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Temporarily remove DisGeNET integration
Supplying the custom background results in internal server errors on the DisGeNET backend. We don't want to present results without a proper background set.
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3 changed files with 0 additions and 51 deletions
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@ -19,7 +19,6 @@ RoxygenNote: 7.2.0
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Imports:
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bslib,
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data.table,
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disgenet2r,
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DT,
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geposan,
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glue,
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43
R/server.R
43
R/server.R
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@ -267,48 +267,5 @@ server <- function(options) {
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digits = 1
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)
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})
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output$disgenet <- DT::renderDT({
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withProgress(
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message = "Querying DisGeNET",
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value = 0.0,
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{ # nolint
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setProgress(0.2)
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all_gene_names <- unique(results()[name != "", name])
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filtered_gene_names <- unique(results_filtered()[name != "", name])
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diseases <- suppressMessages(
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disgenet2r::disease_enrichment(
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all_gene_names,
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custom_universe = list(filtered_gene_names)
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)
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)
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data <- data.table(diseases@qresult)
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data <- data[, .(Description, Ratio, BgRatio, pvalue)]
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setorder(data, pvalue)
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dt <- DT::datatable(
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data,
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rownames = FALSE,
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colnames = c(
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"Disease",
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"Query ratio",
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"Total ratio",
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"p-value"
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),
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options = list(
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pageLength = 25
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)
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)
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dt <- DT::formatRound(dt, "pvalue", digits = 4)
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dt
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}
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)
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})
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}
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}
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7
R/ui.R
7
R/ui.R
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@ -101,13 +101,6 @@ ui <- function(options) {
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style = "margin-top: 16px",
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DT::DTOutput("gost_details")
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)
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),
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tabPanel(
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title = "DisGeNET",
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div(
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style = "margin-top: 16px",
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DT::DTOutput("disgenet")
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)
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)
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)
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)
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