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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"
)
),
div(
style = "margin-top: 16px",
plotly::plotlyOutput(NS(id, "plot")),
),
div(
style = "margin-top: 16px",
DT::DTOutput(NS(id, "details"))
tabsetPanel(
id = NS(id, "results"),
type = "hidden",
tabPanelBody(
"some",
div(
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()) |>
bindEvent(input$gsea_run, ignoreNULL = FALSE)
output$plot <- plotly::renderPlotly({
gprofiler2::gostplot(
gsea_analysis(),
capped = FALSE,
interactive = TRUE
observe({
updateTabsetPanel(
session,
"results",
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({
data <- data.table(gsea_analysis()$result)
setorder(data, p_value)
if (!is.null(gsea_analysis()$result)) {
data <- data.table(gsea_analysis()$result)
setorder(data, p_value)
data[, total_ratio := term_size / effective_domain_size]
data[, query_ratio := intersection_size / query_size]
data[, increase := (query_ratio - total_ratio) / total_ratio]
data[, total_ratio := term_size / effective_domain_size]
data[, query_ratio := intersection_size / query_size]
data[, increase := (query_ratio - total_ratio) / total_ratio]
data <- data[, .(
source,
term_name,
total_ratio,
query_ratio,
increase,
p_value
)]
data <- data[, .(
source,
term_name,
total_ratio,
query_ratio,
increase,
p_value
)]
DT::datatable(
data,
rownames = FALSE,
colnames = c(
"Source",
"Term",
"Total ratio",
"Query ratio",
"Increase",
"p-value"
),
options = list(
pageLength = 25
)
) |>
DT::formatRound("p_value", digits = 4) |>
DT::formatPercentage(
c("total_ratio", "query_ratio", "increase"),
digits = 2
)
DT::datatable(
data,
rownames = FALSE,
colnames = c(
"Source",
"Term",
"Total ratio",
"Query ratio",
"Increase",
"p-value"
),
options = list(
pageLength = 25
)
) |>
DT::formatRound("p_value", digits = 4) |>
DT::formatPercentage(
c("total_ratio", "query_ratio", "increase"),
digits = 2
)
} else {
DT::datatable(data.table())
}
})
})
}