Skip to content

Replace table by plot on tm_missing_data #922

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 72 commits into
base: main
Choose a base branch
from
+247 −148
Open

Replace table by plot on tm_missing_data #922

Show file tree
Hide file tree
Changes from 44 commits
Commits
Show all changes
72 commits
Select commit Hold shift + click to select a range
ec44372
Explore heatmap and tile map
llrs-roche Sep 23, 2025
4593c88
Fix lintr names
llrs-roche Oct 3, 2025
586b960
Replace table by a plot
llrs-roche Oct 3, 2025
c4a13cc
Fix lint comments
llrs-roche Oct 3, 2025
dda7615
[skip style] [skip vbump] Restyle files
github-actions[bot] Oct 3, 2025
ea38ac1
Fix lintr issues
llrs-roche Oct 3, 2025
ee7f4b6
Merge branch '495_plot_missing@main' of github.com:insightsengineerin…
llrs-roche Oct 3, 2025
1159a49
Merge branch 'main' into 495_plot_missing@main
llrs-roche Oct 3, 2025
c296936
Split evaluation to load libraries
llrs-roche Oct 3, 2025
56020d4
Merge branch 'main' into 495_plot_missing@main
m7pr Oct 8, 2025
5e3080d
Use "library(pkg)" instead of 'library("pkg")' #nolint
llrs-roche Oct 9, 2025
484b91c
Use dot at the end of lint comment
llrs-roche Oct 9, 2025
d2673e6
Simplify code branch
llrs-roche Oct 13, 2025
558f666
[skip style] [skip vbump] Restyle files
github-actions[bot] Oct 13, 2025
5c4b580
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
github-actions[bot] Oct 13, 2025
d2a903f
Merge branch 'main' into 495_plot_missing@main
llrs-roche Oct 15, 2025
08951f5
Merge branch 'main' into 495_plot_missing@main
llrs-roche Oct 16, 2025
bcf8803
Merge branch 'main' into 495_plot_missing@main
m7pr Oct 17, 2025
ef399e0
Fix logic
llrs-roche Oct 17, 2025
f383cc7
Avoid ggplot2 warnings
llrs-roche Oct 17, 2025
fed8c46
Check feedback from copilot
llrs-roche Oct 17, 2025
6d71798
[skip style] [skip vbump] Restyle files
github-actions[bot] Oct 17, 2025
22faabd
Fix misspelling on linters
llrs-roche Oct 20, 2025
3cb8e61
Fix style
llrs-roche Oct 20, 2025
463f61e
Do not reduce the timeout from the default 4s
llrs-roche Oct 20, 2025
b576f8e
[skip style] [skip vbump] Restyle files
github-actions[bot] Oct 20, 2025
3696675
Fix typo
llrs-roche Oct 20, 2025
949a35b
Avoid skipping tests
llrs-roche Oct 20, 2025
ed17c6b
Update code based on https://github.com/insightsengineering/teal.modu…
llrs-roche Oct 20, 2025
188fa05
Add req to resolve the app faster
llrs-roche Oct 21, 2025
f1a180b
[skip style] [skip vbump] Restyle files
github-actions[bot] Oct 21, 2025
1006fa9
Prefix functions with their packages
llrs-roche Oct 21, 2025
8a311f1
Fix typo
llrs-roche Oct 21, 2025
5b4226a
Fix package
llrs-roche Oct 21, 2025
5a3bea4
Merge branch 'main' into 495_plot_missing@main
llrs-roche Nov 17, 2025
4b6e867
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
github-actions[bot] Nov 17, 2025
4c1692e
Merge branch 'main' into 495_plot_missing@main
m7pr Nov 17, 2025
46c9ec3
Merge from main
llrs-roche Nov 20, 2025
8845ead
Test CI changes
llrs-roche Nov 21, 2025
ef59971
ci: test ci and revert in the next commit
averissimo Nov 21, 2025
1732dfd
Update R/tm_g_association.R
llrs-roche Nov 21, 2025
7329984
adds new file to remove later
averissimo Nov 21, 2025
c13063f
chore: cleanup extra files and fix name
averissimo Nov 21, 2025
ad5c396
chore: remove added file
averissimo Nov 21, 2025
31957c5
Remove mention to ggmosaic
llrs-roche Nov 24, 2025
d17b93b
Remove extra dependency
llrs-roche Nov 24, 2025
5626cc3
Apply suggestions from code review
llrs-roche Nov 24, 2025
cd0880a
Use main now that https://github.com/insightsengineering/r.pkg.templa…
llrs-roche Nov 24, 2025
b89baee
Merge branch '495_plot_missing@main' of github.com:insightsengineerin…
llrs-roche Nov 24, 2025
5c1bd30
Merge branch 'main' into 495_plot_missing@main
llrs-roche Nov 25, 2025
a2eabe6
Merged origin/495_plot_missing@main into 495_plot_missing@main
llrs-roche Nov 25, 2025
ce2abbe
Merge branch 'main' into 495_plot_missing@main
m7pr Nov 25, 2025
b77b58e
Merge branch 'main' into 495_plot_missing@main
llrs-roche Nov 26, 2025
4bedaa3
update insightsengineering/teal@bring_tests
m7pr Nov 27, 2025
e65605f
Update DESCRIPTION
m7pr Nov 27, 2025
5eed0fe
Update check.yaml to allow PR events on any branch
m7pr Nov 27, 2025
1a5e934
Add lintr issue
llrs-roche Nov 28, 2025
b46d233
Fix summary plot from anyna
llrs-roche Nov 28, 2025
3d60bc4
Update id
llrs-roche Dec 1, 2025
e183a3c
Fix module so plot is shown
llrs-roche Dec 1, 2025
6d7b42f
Fix file_viewer tests
llrs-roche Dec 1, 2025
466d5e7
Simplify selectors (and lintr notes)
llrs-roche Dec 1, 2025
70bbaf0
Add more pause to ensure the checks are when the app is ready
llrs-roche Dec 1, 2025
d480e4a
Update ids
llrs-roche Dec 1, 2025
ddc10db
Remove test about a table no longer present
llrs-roche Dec 2, 2025
b72941c
Remove requirements that prevented displaying the output
llrs-roche Dec 2, 2025
9c17dd9
Update the ids of the plots
llrs-roche Dec 2, 2025
d1f46c9
Apply suggestions from code review
llrs-roche Dec 2, 2025
605abe2
Update R/tm_missing_data.R
llrs-roche Dec 2, 2025
78021ce
Update R/tm_missing_data.R
llrs-roche Dec 2, 2025
5677cc2
Fix logic for validation error
llrs-roche Dec 2, 2025
a95713e
Update R/tm_missing_data.R
llrs-roche Dec 2, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions .github/workflows/check.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ jobs:
uses: insightsengineering/r.pkg.template/.github/workflows/audit.yaml@main
r-cmd:
name: R CMD Check 🧬
uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@skip_missing_files
Copy link
Contributor Author

