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Additional pVACview improvements #1384

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d4ae1c0
Make binding, presentation, and immunogenicity table rows not clickable
susannasiebert Mar 27, 2026
6073d22
Replace the individual MANE Select, Canonical, and TSL columns with a…
susannasiebert Mar 27, 2026
72db25f
Hide WT %ile columns by default
susannasiebert Mar 27, 2026
f7cb713
Merge remote-tracking branch 'origin/7.0.0' into 7.0.0_pvacview
susannasiebert Mar 27, 2026
920b060
Merge remote-tracking branch 'origin/7.0.0' into 7.0.0_pvacview
susannasiebert Mar 27, 2026
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135 changes: 92 additions & 43 deletions pvactools/tools/pvacview/server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -186,9 +186,21 @@ server <- shinyServer(function(input, output, session) {
df$mainTable$`RNA VAF Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA VAF']) && as.numeric(x['RNA VAF']) <= as.numeric(df$metricsData['trna_vaf'])})
df$mainTable$`RNA Depth Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA Depth']) && as.numeric(x['RNA Depth']) <= as.numeric(df$metricsData['trna_cov'])})
df$mainTable$`Prob Pos Pass` <- apply(df$mainTable, 1, function(x) {is_probaa_pass(x["Prob Pos"])})
df$mainTable$`TSL Fail` <- apply(df$mainTable, 1, function(x) {'tsl' %in% df$transcript_prioritization_strategy && !is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))})
df$mainTable$`MANE Select Fail` <- apply(df$mainTable, 1, function(x) {'mane_select' %in% df$transcript_prioritization_strategy && !is_mane_select_pass(x["MANE Select"])})
df$mainTable$`Canonical Fail` <- apply(df$mainTable, 1, function(x) {'canonical' %in% df$transcript_prioritization_strategy && !is_canonical_pass(x["Canonical"])})
transcript_pass <- apply(df$mainTable, 1, function(x) {
if ('tsl' %in% df$transcript_prioritization_strategy && is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))) {
return("True")
}
else if ('mane_select' %in% df$transcript_prioritization_strategy && is_mane_select_pass(x["MANE Select"])) {
return("True")
}
else if ('canonical' %in% df$transcript_prioritization_strategy && is_canonical_pass(x["Canonical"])) {
return("True")
}
else {
return("False")
}
})
df$mainTable <- add_column(df$mainTable, `Transcript Pass` = transcript_pass, .after = "TSL")
})
#Option 1: User uploaded additional data file
observeEvent(input$additionalDataInput, {
Expand Down Expand Up @@ -310,9 +322,19 @@ server <- shinyServer(function(input, output, session) {
df$mainTable$`RNA VAF Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA VAF']) && as.numeric(x['RNA VAF']) <= as.numeric(df$metricsData['trna_vaf'])})
df$mainTable$`RNA Depth Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA Depth']) && as.numeric(x['RNA Depth']) <= as.numeric(df$metricsData['trna_cov'])})
df$mainTable$`Prob Pos Pass` <- apply(df$mainTable, 1, function(x) {is_probaa_pass(x["Prob Pos"])})
df$mainTable$`TSL Fail` <- apply(df$mainTable, 1, function(x) {'tsl' %in% df$transcript_prioritization_strategy && !is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))})
df$mainTable$`MANE Select Fail` <- apply(df$mainTable, 1, function(x) {'mane_select' %in% df$transcript_prioritization_strategy && !is_mane_select_pass(x["MANE Select"])})
df$mainTable$`Canonical Fail` <- apply(df$mainTable, 1, function(x) {'canonical' %in% df$transcript_prioritization_strategy && !is_canonical_pass(x["Canonical"])})
transcript_pass <- apply(df$mainTable, TRUE, function(x) {
if ('tsl' %in% df$transcript_prioritization_strategy && is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))) {
return("True")
}
if ('mane_select' %in% df$transcript_prioritization_strategy && is_mane_select_pass(x["MANE Select"])) {
return("True")
}
if ('canonical' %in% df$transcript_prioritization_strategy && is_canonical_pass(x["Canonical"])) {
return("True")
}
return("False")
})
df$mainTable <- add_column(df$mainTable, `Transcript Pass` = transcript_pass, .after = "TSL")
df$lastSelectedRow <- 1
updateTabItems(session, "tabs", "explore")
incProgress(0.1)
Expand Down Expand Up @@ -497,9 +519,19 @@ server <- shinyServer(function(input, output, session) {
df$mainTable$`RNA VAF Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA VAF']) && as.numeric(x['RNA VAF']) <= as.numeric(df$metricsData['trna_vaf'])})
df$mainTable$`RNA Depth Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA Depth']) && as.numeric(x['RNA Depth']) <= as.numeric(df$metricsData['trna_cov'])})
df$mainTable$`Prob Pos Pass` <- apply(df$mainTable, 1, function(x) {is_probaa_pass(x["Prob Pos"])})
df$mainTable$`TSL Fail` <- apply(df$mainTable, 1, function(x) {'tsl' %in% df$transcript_prioritization_strategy && !is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))})
df$mainTable$`MANE Select Fail` <- apply(df$mainTable, 1, function(x) {'mane_select' %in% df$transcript_prioritization_strategy && !is_mane_select_pass(x["MANE Select"])})
df$mainTable$`Canonical Fail` <- apply(df$mainTable, 1, function(x) {'canonical' %in% df$transcript_prioritization_strategy && !is_canonical_pass(x["Canonical"])})
transcript_pass <- apply(df$mainTable, TRUE, function(x) {
if ('tsl' %in% df$transcript_prioritization_strategy && is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))) {
return("True")
}
if ('mane_select' %in% df$transcript_prioritization_strategy && is_mane_select_pass(x["MANE Select"])) {
return("True")
}
if ('canonical' %in% df$transcript_prioritization_strategy && is_canonical_pass(x["Canonical"])) {
return("True")
}
return("False")
})
df$mainTable <- add_column(df$mainTable, `Transcript Pass` = transcript_pass, .after = "TSL")
tier_sorter <- c("Pass", "PoorBinder", "PoorImmunogenicity", "PoorPresentation", "RefMatch", "PoorTranscript", "LowExpr", "Anchor", "Subclonal", "ProbPos", "Poor", "NoExpr")
df$mainTable$`Rank` <- rank(desc(as.numeric(replace(df$mainTable$`Allele Expr`, is.na(df$mainTable$`Allele Expr`), 0))), ties.method = "first")
for (metric in df$scoring_candidate_metric) {
Expand Down Expand Up @@ -559,9 +591,19 @@ server <- shinyServer(function(input, output, session) {
df$mainTable$`RNA VAF Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA VAF']) && as.numeric(x['RNA VAF']) <= as.numeric(df$metricsData['trna_vaf'])})
df$mainTable$`RNA Depth Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA Depth']) && as.numeric(x['RNA Depth']) <= as.numeric(df$metricsData['trna_cov'])})
df$mainTable$`Prob Pos Pass` <- apply(df$mainTable, 1, function(x) {is_probaa_pass(x["Prob Pos"])})
df$mainTable$`TSL Fail` <- apply(df$mainTable, 1, function(x) {'tsl' %in% df$transcript_prioritization_strategy && !is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))})
df$mainTable$`MANE Select Fail` <- apply(df$mainTable, 1, function(x) {'mane_select' %in% df$transcript_prioritization_strategy && !is_mane_select_pass(x["MANE Select"])})
df$mainTable$`Canonical Fail` <- apply(df$mainTable, 1, function(x) {'canonical' %in% df$transcript_prioritization_strategy && !is_canonical_pass(x["Canonical"])})
transcript_pass <- apply(df$mainTable, TRUE, function(x) {
if ('tsl' %in% df$transcript_prioritization_strategy && is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))) {
return("True")
}
