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gsea: Properly show empty results

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This commit is contained in:
Elias Projahn 2022-08-30 10:13:28 +02:00
parent 49d5a3f281
commit f0a8bce297
1 changed files with 85 additions and 45 deletions
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130
R/gsea.R
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@ -17,13 +17,33 @@ gsea_ui <- function(id) {
style = "margin-left: 16px" style = "margin-left: 16px"
) )
), ),
div( tabsetPanel(
style = "margin-top: 16px", id = NS(id, "results"),
plotly::plotlyOutput(NS(id, "plot")), type = "hidden",
), tabPanelBody(
div( "some",
style = "margin-top: 16px", div(
DT::DTOutput(NS(id, "details")) style = "margin-top: 16px",
plotly::plotlyOutput(NS(id, "plot")),
),
div(
style = "margin-top: 16px",
DT::DTOutput(NS(id, "details"))
)
),
tabPanelBody(
"none",
div(
style = "margin-top: 32px",
h5("No results"),
div(
"The enrichment analysis using g:Profiler yielded no results. ",
"You can change the parameters of the ranking and the filter ",
"criteria. Click the \"Update analysis\" button to rerun the ",
"analysis."
)
)
)
) )
) )
} }
@ -55,51 +75,71 @@ gsea_server <- function(id, ranking) {
bindCache(ranking_filtered()) |> bindCache(ranking_filtered()) |>
bindEvent(input$gsea_run, ignoreNULL = FALSE) bindEvent(input$gsea_run, ignoreNULL = FALSE)
output$plot <- plotly::renderPlotly({ observe({
gprofiler2::gostplot( updateTabsetPanel(
gsea_analysis(), session,
capped = FALSE, "results",
interactive = TRUE selected = if (!is.null(gsea_analysis()$result)) {
"some"
} else {
"none"
}
) )
}) })
output$plot <- plotly::renderPlotly({
if (!is.null(gsea_analysis()$result)) {
gprofiler2::gostplot(
gsea_analysis(),
capped = FALSE,
interactive = TRUE
)
} else {
plotly::plotly_empty()
}
})
output$details <- DT::renderDT({ output$details <- DT::renderDT({
data <- data.table(gsea_analysis()$result) if (!is.null(gsea_analysis()$result)) {
setorder(data, p_value) data <- data.table(gsea_analysis()$result)
setorder(data, p_value)
data[, total_ratio := term_size / effective_domain_size] data[, total_ratio := term_size / effective_domain_size]
data[, query_ratio := intersection_size / query_size] data[, query_ratio := intersection_size / query_size]
data[, increase := (query_ratio - total_ratio) / total_ratio] data[, increase := (query_ratio - total_ratio) / total_ratio]
data <- data[, .( data <- data[, .(
source, source,
term_name, term_name,
total_ratio, total_ratio,
query_ratio, query_ratio,
increase, increase,
p_value p_value
)] )]
DT::datatable( DT::datatable(
data, data,
rownames = FALSE, rownames = FALSE,
colnames = c( colnames = c(
"Source", "Source",
"Term", "Term",
"Total ratio", "Total ratio",
"Query ratio", "Query ratio",
"Increase", "Increase",
"p-value" "p-value"
), ),
options = list( options = list(
pageLength = 25 pageLength = 25
) )
) |> ) |>
DT::formatRound("p_value", digits = 4) |> DT::formatRound("p_value", digits = 4) |>
DT::formatPercentage( DT::formatPercentage(
c("total_ratio", "query_ratio", "increase"), c("total_ratio", "query_ratio", "increase"),
digits = 2 digits = 2
) )
} else {
DT::datatable(data.table())
}
}) })
}) })
} }