@llrs-roche llrs-roche Nov 21, 2025 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Do not merge till this is removed (uses insightsengineering/r.pkg.template#290). This is to prevent GHA failures on Check only affected modules 🎯:

No TESTING_DEPTH default.
Setting TESTING_DEPTH=5
Commit msg is: Merge 46c9ec30e1f1947b3aeef81b955822ea6901dd36 into ac4deefcc5fa28dfa671e7698e37829dcd4e411f
Check for tests/testthat/test-shinytest2-tm_missing_data.R.
sed: can't read tests/testthat/test-shinytest2-tm_missing_data.R
tests/testthat/test-shinytest2-tm_misssing_data.R: No such file or directory

Copy link
Contributor

@averissimo averissimo Nov 21, 2025 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Do not merge until test-shinytest2-tm_missing_data_remove_this_suffix.R is renamed back! no longer applies

secrets:
REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
with:
Expand All @@ -46,7 +46,7 @@ jobs:
selected-shinytests: true
r-cmd-non-cran:
name: R CMD Check (non-CRAN) 🧬
uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@skip_missing_files
secrets:
REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
with:
Expand Down
1 change: 1 addition & 0 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,7 @@ Imports:
tools,
utils
Suggests:
formatters (>= 0.5.11),
knitr (>= 1.42),
logger (>= 0.4.0),
nestcolor (>= 0.1.0),
Expand Down
6 changes: 6 additions & 0 deletions R/teal.modules.general.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,5 +14,11 @@
#' @keywords internal
"_PACKAGE"

# nolint start.
# Note ggmosaic (version <= 0.3.3) needs to be in DEPENDS as the following does not work if it is imported
# df <- data.frame(x = c("A", "B", "C", "A"), y = c("Z", "Z", "W", "W"))
# ggplot(df) + ggmosaic::geom_mosaic(aes(x = ggmosaic::product(x), fill = y))
# nolint end.

