q <- reactive({

‎R/tm_g_scatterplotmatrix.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -330,7 +330,7 @@ srv_g_scatterplotmatrix <- function(id,
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teal.reporter::teal_card(obj),
331331
teal.reporter::teal_card("## Module's output(s)")
332332
)
333-
qenv <- teal.code::eval_code(obj, 'library("dplyr");library("lattice")') # nolint quotes
333+
qenv <- teal.code::eval_code(obj, "library(dplyr);library(lattice)")
334334
teal.code::eval_code(qenv, as.expression(anl_merged_input()$expr))
335335
})
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