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Public data analysis #1541

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c002ffa
wip
zitoa Aug 7, 2025
f066a21
wip
zitoa Aug 8, 2025
9049df9
improve upload UI
zitoa Aug 8, 2025
0e69c24
refactoring and polishing
zitoa Aug 12, 2025
8b43998
refactoring and polishing
zitoa Aug 13, 2025
5a682fa
Only transcriptomics for now
zitoa Aug 13, 2025
bb8597b
refactor proteomics type box && cleaning
zitoa Aug 14, 2025
5b0703f
add timer to success box
zitoa Aug 14, 2025
38ee72e
polishing
zitoa Aug 14, 2025
d3cf5eb
merge devel into public-data-analysis branch
zitoa Aug 18, 2025
c40d9b8
add specification
zitoa Aug 18, 2025
9c04425
fixes to display public metadata
zitoa Aug 19, 2025
56e5b86
polishing
zitoa Aug 19, 2025
47f3a80
polishing and set GEO NULL
zitoa Aug 19, 2025
ca65631
remove unneded alerts
ESCRI11 Aug 20, 2025
63ec8a8
remove inserted html/move style to scss
ESCRI11 Aug 20, 2025
6fa743d
open sidebar on data upload
ESCRI11 Aug 20, 2025
2f04110
handle public data selectors
ESCRI11 Aug 20, 2025
357edde
reshufle public data upload UI
ESCRI11 Aug 20, 2025
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285 changes: 173 additions & 112 deletions components/board.upload/R/upload_module_preview_counts.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,29 +13,33 @@ upload_table_preview_counts_ui <- function(id) {
}

upload_table_preview_counts_server <- function(
id,
create_raw_dir,
auth,
uploaded,
checked_matrix,
is_logscale,
checklist,
scrollY,
width,
height,
title,
info.text,
caption,
upload_datatype,
is.olink
) {
id,
create_raw_dir,
auth,
uploaded,
checked_matrix,
is_logscale,
checklist,
scrollY,
width,
height,
title,
info.text,
caption,
upload_datatype,
is.olink,
public_dataset_id
) {

moduleServer(id, function(input, output, session) {

ns <- session$ns

GEO_alert_shown <- reactiveVal(FALSE)

table_data <- shiny::reactive({
shiny::req(!is.null(uploaded$counts.csv))
dt <- uploaded$counts.csv
dt <- uploaded$counts.csv
nrow0 <- nrow(dt)
ncol0 <- ncol(dt)
MAXROW <- 1000
Expand All @@ -58,10 +62,8 @@ upload_table_preview_counts_server <- function(
table.RENDER <- function() {
dt <- table_data()
req(!is.null(dt))

is.integer <- is.integer(dt) || all(round(dt) == dt, na.rm = TRUE)
digits <- ifelse(is.integer, 0, 2)

DT::datatable(dt,
class = "compact hover",
rownames = TRUE,
Expand All @@ -82,6 +84,7 @@ upload_table_preview_counts_server <- function(
}

output$table_counts <- shiny::renderUI({

action_buttons <- div(
style = "display: flex; justify-content: left; margin: 8px;",
if (is.null(uploaded$counts.csv)) {
Expand Down Expand Up @@ -115,95 +118,31 @@ upload_table_preview_counts_server <- function(
)
)

