rewrite scatterplotmatrix so it uses ggally

[m7pr]

Part of

• UAT Exploratory App: scatterplot matrix, correlation NA #63

Satisfies last comment from 2025

• UAT Exploratory App: scatterplot matrix, correlation NA #63 (comment)

Alternative to

• rewrite scatterplotmatrix so it uses patchwork #986

This PR rewrite scatterplotmatrix so it uses ggally

Coe do generate plots

library(ggplot2)
library(GGally)
library(dplyr)

set.seed(42)
n <- 200
demo_data <- data.frame(
  AGE = rnorm(n, mean = 55, sd = 12),
  BMRKR1 = rlnorm(n, meanlog = 1.5, sdlog = 0.8),
  AVAL = rnorm(n, mean = 100, sd = 25),
  BMRKR2 = sample(c("LOW", "MEDIUM", "HIGH"), n, replace = TRUE, prob = c(0.3, 0.4, 0.3))
) %>%
  mutate(BMRKR2 = factor(BMRKR2, levels = c("LOW", "MEDIUM", "HIGH")))

demo_data$AGE[sample(n, 10)] <- NA
demo_data$BMRKR1[sample(n, 5)] <- NA

plot_with_cor <- GGally::ggpairs(
  demo_data,
  columnLabels = c("Age", "Biomarker 1", "Analysis Value", "Biomarker 2"),
  upper = list(
    continuous = GGally::wrap("cor", method = "pearson", use = "pairwise.complete.obs")
  ),
  lower = list(
    continuous = GGally::wrap("points", alpha = 0.5, size = 1.5)
  ),
  diag = list(
    continuous = GGally::wrap("densityDiag", alpha = 0.5)
  )
) +
  ggplot2::ggtitle("Scatterplot Matrix - With Correlation (Pearson)") +
  ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 14))

plot_without_cor <- GGally::ggpairs(
  demo_data,
  columnLabels = c("Age", "Biomarker 1", "Analysis Value", "Biomarker 2"),
  upper = list(
    continuous = GGally::wrap("points", alpha = 0.5, size = 1.5)
  ),
  lower = list(
    continuous = GGally::wrap("points", alpha = 0.5, size = 1.5)
  ),
  diag = list(
    continuous = GGally::wrap("densityDiag", alpha = 0.5)
  )
) +
  ggplot2::ggtitle("Scatterplot Matrix - Without Correlation") +
  ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 14))

plot_spearman <- GGally::ggpairs(
  demo_data,
  columnLabels = c("Age", "Biomarker 1", "Analysis Value", "Biomarker 2"),
  upper = list(
    continuous = GGally::wrap("cor", method = "spearman", use = "pairwise.complete.obs")
  ),
  lower = list(
    continuous = GGally::wrap("points", alpha = 0.5, size = 1.5)
  ),
  diag = list(
    continuous = GGally::wrap("densityDiag", alpha = 0.5)
  )
) +
  ggplot2::ggtitle("Scatterplot Matrix - With Correlation (Spearman)") +
  ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 14))

numeric_data <- demo_data %>% select(AGE, BMRKR1, AVAL)

plot_numeric_only <- GGally::ggpairs(
  numeric_data,
  columnLabels = c("Age", "Biomarker 1", "Analysis Value"),
  upper = list(
    continuous = GGally::wrap("cor", method = "pearson", use = "pairwise.complete.obs")
  ),
  lower = list(
    continuous = GGally::wrap("points", alpha = 0.5, size = 1.5)
  ),
  diag = list(
    continuous = GGally::wrap("densityDiag", alpha = 0.5)
  )
) +
  ggplot2::ggtitle("Numeric Only - Correlation Matrix Style") +
  ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 14))

output_dir <- file.path("dev", "demo_plots")
dir.create(output_dir, showWarnings = FALSE, recursive = TRUE)

ggsave(file.path(output_dir, "1_with_correlation_pearson.png"), plot_with_cor, width = 10, height = 10, dpi = 150)
ggsave(file.path(output_dir, "2_without_correlation.png"), plot_without_cor, width = 10, height = 10, dpi = 150)
ggsave(file.path(output_dir, "3_with_correlation_spearman.png"), plot_spearman, width = 10, height = 10, dpi = 150)
ggsave(file.path(output_dir, "4_numeric_only_correlation.png"), plot_numeric_only, width = 8, height = 8, dpi = 150)

