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Merged
tonywu1999 merged 3 commits into from
Nov 21, 2025
Merged

refactor(statmodel): Finalize namespaces for comparisons components #131

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f5bb098
refactor(statmodel): Finalize namespaces for comparisons components
tonywu1999 Nov 20, 2025
b7d164a
fix one set of unit tests
tonywu1999 Nov 20, 2025
ca08aa1
finalize all unit tests
tonywu1999 Nov 20, 2025
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38 changes: 18 additions & 20 deletions R/module-statmodel-server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,32 +41,29 @@ render_all_against_one_inputs = function(output, session, condition_list) {
ns = session$ns

output[[NAMESPACE_STATMODEL$comparisons_all_vs_one_choice]] = renderUI({
selectInput(ns("group3"), "", condition_list())
selectInput(ns(NAMESPACE_STATMODEL$comparisons_all_vs_one_choice), "", condition_list())
})
}

render_custom_pairwise_inputs = function(output, session, condition_list) {
ns = session$ns

output[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] = renderUI({
selectInput(ns("group1"), "Group 1", condition_list())
selectInput(ns(NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1), "Group 1", condition_list())
})

output[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]] = renderUI({
selectInput(ns("group2"), "Group 2", condition_list())
selectInput(ns(NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2), "Group 2", condition_list())
})
}

render_custom_non_pairwise_inputs = function(output, session, condition_list) {
ns = session$ns

output[[NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_name]] = renderUI({
textInput(ns("comp_name"), label = "Comparison Name", value = "")
})

output[[NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights]] = renderUI({
lapply(1:length(condition_list()), function(i) {
list(numericInput(ns(paste0("weight", i)),
list(numericInput(ns(paste0(
NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, i)
),
label = condition_list()[i], value = 0))
})
})
Expand All @@ -77,11 +74,11 @@ render_custom_non_pairwise_inputs = function(output, session, condition_list) {
validate_contrast_inputs = function(input, contrast_mode, condition_list) {
if (contrast_mode == CONSTANTS_STATMODEL$comparison_mode_custom_pairwise) {
validate(
need(input$group1 != input$group2, "Please select different groups")
need(input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] != input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]], "Please select different groups")
)
} else if (contrast_mode == CONSTANTS_STATMODEL$comparison_mode_custom_nonpairwise) {
wt_sum = sum(sapply(1:length(condition_list), function(i) {
input[[paste0("weight", i)]]
input[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, i)]]
}))

validate(
Expand All @@ -91,15 +88,15 @@ validate_contrast_inputs = function(input, contrast_mode, condition_list) {
}

build_custom_pairwise_contrast = function(input, condition_list, contrast, comp_list, row) {
if (input$group1 == input$group2) {
if (input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] == input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]]) {
return(contrast$matrix)
}

index1 = which(condition_list == input$group1)
index2 = which(condition_list == input$group2)
index1 = which(condition_list == input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]])
index2 = which(condition_list == input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]])

comp_list$dList = unique(c(isolate(comp_list$dList),
paste(input$group1, "vs", input$group2, sep = " ")))
paste(input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]], "vs", input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]], sep = " ")))

contrast$row = matrix(row, nrow = 1)
contrast$row[index1] = 1
Expand All @@ -120,18 +117,19 @@ build_custom_pairwise_contrast = function(input, condition_list, contrast, comp_

build_custom_non_pairwise_contrast = function(input, condition_list, contrast, comp_list, row) {
wt_sum = sum(sapply(1:length(condition_list), function(i) {
input[[paste0("weight", i)]]
input[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, i)]]
}))

if (wt_sum != 0) {
return(contrast$matrix)
}

comp_list$dList = unique(c(isolate(comp_list$dList), input$comp_name))
comp_list$dList = unique(c(isolate(comp_list$dList),
input[[NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_name]]))
contrast$row = matrix(row, nrow = 1)

for (index in 1:length(condition_list)) {
contrast$row[index] = input[[paste0("weight", index)]]
contrast$row[index] = input[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, index)]]
}

if (is.null(contrast$matrix)) {
Expand All @@ -148,13 +146,13 @@ build_custom_non_pairwise_contrast = function(input, condition_list, contrast, c
}

build_all_against_one_contrast = function(input, condition_list, contrast, comp_list, row, loadpage_input) {
index3 = which(condition_list == input$group3)
index3 = which(condition_list == input[[NAMESPACE_STATMODEL$comparisons_all_vs_one_choice]])