div(
bslib::as_fill_carrier(),
style = "width: 100%; display: flex; ",
if (is.null(uploaded$counts.csv)) {
if (upload_datatype() == "proteomics") {
msg <- "The counts file (counts.csv) contains the gene counts for all samples. For proteomics data types other than Olink NPX, the file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample. For Olink NPX, the uploaded file needs to be the standard Olink format."
} else {
msg <- "The counts file (counts.csv) contains the gene counts for all samples. The file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample."
}
bslib::layout_columns(
col_widths = c(-3, 6, -3),
row_heights = list("auto", 8, 1, 2),
gap = "0.5rem",
bslib::as_fill_carrier(bs_alert(tspan(msg), closable = FALSE, translate_js = FALSE)),
bslib::card(
if (upload_datatype() == "multi-omics") {
shiny::radioButtons(
ns("data_source"),
label = "Select input files from:",
choices = c("multi-csv", "pgx", "single-csv"),
selected = "multi-csv",
inline = TRUE
)
},
if (upload_datatype() == "multi-omics") {
shiny::conditionalPanel(
condition = sprintf("input['%s'] == 'pgx'", ns("data_source")),
div(
div(
style = "margin-bottom: 15px;",
shiny::radioButtons(
ns("data_processing"),
label = "Select data processing level:",
choices = c("Raw" = "raw", "Normalized (also batch corrected if selected on computation)" = "normalized"),
selected = "raw",
inline = TRUE
)
),
div(
style = "display: flex; align-items: center; gap: 10px; margin-bottom: 10px;",
span("Selected:", style = "font-weight: bold;"),
textOutput(ns("selected_rows_text")),
),
div(
style = "height: 350px; overflow-y: auto;",
DT::DTOutput(ns("available_data_table"))
),
style = "width: 100%; max-height: 400px; overflow-y: auto;"
),
selection = "multiple",
options = list(pageLength = 5, dom = "tp", scrollY = TRUE)
)
},

if (upload_datatype() == "multi-omics") {
shiny::conditionalPanel(
condition = sprintf("input['%s'] == 'multi-csv'", ns("data_source")),
shiny::uiOutput(ns("dynamic_file_inputs"))#,
)
},
if (public_dataset_id() != "") {

if (upload_datatype() == "multi-omics") {
shiny::conditionalPanel(
condition = sprintf("input['%s'] == 'single-csv'", ns("data_source")),
fileInputArea(
ns("counts_csv"),
shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
multiple = FALSE,
accept = c(".csv"),
width = "100%"
)
)
},

if (upload_datatype() != "multi-omics") {
fileInputArea(
ns("counts_csv"),
shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
multiple = FALSE,
accept = c(".csv"),
width = "100%"
)
},
style = "background-color: aliceblue; border: 0.07rem dashed steelblue;"
),
action_buttons,
br()
)
},
ID <- public_dataset_id()
msg <- paste0("Retrieving ", ID, " from GEO, ReCount, or ArrayExpress...<br>", "Please wait. Most datasets take 2-3 mins.")

showModal(modalDialog(
div(id = "custom-progress-modal", HTML(msg),
div(id = "custom-progress-container",
div(id = "custom-progress-bar"))),
footer = NULL, fade = FALSE))
GEO <- tryCatch({ playbase::pgx.getGEOseries(accession = ID, archs.h5 = NULL, get.info = FALSE)},
error = function(w) { NULL })
removeModal()

if (!is.null(GEO)) {
if (!GEO_alert_shown()) {
msg <- paste0("Success! ", ID, " found in ", GEO[["source"]], ".\nWe're preparing it...")
GEO_alert_shown(TRUE)
}
uploaded$counts.csv <- GEO[["counts"]]
uploaded$samples.csv <- GEO[["samples"]]
cm <- intersect(colnames(GEO[["counts"]]), rownames(GEO[["samples"]]))
GEO <- NULL
}

if (!is.null(uploaded$counts.csv)) {
bslib::layout_columns(
col_widths = 12,
Expand All @@ -227,8 +166,129 @@ upload_table_preview_counts_server <- function(
),
bslib::layout_columns(action_buttons, br(), uiOutput(ns("error_summary")))
)
} ## end of if-else
) ## end of div
} else {
div("No counts data available for this public dataset.")
}

