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Merged
Cristianetaniguti merged 3 commits into from
Jul 21, 2026
Merged

Development #11

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77a8ddb
add cores box
Cristianetaniguti Jun 30, 2026
cc5917f
Merge pull request #10 from Breeding-Insight/add_parallel
Cristianetaniguti Jun 30, 2026
c98cc05
fix download buttons
Cristianetaniguti Jul 15, 2026
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119 changes: 59 additions & 60 deletions R/mod_cnv.R
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Original file line number Diff line number Diff line change
Expand Up @@ -224,6 +224,10 @@ mod_cnv_ui <- function(id){
inline = TRUE,
status = "info"
)
),
column(width = 3,
numericInput(ns("n_cores"), label = "Number of cores",
value = 1L, min = 1L, step = 1L, width = "50%")
)
),
column(width = 6,
Expand Down Expand Up @@ -256,14 +260,22 @@ mod_cnv_ui <- function(id){
sliderInput(ns("cnv_image_res"), "Resolution", value = 300, min = 50, max = 1000, step = 50),
sliderInput(ns("cnv_image_width"), "Width", value = 10, min = 1, max = 20, step = 0.5),
sliderInput(ns("cnv_image_height"), "Height", value = 6, min = 1, max = 20, step = 0.5),
downloadButton(ns("download_cnv_plot"), "Save Image"),
downloadButton(ns("download_cnv_plot"), "Save Image",
onclick = "event.stopPropagation();"),
circle = FALSE, status = "danger",
icon = icon("floppy-disk"), width = "300px", label = "Save",
tooltip = tooltipOptions(title = "Save CNV Compare plot")
)
)
)
)
),
fluidRow(
column(width = 12,
progressBar(id = ns("save_image_bar"), value = 0,
title = "", display_pct = FALSE,
status = "info", striped = TRUE)
)
)
), br(),
box(
title = "BAF and Z-scores", status = "info", solidHeader = FALSE,
Expand Down Expand Up @@ -488,7 +500,8 @@ mod_cnv_ui <- function(id){
sliderInput(ns("baf_image_res"), "Resolution", value = 300, min = 50, max = 1000, step = 50),
sliderInput(ns("baf_image_width"), "Width", value = 10, min = 1, max = 20, step = 0.5),
sliderInput(ns("baf_image_height"), "Height", value = 6, min = 1, max = 20, step = 0.5),
downloadButton(ns("download_baf_plot"), "Save Image"),
downloadButton(ns("download_baf_plot"), "Save Image",
onclick = "event.stopPropagation();"),
circle = FALSE, status = "danger",
icon = icon("floppy-disk"), width = "300px", label = "Save",
tooltip = tooltipOptions(title = "Save CNV plot")
Expand Down Expand Up @@ -768,7 +781,7 @@ mod_cnv_server <- function(input, output, session, parent_session){
if(input$add_heterozygosity == "TRUE") {
updateProgressBar(session, "cnv_plot", value = 50, title = "Calling dosages for heterozygosity estimation...")

call_hmm_dosages(cnv_items$hmm_CN, bw = 0.15, dist = "gaussian", add_uniform = FALSE, uniform_weight = 0.01)
call_hmm_dosages(cnv_items$hmm_CN, bw = 0.15, dist = "gaussian", add_uniform = FALSE, uniform_weight = 0.01, n.cores = input$n_cores)
} else NULL
})

Expand Down Expand Up @@ -822,31 +835,7 @@ mod_cnv_server <- function(input, output, session, parent_session){
output$cnv_compare_plot_ui <- renderUI({
plotlyOutput(ns("cnv_compare_plotly"), height = "600px")
})

# Simple ggplot click handler - manual coordinate detection
# observeEvent(input$cnv_plot_click, {
# if (!is.null(input$cnv_plot_click)) {
# tryCatch({
# data <- cnv_profile()@data
# click_y <- input$cnv_plot_click$y
#
# # Get unique samples and their order (bottom to top)
# samples <- unique(data$Sample)
# sample_levels <- rev(samples) # reversed because ggplot plots bottom to top
#
# # Find which sample was clicked based on y coordinate
# sample_index <- round(click_y)
#
# if (sample_index >= 1 && sample_index <= length(sample_levels)) {
# clicked_sample <- sample_levels[sample_index]
# updatePickerInput(session, "cnv_filter_samples_baf", selected = as.character(clicked_sample))
# }
# }, error = function(e) {
# # Silently handle errors
# })
# }
# })


# Plotly click handler - try different event source
observeEvent(event_data("plotly_click"), {
click_data <- event_data("plotly_click")
Expand All @@ -864,6 +853,46 @@ mod_cnv_server <- function(input, output, session, parent_session){
})
}
})

# Download handler for CNV plot
output$download_cnv_plot <- downloadHandler(
filename = function() {
paste0("CNV_Plot_", Sys.Date(), ".", input$cnv_image_type)
},
content = function(file) {
print("Download triggered!")
updateProgressBar(session, "save_image_bar", value = 10, title = "Saving image...")

if (input$cnv_image_type == "html") {
updateProgressBar(session, "save_image_bar", value = 20, title = "Saving image to HTML...")
htmlwidgets::saveWidget(cnv_profile(), file)

} else {
updateProgressBar(session, "save_image_bar", value = 30, title = "Saving image to file...")

# Re-generate as static ggplot (without interactive = TRUE)
p_static <- compare_cn_track(
cnv_items$hmm_CN,
samples_to_plot = cnv_items$samples_to_plot,
facet_nrow = 1,
gray_CN = input$gray_CN,
add_het = input$add_heterozygosity == "TRUE",
hmm_dosage_calls = dosages(),
interactive = FALSE # <-- key change
)

ggsave(
filename = file,
plot = p_static,
device = input$cnv_image_type,
dpi = input$cnv_image_res,
width = input$cnv_image_width,
height = input$cnv_image_height
)
}
updateProgressBar(session, "save_image_bar", value = 100, title = "Done!")
}
)

######

Expand Down Expand Up @@ -1013,37 +1042,7 @@ mod_cnv_server <- function(input, output, session, parent_session){
download.file(url, file, mode = "wb")
}
)

# Download handler for CNV plot
output$download_cnv_plot <- downloadHandler(
filename = function() {
paste("CNV_Plot", Sys.Date(), ".", input$cnv_image_type, sep = "")
},
content = function(file) {
req(cnv_profile())
if(input$cnv_image_type == "html") {
htmlwidgets::saveWidget(cnv_profile(), file)
} else {

plot <- compare_cn_track(cnv_items$hmm_CN,
samples_to_plot = cnv_items$samples_to_plot,
facet_nrow = 1,
gray_CN = input$gray_CN,
add_het = input$add_heterozygosity == "TRUE",
hmm_dosage_calls = dosages(),
interactive = FALSE)
ggsave(
filename = file,
plot = plot,
device = input$cnv_image_type,
dpi = input$cnv_image_res,
width = input$cnv_image_width,
height = input$cnv_image_height
)
}
}
)


# Download handler for BAF and Z-scores plot
output$download_baf_plot <- downloadHandler(
filename = function() {
Expand Down
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