for (index in 1:length(condition_list)) {
if (index == index3) next

comp_list$dList = c(isolate(comp_list$dList),
paste(condition_list[index], "vs", input$group3, sep = " "))
paste(condition_list[index], "vs", input[[NAMESPACE_STATMODEL$comparisons_all_vs_one_choice]], sep = " "))

contrast$row = matrix(row, nrow = 1)
contrast$row[index] = 1
Expand Down
3 changes: 2 additions & 1 deletion R/statmodel-ui-options-contrasts.R → R/statmodel-ui-comparisons.R
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,8 @@ build_all_pairwise_panel <- function(ns) {
build_custom_nonpairwise_panel <- function(ns) {
tagList(
h5("Non-pairwise Comparison:"),
uiOutput(ns(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_name)),
textInput(ns(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_name),
label = "Comparison Name", value = ""),
uiOutput(ns(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights)),
actionButton(ns(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_submit), "Add"),
actionButton(ns(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_clear), "Clear matrix")
Expand Down
34 changes: 17 additions & 17 deletions tests/testthat/test-module-statmodel-server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -189,8 +189,8 @@ test_that("matrix_build creates correct pairwise comparison", {
# Set up custom comparison
inputs <- list()
inputs[[NAMESPACE_STATMODEL$comparison_mode]] <- CONSTANTS_STATMODEL$comparison_mode_custom_pairwise
inputs$group1 <- "Group1"
inputs$group2 <- "Group2"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] = "Group1"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]] = "Group2"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_submit]] <- 1
do.call(session$setInputs, inputs)

Expand Down Expand Up @@ -280,7 +280,7 @@ test_that("matrix_build creates all vs one comparisons", {
# Set up all vs one comparison
inputs <- list()
inputs[[NAMESPACE_STATMODEL$comparison_mode]] <- CONSTANTS_STATMODEL$comparison_mode_all_vs_one
inputs$group3 <- "Group3"
inputs[[NAMESPACE_STATMODEL$comparisons_all_vs_one_choice]] = "Group3"
inputs[[NAMESPACE_STATMODEL$comparisons_all_vs_one_submit]] <- 1
do.call(session$setInputs, inputs)

Expand Down Expand Up @@ -323,10 +323,10 @@ test_that("matrix_build creates custom non-pairwise comparison", {
# Set up custom non-pairwise comparison
inputs <- list()
inputs[[NAMESPACE_STATMODEL$comparison_mode]] <- CONSTANTS_STATMODEL$comparison_mode_custom_nonpairwise
inputs$comp_name <- "CustomComparison"
inputs$weight1 <- 1
inputs$weight2 <- 1
inputs$weight3 <- -2
inputs[[NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_name]] = "CustomComparison"
inputs[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 1)]] = 1
inputs[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 2)]] = 1
inputs[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 3)]] = -2
inputs[[NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_submit]] <- 1
do.call(session$setInputs, inputs)

Expand Down Expand Up @@ -374,8 +374,8 @@ test_that("check_cond validates same group selection", {
# Set up invalid comparison (same groups)
inputs <- list()
inputs[[NAMESPACE_STATMODEL$comparison_mode]] <- CONSTANTS_STATMODEL$comparison_mode_custom_pairwise
inputs$group1 <- "Group1"
inputs$group2 <- "Group1"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] = "Group1"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]] = "Group1"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_submit]] <- 1
do.call(session$setInputs, inputs)

Expand Down Expand Up @@ -412,10 +412,10 @@ test_that("check_cond validates contrast weights sum to zero", {
# Set up invalid weights (don't sum to 0)
inputs <- list()
inputs[[NAMESPACE_STATMODEL$comparison_mode]] <- CONSTANTS_STATMODEL$comparison_mode_custom_nonpairwise
inputs$comp_name <- "BadComparison"
inputs$weight1 <- 1
inputs$weight2 <- 1
inputs$weight3 <- 1
inputs[[NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_name]] = "BadComparison"
inputs[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 1)]] = 1
inputs[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 2)]] = 1
inputs[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 3)]] = 1
inputs[[NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_submit]] <- 1
do.call(session$setInputs, inputs)

Expand Down Expand Up @@ -452,8 +452,8 @@ test_that("contrast_mode change resets matrix", {
# Build a matrix
inputs <- list()
inputs[[NAMESPACE_STATMODEL$comparison_mode]] <- CONSTANTS_STATMODEL$comparison_mode_custom_pairwise
inputs$group1 <- "Group1"
inputs$group2 <- "Group2"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] = "Group1"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]] = "Group2"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_submit]] <- 1
do.call(session$setInputs, inputs)
matrix_build()
Expand Down Expand Up @@ -497,8 +497,8 @@ test_that("matrix doesn't add duplicate rows", {
# Add same comparison twice
inputs <- list()
inputs[[NAMESPACE_STATMODEL$comparison_mode]] <- CONSTANTS_STATMODEL$comparison_mode_custom_pairwise
inputs$group1 <- "Group1"
inputs$group2 <- "Group2"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] = "Group1"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]] = "Group2"
inputs[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_submit]] <- 1
do.call(session$setInputs, inputs)
matrix_build()
Expand Down
40 changes: 23 additions & 17 deletions tests/testthat/test-utils-statmodel-server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,9 @@ test_that("get_experimental_conditions returns GROUP for standard analysis", {
# ============================================================================

test_that("build_custom_pairwise_contrast creates correct matrix", {
input <- list(group1 = "A", group2 = "B")
input <- list()
input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] = "A"
input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]] = "B"
condition_list <- c("A", "B", "C")
contrast <- list(matrix = NULL, row = NULL)
comp_list <- list(dList = NULL)
Expand All @@ -78,7 +80,9 @@ test_that("build_custom_pairwise_contrast creates correct matrix", {
})

test_that("build_custom_pairwise_contrast handles multiple comparisons", {
input <- list(group1 = "C", group2 = "A")
input <- list()
input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] = "C"
input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]] = "A"
condition_list <- c("A", "B", "C")
existing_matrix <- matrix(c(1, -1, 0), nrow = 1)
rownames(existing_matrix) <- "A vs B"
Expand All @@ -98,7 +102,9 @@ test_that("build_custom_pairwise_contrast handles multiple comparisons", {
})

test_that("build_custom_pairwise_contrast returns unchanged matrix for same groups", {
input <- list(group1 = "A", group2 = "A")
input <- list()
input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice1]] = "A"
input[[NAMESPACE_STATMODEL$comparisons_custom_pairwise_choice2]] = "A"
condition_list <- c("A", "B", "C")
existing_matrix <- matrix(c(1, -1, 0), nrow = 1)

Expand All @@ -118,12 +124,11 @@ test_that("build_custom_pairwise_contrast returns unchanged matrix for same grou
# ============================================================================

test_that("build_custom_non_pairwise_contrast creates correct matrix", {
input <- list(
weight1 = 0.5,
weight2 = 0.5,
weight3 = -1,
comp_name = "AB vs C"
)
input <- list()
input[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 1)]] = 0.5
input[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 2)]] = 0.5
input[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 3)]] = -1
input[[NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_name]] = "AB vs C"
condition_list <- c("A", "B", "C")
contrast <- list(matrix = NULL, row = NULL)
comp_list <- list(dList = NULL)
Expand All @@ -141,12 +146,11 @@ test_that("build_custom_non_pairwise_contrast creates correct matrix", {
})

test_that("build_custom_non_pairwise_contrast rejects non-zero sum", {
input <- list(
weight1 = 1,
weight2 = 1,
weight3 = 1,
comp_name = "Invalid"
)
input <- list()
input[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 1)]] = 1
input[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 2)]] = 1
input[[paste0(NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_weights, 3)]] = 1
input[[NAMESPACE_STATMODEL$comparisons_custom_nonpairwise_name]] = "invalid"
condition_list <- c("A", "B", "C")
existing_matrix <- matrix(c(1, -1, 0), nrow = 1)

Expand All @@ -166,7 +170,8 @@ test_that("build_custom_non_pairwise_contrast rejects non-zero sum", {
# ============================================================================

test_that("build_all_against_one_contrast creates all comparisons", {
input <- list(group3 = "Control")
input <- list()
input[[NAMESPACE_STATMODEL$comparisons_all_vs_one_choice]] = "Control"
condition_list <- c("TreatA", "TreatB", "Control")
contrast <- list(matrix = NULL, row = NULL)
comp_list <- list(dList = NULL)
Expand All @@ -187,7 +192,8 @@ test_that("build_all_against_one_contrast creates all comparisons", {
})

test_that("build_all_against_one_contrast handles single comparison", {
input <- list(group3 = "B")
input <- list()
input[[NAMESPACE_STATMODEL$comparisons_all_vs_one_choice]] = "B"
condition_list <- c("A", "B")
contrast <- list(matrix = NULL, row = NULL)
comp_list <- list(dList = NULL)
Expand Down
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