} else {

div(
bslib::as_fill_carrier(),
style = "width: 100%; display: flex; ",
if (is.null(uploaded$counts.csv)) {
if (upload_datatype() == "proteomics") {
msg <- "The counts file (counts.csv) contains the gene counts for all samples. For proteomics data types other than Olink NPX, the file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample. For Olink NPX, the uploaded file needs to be the standard Olink format."
} else {
msg <- "The counts file (counts.csv) contains the gene counts for all samples. The file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample."
}
bslib::layout_columns(
col_widths = c(-3, 6, -3),
row_heights = list("auto", 8, 1, 2),
gap = "0.5rem",
bslib::as_fill_carrier(bs_alert(tspan(msg), closable = FALSE, translate_js = FALSE)),
bslib::card(
if (upload_datatype() == "multi-omics") {
shiny::radioButtons(
ns("data_source"),
label = "Select input files from:",
choices = c("multi-csv", "pgx", "single-csv"),
selected = "multi-csv",
inline = TRUE
)
},
if (upload_datatype() == "multi-omics") {
shiny::conditionalPanel(
condition = sprintf("input['%s'] == 'pgx'", ns("data_source")),
div(
div(
style = "margin-bottom: 15px;",
shiny::radioButtons(
ns("data_processing"),
label = "Select data processing level:",
choices = c("Raw" = "raw", "Normalized (also batch corrected if selected on computation)" = "normalized"),
selected = "raw",
inline = TRUE
)
),
div(
style = "display: flex; align-items: center; gap: 10px; margin-bottom: 10px;",
span("Selected:", style = "font-weight: bold;"),
textOutput(ns("selected_rows_text")),
),
div(
style = "height: 350px; overflow-y: auto;",
DT::DTOutput(ns("available_data_table"))
),
style = "width: 100%; max-height: 400px; overflow-y: auto;"
),
selection = "multiple",
options = list(pageLength = 5, dom = "tp", scrollY = TRUE)
)
},

if (upload_datatype() == "multi-omics") {
shiny::conditionalPanel(
condition = sprintf("input['%s'] == 'multi-csv'", ns("data_source")),
shiny::uiOutput(ns("dynamic_file_inputs"))#,
)
},

if (upload_datatype() == "multi-omics") {
shiny::conditionalPanel(
condition = sprintf("input['%s'] == 'single-csv'", ns("data_source")),
fileInputArea(
ns("counts_csv"),
shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
multiple = FALSE,
accept = c(".csv"),
width = "100%"
)
)
},

if (upload_datatype() != "multi-omics") {
fileInputArea(
ns("counts_csv"),
shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
multiple = FALSE,
accept = c(".csv"),
width = "100%"
)
},

style = "background-color: aliceblue; border: 0.07rem dashed steelblue;"
),
action_buttons,
br()
)
},
if (!is.null(uploaded$counts.csv)) {
bslib::layout_columns(
col_widths = 12,
bslib::layout_columns(
col_widths = c(8, 4),
TableModuleUI(
ns("counts_datasets"),
width = width,
height = height,
title = title,
info.text = info.text,
caption = caption,
label = "",
show.maximize = FALSE,
translate_js = FALSE
),
bslib::navset_card_pill(
bslib::nav_panel(title = "Histogram", br(), plotOutput(ns("histogram"))),
bslib::nav_panel(title = "Box plots", br(), plotOutput(ns("boxplots")))
)
),
bslib::layout_columns(action_buttons, br(), uiOutput(ns("error_summary")))
)
} ## end of if-else
) ## end of div
}

})

output$selected_rows_text <- renderText({
Expand Down Expand Up @@ -485,7 +545,7 @@ upload_table_preview_counts_server <- function(
shinyalert::shinyalert(title = "Warning", text = err.html, html = TRUE)
}
})

# pass counts to uploaded when uploaded
observeEvent(input$counts_csv, {
# check if counts is csv (necessary due to drag and drop of any file)
Expand Down Expand Up @@ -526,7 +586,7 @@ upload_table_preview_counts_server <- function(
overwrite = TRUE
)
}

##---counts---##
sel <- grep("count|expression|abundance|concentration", tolower(input$counts_csv$name))
if (length(sel)) {
Expand Down Expand Up @@ -572,7 +632,7 @@ upload_table_preview_counts_server <- function(
if (upload_datatype() == "proteomics" && is.olink() && !is.null(df.samples)) {
uploaded$samples.csv <- df.samples
}

## ##---samples---##
## sel <- grep("samples", tolower(input$counts_csv$name))
## if (length(sel)) {
Expand Down Expand Up @@ -670,3 +730,4 @@ upload_table_preview_counts_server <- function(
)
}) ## end of moduleServer
} ## end of server

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