# Needed to avoid R CMD note on no visible binding
utils::globalVariables("count")
2 changes: 1 addition & 1 deletion R/tm_a_pca.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -435,7 +435,7 @@ srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, deco
teal.reporter::teal_card(obj),
teal.reporter::teal_card("## Module's output(s)")
)
teal.code::eval_code(obj, 'library("ggplot2");library("dplyr");library("tidyr")') # nolint: quotes
teal.code::eval_code(obj, "library(ggplot2);library(dplyr);library(tidyr)")
})
anl_merged_q <- reactive({
req(anl_merged_input())
Expand Down
2 changes: 1 addition & 1 deletion R/tm_a_regression.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -461,7 +461,7 @@ srv_a_regression <- function(id,
teal.reporter::teal_card(obj),
teal.reporter::teal_card("## Module's output(s)")
)
teal.code::eval_code(obj, 'library("ggplot2");library("dplyr")') # nolint: quotes
teal.code::eval_code(obj, "library(ggplot2);library(dplyr)")
})

anl_merged_q <- reactive({
Expand Down
2 changes: 1 addition & 1 deletion R/tm_data_table.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -309,7 +309,7 @@ srv_data_table <- function(id,
teal::validate_has_data(df, min_nrow = 1L, msg = paste("data", dataname, "is empty"))
qenv <- teal.code::eval_code(
data(),
'library("dplyr");library("DT")' # nolint: quotes.
"library(dplyr);library(DT)"
)
teal.code::eval_code(
qenv,
Expand Down
6 changes: 3 additions & 3 deletions R/tm_g_association.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -151,8 +151,8 @@ tm_g_association <- function(label = "Association",
show_association = TRUE,
plot_height = c(600, 400, 5000),
plot_width = NULL,
distribution_theme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"), # nolint: line_length.
association_theme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"), # nolint: line_length.
distribution_theme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"), # nolint line_length_linter.
association_theme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"), # nolint line_length_linter.
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args(),
Expand Down Expand Up @@ -345,7 +345,7 @@ srv_tm_g_association <- function(id,
teal.reporter::teal_card(obj),
teal.reporter::teal_card("## Module's output(s)")
)
teal.code::eval_code(obj, 'library("ggplot2");library("dplyr")') # nolint: quotes
teal.code::eval_code(obj, "library(ggplot2);library(dplyr)")
})
anl_merged_q <- reactive({
req(anl_merged_input())
Expand Down
6 changes: 3 additions & 3 deletions R/tm_g_bivariate.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -558,9 +558,9 @@ srv_g_bivariate <- function(id,
teal.reporter::teal_card(obj),
teal.reporter::teal_card("## Module's output(s)")
)
obj %>%
teal.code::eval_code('library("ggplot2");library("dplyr")') %>%
teal.code::eval_code(as.expression(anl_merged_input()$expr)) # don't mix char with expr in single eval_code
obj |>
teal.code::eval_code("library(ggplot2);library(dplyr)") |>
teal.code::eval_code(as.expression(anl_merged_input()$expr))
})

merged <- list(
Expand Down
14 changes: 7 additions & 7 deletions R/tm_g_distribution.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -523,7 +523,7 @@ srv_distribution <- function(id,
)

qenv <- reactive(
teal.code::eval_code(data(), 'library("ggplot2");library("dplyr")') # nolint quotes
teal.code::eval_code(data(), "library(ggplot2);library(dplyr)")
)

anl_merged_q <- reactive({
Expand Down Expand Up @@ -663,7 +663,7 @@ srv_distribution <- function(id,
"Group by variable must be `factor`, `character`, or `integer`"
)
)
qenv <- teal.code::eval_code(qenv, 'library("forcats")') # nolint quotes
qenv <- teal.code::eval_code(qenv, "library(forcats)")
qenv <- teal.code::eval_code(
qenv,
substitute(
Expand All @@ -681,7 +681,7 @@ srv_distribution <- function(id,
)
)

