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small patch for labeling plots with signature group labels. #20

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Merged
Cvicnaire merged 1 commit into from
Apr 28, 2026
Merged

small patch for labeling plots with signature group labels. #20

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142 changes: 121 additions & 21 deletions shiny/modules/annotate_module.R
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -413,12 +413,99 @@ hype_dotplot_data <- function(hyp, fdr_threshold, top = 30, abrv = 50) {
}


build_enrichment_signatures <- function(sig_objs, sig_list) {
empty_result <- list(
vectors = list(),
metadata = data.frame(
signature = character(),
signature_name = character(),
group_label = character(),
signature_order = numeric(),
group_order = numeric(),
stringsAsFactors = FALSE
)
)

if (length(sig_objs) == 0 || length(sig_list) == 0) {
return(empty_result)
}

sig_names <- vapply(sig_list, `[[`, character(1), "signature_name")
vectors <- list()
metadata <- vector("list", length(sig_objs))
metadata_idx <- 0

for (i in seq_along(sig_objs)) {
sig_obj <- sig_objs[[i]]
sig_name <- sig_names[[i]]

difexp_df <- sig_obj$difexp
if (is.null(difexp_df) || !is.data.frame(difexp_df) || nrow(difexp_df) == 0) {
next
}

difexp_df$symbol <- as.character(difexp_df$symbol)
difexp_df <- difexp_df[!is.na(difexp_df$symbol) & nzchar(difexp_df$symbol), , drop = FALSE]

if (nrow(difexp_df) == 0) {
next
}

if ("group_label" %in% names(difexp_df)) {
difexp_df$group_label <- as.character(difexp_df$group_label)
difexp_df$group_label[is.na(difexp_df$group_label) | !nzchar(difexp_df$group_label)] <- "Ungrouped"
} else {
difexp_df$group_label <- "All Features"
}

group_levels <- unique(difexp_df$group_label)

for (group_label in group_levels) {
group_symbols <- unique(difexp_df$symbol[difexp_df$group_label == group_label])

if (length(group_symbols) == 0) {
next
}

signature_key <- sprintf("%s | %s", sig_name, group_label)
vectors[[signature_key]] <- group_symbols

metadata_idx <- metadata_idx + 1
metadata[[metadata_idx]] <- data.frame(
signature = signature_key,
signature_name = sig_name,
group_label = group_label,
signature_order = i,
group_order = match(group_label, group_levels),
stringsAsFactors = FALSE
)
}
}

metadata <- metadata[seq_len(metadata_idx)]
metadata_df <- if (length(metadata) > 0) do.call(rbind, metadata) else empty_result$metadata

list(
vectors = vectors,
metadata = metadata_df
)
}


annotate_module_server <- function(id, signature_db, user_conn_handler) {
moduleServer(id, function(input, output, session) {
max_signature_count <- 10
active_signatures <- reactiveVal(list())
run_feedback <- reactiveVal(NULL)
hyp_result <- reactiveVal(NULL)
signature_plot_metadata <- reactiveVal(
data.frame(
signature = character(),
signature_name = character(),
group_label = character(),
stringsAsFactors = FALSE
)
)

output$signature_hypeR <- renderDT({
df <- signature_db()
Expand Down Expand Up @@ -469,14 +556,16 @@ annotate_module_server <- function(id, signature_db, user_conn_handler) {
current[[key]] <- list(
experiment = input$experiment_label,
signature_name = sig_row$signature_name,
signature_id = sig_row$signature_id
signature_id = sig_row$signature_id,
perturbation = if ("perturbation" %in% names(sig_row)) sig_row$perturbation else NA_character_
)
added_count <- added_count + 1
}
}

active_signatures(current)
hyp_result(NULL)
signature_plot_metadata(signature_plot_metadata()[0, , drop = FALSE])

run_feedback(list(
type = if (skipped_limit_count > 0) "warning" else if (added_count > 0) "success" else "info",
Expand All @@ -499,6 +588,7 @@ annotate_module_server <- function(id, signature_db, user_conn_handler) {
active_signatures(list())
hyp_result(NULL)
run_feedback(NULL)
signature_plot_metadata(signature_plot_metadata()[0, , drop = FALSE])

updateTextInput(session, "experiment_label", value = "")
updateRadioButtons(session, "enrichment_type", selected = "hypergeo")
Expand Down Expand Up @@ -648,22 +738,8 @@ annotate_module_server <- function(id, signature_db, user_conn_handler) {
signature_id = sig_ids
)

signature_vectors <- lapply(sig_objs, function(x) {
if (is.null(x$signature)) {
return(NULL)
}

symbols <- as.character(x$difexp$symbol)
symbols <- symbols[!is.na(symbols)]

if (length(symbols) == 0) {
return(NULL)
}

symbols
})

signature_vectors <- signature_vectors[!vapply(signature_vectors, is.null, logical(1))]
enrichment_inputs <- build_enrichment_signatures(sig_objs, sig_list)
signature_vectors <- enrichment_inputs$vectors

if (length(signature_vectors) == 0) {
showNotification("No valid signatures were available to run enrichment.", type = "error")
Expand All @@ -681,6 +757,7 @@ annotate_module_server <- function(id, signature_db, user_conn_handler) {
)

hyp_result(hyp)
signature_plot_metadata(enrichment_inputs$metadata)
showNotification("Enrichment analysis completed.", type = "message")
})

