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.
This commit is contained in:
Elias Projahn 2022-07-01 12:40:54 +02:00
parent b5ca619a0d
commit eed1cbe86b
3 changed files with 0 additions and 51 deletions

View file

@ -19,7 +19,6 @@ RoxygenNote: 7.2.0
Imports:
bslib,
data.table,
disgenet2r,
DT,
geposan,
glue,

View file

@ -267,48 +267,5 @@ server <- function(options) {
digits = 1
)
})
output$disgenet <- DT::renderDT({
withProgress(
message = "Querying DisGeNET",
value = 0.0,
{ # nolint
setProgress(0.2)
all_gene_names <- unique(results()[name != "", name])
filtered_gene_names <- unique(results_filtered()[name != "", name])
diseases <- suppressMessages(
disgenet2r::disease_enrichment(
all_gene_names,
custom_universe = list(filtered_gene_names)
)
)
data <- data.table(diseases@qresult)
data <- data[, .(Description, Ratio, BgRatio, pvalue)]
setorder(data, pvalue)
dt <- DT::datatable(
data,
rownames = FALSE,
colnames = c(
"Disease",
"Query ratio",
"Total ratio",
"p-value"
),
options = list(
pageLength = 25
)
)
dt <- DT::formatRound(dt, "pvalue", digits = 4)
dt
}
)
})
}
}

7
R/ui.R
View file

@ -101,13 +101,6 @@ ui <- function(options) {
style = "margin-top: 16px",
DT::DTOutput("gost_details")
)
),
tabPanel(
title = "DisGeNET",
div(
style = "margin-top: 16px",
DT::DTOutput("disgenet")
)
)
)
)