mirror of
https://github.com/johrpan/geposanui.git
synced 2025-10-26 11:17:24 +01:00
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:
parent
6db14c4d4a
commit
9a20abd69b
3 changed files with 0 additions and 51 deletions
|
|
@ -19,7 +19,6 @@ RoxygenNote: 7.2.0
|
||||||
Imports:
|
Imports:
|
||||||
bslib,
|
bslib,
|
||||||
data.table,
|
data.table,
|
||||||
disgenet2r,
|
|
||||||
DT,
|
DT,
|
||||||
geposan,
|
geposan,
|
||||||
glue,
|
glue,
|
||||||
|
|
|
||||||
43
R/server.R
43
R/server.R
|
|
@ -267,48 +267,5 @@ server <- function(options) {
|
||||||
digits = 1
|
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
7
R/ui.R
|
|
@ -101,13 +101,6 @@ ui <- function(options) {
|
||||||
style = "margin-top: 16px",
|
style = "margin-top: 16px",
|
||||||
DT::DTOutput("gost_details")
|
DT::DTOutput("gost_details")
|
||||||
)
|
)
|
||||||
),
|
|
||||||
tabPanel(
|
|
||||||
title = "DisGeNET",
|
|
||||||
div(
|
|
||||||
style = "margin-top: 16px",
|
|
||||||
DT::DTOutput("disgenet")
|
|
||||||
)
|
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue