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Use correct background and show increase for GSEA

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This commit is contained in:
Elias Projahn 2022-07-22 09:35:24 +02:00
parent 12129ac65a
commit c2328c0847
1 changed files with 11 additions and 9 deletions
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20
R/server.R
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@ -212,7 +212,8 @@ server <- function(options) {
setProgress(0.2) setProgress(0.2)
gprofiler2::gost( gprofiler2::gost(
results_filtered()[, gene], results_filtered()[, gene],
custom_bg = preset()$gene_ids custom_bg = preset()$gene_ids,
domain_scope = "custom_annotated"
) )
} }
) )
@ -232,12 +233,14 @@ server <- function(options) {
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 <- data[, .( data <- data[, .(
source, source,
term_name, term_name,
total_ratio, total_ratio,
query_ratio, query_ratio,
increase,
p_value p_value
)] )]
@ -249,19 +252,18 @@ server <- function(options) {
"Term", "Term",
"Total ratio", "Total ratio",
"Query ratio", "Query ratio",
"Increase",
"p-value" "p-value"
), ),
options = list( options = list(
pageLength = 25 pageLength = 25
) )
) ) |>
DT::formatRound("p_value", digits = 4) |>
dt <- DT::formatRound(dt, "p_value", digits = 4) DT::formatPercentage(
dt <- DT::formatPercentage( c("total_ratio", "query_ratio", "increase"),
dt, digits = 2
c("total_ratio", "query_ratio"), )
digits = 1
)
}) })
} }
} }