Expand All @@ -691,8 +768,31 @@ annotate_module_server <- function(id, signature_db, user_conn_handler) {
plot_df <- hype_dotplot_data(hyp, fdr_threshold = input$enrichment_thresh)
validate(need(nrow(plot_df) > 0, "No enriched genesets passed the selected FDR threshold."))

signature_lookup <- unique(plot_df["signature"])
signature_lookup$signature_label <- paste0("S", seq_len(nrow(signature_lookup)))
plot_metadata <- signature_plot_metadata()
validate(need(nrow(plot_metadata) > 0, "Signature grouping metadata was not available for plotting."))

signature_lookup <- unique(
plot_metadata[, c("signature", "signature_name", "group_label", "signature_order", "group_order"), drop = FALSE]
)
signature_lookup <- signature_lookup[order(signature_lookup$signature_order, signature_lookup$group_order), , drop = FALSE]

signature_id_lookup <- unique(signature_lookup[, c("signature_name", "signature_order"), drop = FALSE])
signature_id_lookup <- signature_id_lookup[order(signature_id_lookup$signature_order), , drop = FALSE]
signature_id_lookup$plot_id <- paste0("S", seq_len(nrow(signature_id_lookup)))

signature_lookup <- merge(
signature_lookup,
signature_id_lookup,
by = c("signature_name", "signature_order"),
all.x = TRUE,
sort = FALSE
)
signature_lookup <- signature_lookup[order(signature_lookup$signature_order, signature_lookup$group_order), , drop = FALSE]
signature_lookup$signature_label <- ifelse(
nzchar(signature_lookup$group_label) & signature_lookup$group_label != "All Features",
paste(signature_lookup$plot_id, signature_lookup$group_label),
signature_lookup$plot_id
)

plot_df <- merge(plot_df, signature_lookup, by = "signature", all.x = TRUE, sort = FALSE)
plot_df$signature_label <- factor(plot_df$signature_label, levels = signature_lookup$signature_label)
Expand All @@ -704,7 +804,7 @@ annotate_module_server <- function(id, signature_db, user_conn_handler) {

list(
plot_df = plot_df,
signature_lookup = signature_lookup[, c("signature_label", "signature"), drop = FALSE]
signature_lookup = signature_lookup[, c("plot_id", "signature_label", "signature_name", "group_label"), drop = FALSE]
)
})

Expand Down Expand Up @@ -746,7 +846,7 @@ annotate_module_server <- function(id, signature_db, user_conn_handler) {

output$dotplot_signature_key <- DT::renderDT({
key_df <- dotplot_data()$signature_lookup
names(key_df) <- c("Plot ID", "Signature")
names(key_df) <- c("Signature ID", "Plot Label", "Signature", "Group Label")

DT::datatable(
key_df,
Expand Down
47 changes: 43 additions & 4 deletions shiny/modules/hypeR_module.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,10 +70,31 @@ fetch_msigdb_table <- function(species, collection, subcollection = "") {


msigdb_cache_dir <- function() {
Sys.getenv(
"MSIGDB_CACHE_DIR",
unset = file.path("shiny", "data", "msigdb_genesets")
)
env_cache_dir <- Sys.getenv("MSIGDB_CACHE_DIR", unset = "")

if (nzchar(env_cache_dir)) {
return(env_cache_dir)
}

shiny_path <- getOption("sigrepo.shiny_path", default = "")
server_root <- Sys.getenv("SIGREPO_SERVER_DIR", unset = "")

cache_dir_candidates <- unique(c(
if (nzchar(shiny_path)) file.path(shiny_path, "data", "msigdb_genesets"),
if (nzchar(server_root)) file.path(server_root, "shiny", "data", "msigdb_genesets"),
file.path(getwd(), "data", "msigdb_genesets"),
file.path(getwd(), "shiny", "data", "msigdb_genesets"),
file.path("data", "msigdb_genesets"),
file.path("shiny", "data", "msigdb_genesets")
))

existing_cache_dir <- cache_dir_candidates[dir.exists(cache_dir_candidates)]

if (length(existing_cache_dir) > 0) {
return(existing_cache_dir[[1]])
}

cache_dir_candidates[[1]]
}


Expand Down Expand Up @@ -110,6 +131,12 @@ load_cached_msigdb_genesets <- function(species, collection, subcollection = "")
}


runtime_msigdb_fetch_allowed <- function() {
value <- tolower(Sys.getenv("MSIGDB_ALLOW_RUNTIME_FETCH", unset = "false"))
value %in% c("true", "1", "yes", "y")
}


# hypeR genests ui rewrite
#' Shiny UI for MSigDB subcategory selection
#'
Expand Down Expand Up @@ -248,6 +275,18 @@ genesets_hypeR_Server <- function(id, species, clean = FALSE) {
return()
}

if (!runtime_msigdb_fetch_allowed()) {
showNotification(
sprintf(
"MSigDB cache file was not found: %s. Build the cache or set MSIGDB_CACHE_DIR.",
msigdb_cache_file(species(), input$collection, input$subcategory)
),
type = "error",
duration = 12
)
return()
}

filtered_tbl <- tryCatch(
{
shiny::withProgress(
Expand Down
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