Plots below

[github-actions]

Unit Tests Summary

    1 files     38 suites   22m 44s ⏱️
  686 tests   680 ✅ 5 💤 0 ❌ 1 🔥
1 307 runs  1 301 ✅ 5 💤 0 ❌ 1 🔥

For more details on these errors, see this check.

Results for commit 2e5ff84.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
shinytest2-tm_a_pca	💚	$220.36$	$-3.27$	$0$	$0$	$0$	$0$
shinytest2-tm_a_regression	💚	$86.24$	$-3.26$	$0$	$0$	$0$	$0$
shinytest2-tm_file_viewer	💚	$42.25$	$-1.43$	$0$	$0$	$0$	$0$
shinytest2-tm_g_bivariate	💚	$102.56$	$-38.13$	$-11$	$0$	$0$	$+1$
shinytest2-tm_g_distribution	💚	$117.29$	$-67.46$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplot	💚	$137.99$	$-2.34$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplotmatrix	💔	$44.09$	$+12.22$	$0$	$0$	$0$	$0$
shinytest2-tm_missing_data	💚	$67.03$	$-1.93$	$0$	$0$	$0$	$0$
shinytest2-tm_outliers	💚	$170.99$	$-5.07$	$0$	$0$	$0$	$0$
shinytest2-tm_t_crosstable	💚	$48.25$	$-1.20$	$0$	$0$	$0$	$0$
shinytest2-tm_variable_browser	💚	$97.43$	$-4.33$	$0$	$0$	$0$	$0$
tm_g_association	💚	$12.94$	$-1.14$	$0$	$0$	$0$	$0$
tm_g_scatterplotmatrix	💔	$1.50$	$+1.37$	$0$	$0$	$0$	$0$
tm_outliers	💚	$53.04$	$-2.45$	$0$	$0$	$0$	$0$
variable_browser	💚	$69.33$	$-3.97$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
shinytest2-tm_g_bivariate	💚	$10.66$	$-1.19$	e2e_tm_g_bivariate_Module_is_initialised_with_the_specified_defaults.
shinytest2-tm_g_bivariate	💚	$39.19$	$-35.34$	e2e_tm_g_bivariate_Setting_encoding_inputs_produces_outputs_without_validation_errors.
shinytest2-tm_g_distribution	💚	$77.64$	$-66.47$	e2e_tm_g_distribution_Module_is_initialised_with_the_specified_defaults.
shinytest2-tm_g_scatterplotmatrix	💔	$13.06$	$+6.60$	e2e_tm_g_scatterplotmatrix_Change_plot_settings
shinytest2-tm_g_scatterplotmatrix	💔	$9.04$	$+1.65$	e2e_tm_g_scatterplotmatrix_Initializes_without_errors
shinytest2-tm_g_scatterplotmatrix	💔	$10.73$	$+2.43$	e2e_tm_g_scatterplotmatrix_Verify_default_values_and_settings_data_extracts_for_data_selection
shinytest2-tm_g_scatterplotmatrix	💔	$11.26$	$+1.53$	e2e_tm_g_scatterplotmatrix_Verify_module_displays_data_table
shinytest2-tm_variable_browser	💚	$22.26$	$-1.10$	e2e_tm_variable_browser_changing_plot_setting_encodings_doesn_t_show_errors.
variable_browser	💚	$13.12$	$-1.39$	UI_switches_and_controls_server_handles_different_outlier_definition_thresholds

Results for commit 2f335b3

♻️ This comment has been updated with latest results.

[donyunardi]

User prefer that patchwork solution. Closing without merging.