qenv <- teal.code::eval_code(qenv, 'library("forcats")') # nolint quotes
qenv <- teal.code::eval_code(qenv, "library(forcats)")
qenv <- teal.code::eval_code(
qenv,
substitute(
Expand Down Expand Up @@ -891,7 +891,7 @@ srv_distribution <- function(id,
}

if (length(t_dist) != 0 && main_type_var == "Density" && length(g_var) == 0 && length(s_var) == 0) {
qenv <- teal.code::eval_code(qenv, 'library("ggpp")') # nolint quotes
qenv <- teal.code::eval_code(qenv, "library(ggpp)")
qenv <- teal.code::eval_code(
qenv,
substitute(
Expand Down Expand Up @@ -1037,7 +1037,7 @@ srv_distribution <- function(id,
)

if (length(t_dist) != 0 && length(g_var) == 0 && length(s_var) == 0) {
qenv <- teal.code::eval_code(qenv, 'library("ggpp")') # nolint quotes
qenv <- teal.code::eval_code(qenv, "library(ggpp)")
qenv <- teal.code::eval_code(
qenv,
substitute(
Expand Down Expand Up @@ -1233,7 +1233,7 @@ srv_distribution <- function(id,
qenv <- common_q()

if (length(s_var) == 0 && length(g_var) == 0) {
qenv <- teal.code::eval_code(qenv, 'library("generics")') # nolint quotes
qenv <- teal.code::eval_code(qenv, "library(generics)")
qenv <- teal.code::eval_code(
qenv,
substitute(
Expand All @@ -1247,7 +1247,7 @@ srv_distribution <- function(id,
)
)
} else {
qenv <- teal.code::eval_code(qenv, 'library("tidyr")') # nolint quotes
qenv <- teal.code::eval_code(qenv, "library(tidyr)")
qenv <- teal.code::eval_code(
qenv,
substitute(
Expand Down
4 changes: 2 additions & 2 deletions R/tm_g_response.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -387,7 +387,7 @@ srv_g_response <- function(id,
)

qenv <- reactive(
teal.code::eval_code(data(), 'library("ggplot2");library("dplyr")') # nolint quotes
teal.code::eval_code(data(), "library(ggplot2);library(dplyr)")
)

anl_merged_q <- reactive({
Expand Down Expand Up @@ -520,7 +520,7 @@ srv_g_response <- function(id,
resp_cl = resp_cl,
hjust_value = if (swap_axes) "left" else "middle",
vjust_value = if (swap_axes) "middle" else -1,
position_anl2_value = if (!freq) quote(position_fill(0.5)) else quote(position_stack(0.5)), # nolint: line_length.
position_anl2_value = if (!freq) quote(position_fill(0.5)) else quote(position_stack(0.5)), # nolint line_length_linter
anl3_y = if (!freq) 1.1 else as.name("ns"),
position_anl3_value = if (!freq) "fill" else "stack"
)
Expand Down
2 changes: 1 addition & 1 deletion R/tm_g_scatterplot.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -587,7 +587,7 @@ srv_g_scatterplot <- function(id,
teal.reporter::teal_card(obj),
teal.reporter::teal_card("## Module's output(s)")
)
teal.code::eval_code(data(), 'library("ggplot2");library("dplyr")') # nolint quotes
teal.code::eval_code(data(), "library(ggplot2);library(dplyr)")
})

anl_merged_q <- reactive({
Expand Down
2 changes: 1 addition & 1 deletion R/tm_g_scatterplotmatrix.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -330,7 +330,7 @@ srv_g_scatterplotmatrix <- function(id,
teal.reporter::teal_card(obj),
teal.reporter::teal_card("## Module's output(s)")
)
qenv <- teal.code::eval_code(obj, 'library("dplyr");library("lattice")') # nolint quotes
qenv <- teal.code::eval_code(obj, "library(dplyr);library(lattice)")
teal.code::eval_code(qenv, as.expression(anl_merged_input()$expr))
})

Expand Down
Loading
Loading