Skip to content

Added sortability to Acpt/Rej/Rev columns #1270

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: staging
Choose a base branch
from
Open

Added sortability to Acpt/Rej/Rev columns #1270

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
35 changes: 32 additions & 3 deletions pvactools/tools/pvacview/server.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,9 @@ server <- shinyServer(function(input, output, session) {
mainData$`%ile MT` <- as.numeric(mainData$`%ile MT`)
mainData$`RNA Depth` <- as.character(as.integer(mainData$`RNA Depth`))
mainData$`TSL`[is.na(mainData$`TSL`)] <- "NA"
mainData$Acpt_val <- ifelse(mainData$Evaluation == "Accept", 1, 0)
mainData$Rej_val <- ifelse(mainData$Evaluation == "Reject", 1, 0)
mainData$Rev_val <- ifelse(mainData$Evaluation == "Review", 1, 0)
df$evaluations <- data.frame(data = mainData$Evaluation, row.names = mainData$ID)
df$mainTable <- mainData
df$metricsData <- NULL
Expand Down Expand Up @@ -208,6 +211,9 @@ server <- shinyServer(function(input, output, session) {
mainData$`%ile MT` <- as.numeric(mainData$`%ile MT`)
mainData$`RNA Depth` <- as.character(as.integer(mainData$`RNA Depth`))
mainData$`TSL`[is.na(mainData$`TSL`)] <- "NA"
mainData$Acpt_val <- ifelse(mainData$Evaluation == "Accept", 1, 0)
mainData$Rej_val <- ifelse(mainData$Evaluation == "Reject", 1, 0)
mainData$Rev_val <- ifelse(mainData$Evaluation == "Review", 1, 0)
df$evaluations <- data.frame(data = mainData$Evaluation, row.names = mainData$ID)
df$mainTable <- mainData
incProgress(0.1)
Expand Down Expand Up @@ -240,7 +246,7 @@ server <- shinyServer(function(input, output, session) {
}
columns_needed <- c("ID", "Index", df$converted_hla_names, "Gene", "AA Change", "Num Passing Transcripts", "Best Peptide", "Best Transcript", "TSL", "Allele",
"Pos", "Prob Pos", "Num Included Peptides", "Num Passing Peptides", "IC50 MT", "IC50 WT", "%ile MT", "%ile WT", "RNA Expr", "RNA VAF",
"Allele Expr", "RNA Depth", "DNA VAF", "Tier", "Ref Match", "Acpt", "Rej", "Rev")
"Allele Expr", "RNA Depth", "DNA VAF", "Tier", "Ref Match", "Acpt", "Rej", "Rev", "Acpt_val", "Rej_val", "Rev_val")
if ("Comments" %in% colnames(df$mainTable)) {
columns_needed <- c(columns_needed, "Comments")
df$comments <- data.frame(data = df$mainTable$`Comments`, nrow = nrow(df$mainTable), ncol = 1)
Expand Down Expand Up @@ -564,7 +570,8 @@ server <- shinyServer(function(input, output, session) {
# Columns that should be hidden from the display
additional_hidden_columns <- which(colnames(filtered_table) %in% c("Num Passing Transcripts", "Best Transcript", "Has Prob Pos", "Percentile Fail",
"Col DNA VAF", "Col RNA Depth", "Col Allele Expr", "Col RNA VAF", "Col RNA Expr",
"Bad TSL", "Scaled percentile", "Scaled BA", "Gene of Interest", "Tier Count"))
"Bad TSL", "Scaled percentile", "Scaled BA", "Gene of Interest", "Tier Count",
"Acpt_val", "Rej_val", "Rev_val"))
hidden_targets <- c(hla_columns, additional_hidden_columns)

# Applies a CSS class to the specified columns
Expand All @@ -576,6 +583,13 @@ server <- shinyServer(function(input, output, session) {
list(targets = i, render = render_na)
})

# Modify default sort logic for 'Acpt', 'Rej', and 'Rev' columns
eval_sort_defs <- list(
list(targets = which(colnames(filtered_table) == "Acpt"), orderData = which(colnames(filtered_table) == "Acpt_val")),
list(targets = which(colnames(filtered_table) == "Rej"), orderData = which(colnames(filtered_table) == "Rej_val")),
list(targets = which(colnames(filtered_table) == "Rev"), orderData = which(colnames(filtered_table) == "Rev_val"))
)

datatable(filtered_table,
escape = FALSE,
callback = JS(callback(hla_count(), df$metricsData$mt_top_score_metric)),
Expand All @@ -589,7 +603,7 @@ server <- shinyServer(function(input, output, session) {
list(visible = FALSE, targets = hidden_targets),
list(orderable = TRUE, targets = 0)
),
na_render_defs
c(eval_sort_defs, na_render_defs)
),
buttons = list(I("colvis")),
drawCallback = htmlwidgets::JS(
Expand Down Expand Up @@ -698,6 +712,11 @@ server <- shinyServer(function(input, output, session) {
}
selectedID <- strsplit(input$accept_eval, "_")[[1]][2]
df$evaluations[selectedID, 1] <- "Accept"

df$mainTable$Acpt_val[df$mainTable$ID == selectedID] <- 1
df$mainTable$Rej_val[df$mainTable$ID == selectedID] <- 0
df$mainTable$Rev_val[df$mainTable$ID == selectedID] <- 0

html <- paste0("#button-acpt_", selectedID ," { color: green !important; }")
insertUI("head", ui = tags$style(HTML(html)))
removeUI(selector = paste0("style:contains(#button-rej_", selectedID, ')'), multiple = TRUE)
Expand All @@ -709,6 +728,11 @@ server <- shinyServer(function(input, output, session) {
}
selectedID <- strsplit(input$reject_eval, "_")[[1]][2]
df$evaluations[selectedID, 1] <- "Reject"

df$mainTable$Acpt_val[df$mainTable$ID == selectedID] <- 0
df$mainTable$Rej_val[df$mainTable$ID == selectedID] <- 1
df$mainTable$Rev_val[df$mainTable$ID == selectedID] <- 0

html <- paste0("#button-rej_", selectedID ," { color: red !important; }")
insertUI("head", ui = tags$style(HTML(html)))
removeUI(selector = paste0("style:contains(#button-acpt_", selectedID, ')'), multiple = TRUE)
Expand All @@ -720,6 +744,11 @@ server <- shinyServer(function(input, output, session) {
}
selectedID <- strsplit(input$review_eval, "_")[[1]][2]
df$evaluations[selectedID, 1] <- "Review"

df$mainTable$Acpt_val[df$mainTable$ID == selectedID] <- 0
df$mainTable$Rej_val[df$mainTable$ID == selectedID] <- 0
df$mainTable$Rev_val[df$mainTable$ID == selectedID] <- 1

html <- paste0("#button-rev_", selectedID ," { color: orange !important; }")
insertUI("head", ui = tags$style(HTML(html)))
removeUI(selector = paste0("style:contains(#button-acpt_", selectedID, ')'), multiple = TRUE)
Expand Down