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Add rankings correlation plot

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This commit is contained in:
Elias Projahn 2022-08-14 18:04:40 +02:00
parent c78802425c
commit 4e31d4ef79
2 changed files with 101 additions and 1 deletions
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48
R/server.R
View file

@ -116,6 +116,54 @@ server <- function(options) {
geposan::plot_rankings(rankings, gene_sets)
})
output$ranking_correlation_plot <- plotly::renderPlotly({
preset <- preset()
ranking <- ranking()
ranking_x <- if (input$ranking_x == "combined") {
ranking
} else {
weights <- list()
weights[[input$ranking_x]] <- 1.0
geposan::ranking(ranking, weights)
}
ranking_y <- if (input$ranking_y == "combined") {
ranking
} else {
weights <- list()
weights[[input$ranking_y]] <- 1.0
geposan::ranking(ranking, weights)
}
gene_sets <- list("Reference genes" = preset$reference_gene_ids)
comparison_gene_ids <- comparison_gene_ids()
if (length(comparison_gene_ids) >= 1) {
gene_sets <- c(
gene_sets,
list("Comparison genes" = comparison_gene_ids)
)
}
method_names <- geposan::all_methods() |> purrr::lmap(function(method) {
l <- list()
l[[method[[1]]$id]] <- method[[1]]$name
l
})
method_names[["combined"]] <- "Combined"
geposan::plot_rankings_correlation(
ranking_x,
ranking_y,
method_names[[input$ranking_x]],
method_names[[input$ranking_y]],
gene_sets = gene_sets,
use_ranks = input$use_ranks
)
})
output$comparison_text <- renderUI({
reference <- geposan::compare(
ranking(),

54
R/ui.R
View file

@ -4,6 +4,14 @@
#'
#' @noRd
ui <- function(options) {
ranking_choices <- purrr::lmap(geposan::all_methods(), function(method) {
l <- list()
l[[method[[1]]$name]] <- method[[1]]$id
l
})
ranking_choices <- c(ranking_choices, "Combined" = "combined")
div(
custom_css(),
shinyjs::useShinyjs(),
@ -46,7 +54,7 @@ ui <- function(options) {
)
),
tabPanel(
title = "Methods & Distribution",
title = "Method comparison",
div(
style = "margin-top: 16px",
plotly::plotlyOutput(
@ -56,6 +64,50 @@ ui <- function(options) {
)
)
),
tabPanel(
title = "Method correlation",
div(
style = "margin-top: 16px",
div(
class = "flow-layout",
selectInput(
"ranking_y",
label = NULL,
choices = ranking_choices
),
span(
style = paste0(
"display: inline-block;",
"margin-right: 12px;",
"padding: 0.375rem 0.75rem;"
),
"~"
),
selectInput(
"ranking_x",
label = NULL,
choices = ranking_choices,
selected = "combined"
),
div(
style = paste0(
"display: inline-block;",
"padding: 0.375rem 0.75rem;"
),
checkboxInput(
"use_ranks",
"Use ranks instead of scores",
value = TRUE
)
)
),
plotly::plotlyOutput(
"ranking_correlation_plot",
width = "100%",
height = "600px"
)
)
),
tabPanel(
title = "Comparison",
div(