if ('mane_select' %in% df$transcript_prioritization_strategy && is_mane_select_pass(x["MANE Select"])) {
return("True")
}
if ('canonical' %in% df$transcript_prioritization_strategy && is_canonical_pass(x["Canonical"])) {
return("True")
}
return("False")
})
df$mainTable <- add_column(df$mainTable, `Transcript Pass` = transcript_pass, .after = "TSL")
tier_sorter <- c("Pass", "PoorBinder", "PoorImmunogenicity", "PoorPresentation", "RefMatch", "PoorTranscript", "LowExpr", "Anchor", "Subclonal", "ProbPos", "Poor", "NoExpr")
df$mainTable$`Rank` <- rank(desc(as.numeric(replace(df$mainTable$`Allele Expr`, is.na(df$mainTable$`Allele Expr`), 0))), ties.method = "first")
for (metric in df$scoring_candidate_metric) {
Expand Down Expand Up @@ -720,12 +762,13 @@ server <- shinyServer(function(input, output, session) {
"RNA Expr", "RNA VAF", "Allele Expr", "RNA Depth", "DNA VAF"))

# Columns that should be hidden from the display
additional_hidden_columns <- which(colnames(filtered_table) %in% c("Num Passing Transcripts", "Best Transcript",
additional_hidden_columns <- which(colnames(filtered_table) %in% c("Num Passing Transcripts", "Best Transcript", "MANE Select", "Canonical", "TSL",
"%ile WT", "IC50 %ile WT", "IM %ile WT", "Pres %ile WT",
"Col DNA VAF", "Col RNA Depth", "Col Allele Expr", "Col RNA VAF", "Col RNA Expr",
"Scaled binding percentile", "Scaled immunogenicity percentile", "Scaled presentation percentile", "Scaled BA", "Gene of Interest",
"IC50 Pass", "Binding Percentile Pass", "Immunogenicity Percentile Pass", "Presentation Percentile Pass", "Anchor Pass",
"VAF Clonal Pass", "Allele Expr Pass", "RNA Expr Fail", "RNA VAF Fail", "RNA Depth Fail",
"Prob Pos Pass", "TSL Fail", "MANE Select Fail", "Canonical Fail"))
"Prob Pos Pass"))
hidden_targets <- c(hla_columns, additional_hidden_columns)

# Applies a CSS class to the specified columns
Expand Down Expand Up @@ -800,15 +843,13 @@ server <- shinyServer(function(input, output, session) {
%>% formatStyle(c("RNA Expr"), "RNA Expr Fail", fontWeight = styleEqual(c(TRUE), c("bold")), border = styleEqual(c(TRUE), c("2px solid red")))
%>% formatStyle(c("RNA VAF"), "RNA VAF Fail", fontWeight = styleEqual(c(TRUE), c("bold")), border = styleEqual(c(TRUE), c("2px solid red")))
%>% formatStyle(c("RNA Depth"), "RNA Depth Fail", fontWeight = styleEqual(c(TRUE), c("bold")), border = styleEqual(c(TRUE), c("2px solid red")))
%>% formatStyle(c("TSL"), "TSL Fail", fontWeight = styleEqual(c(TRUE), c("bold")), border = styleEqual(c(TRUE), c("2px solid red")))
%>% formatStyle(c("MANE Select"), "MANE Select Fail", fontWeight = styleEqual(c(TRUE), c("bold")), border = styleEqual(c(TRUE), c("2px solid red")))
%>% formatStyle(c("Canonical"), "Canonical Fail", fontWeight = styleEqual(c(TRUE), c("bold")), border = styleEqual(c(TRUE), c("2px solid red")))
%>% formatStyle(c("IC50 MT"), "IC50 Pass",fontWeight = styleEqual(c(FALSE), c("bold")), border = styleEqual(c(FALSE), c("2px solid red")))
%>% formatStyle(c("IC50 %ile MT"), "Binding Percentile Pass",fontWeight = styleEqual(c(FALSE), c("bold")), border = styleEqual(c(FALSE), c("2px solid red")))
%>% formatStyle(c("IM %ile MT"), "Immunogenicity Percentile Pass",fontWeight = styleEqual(c(FALSE), c("bold")), border = styleEqual(c(FALSE), c("2px solid red")))
%>% formatStyle(c("Pres %ile MT"), "Presentation Percentile Pass",fontWeight = styleEqual(c(FALSE), c("bold")), border = styleEqual(c(FALSE), c("2px solid red")))
%>% formatStyle(c("Prob Pos"), "Prob Pos Pass", fontWeight = styleEqual(c(FALSE), c("bold")), border = styleEqual(c(FALSE), c("2px solid red")))
%>% formatStyle(c("Ref Match"), "Ref Match", fontWeight = styleEqual(c("True"), c("bold")), border = styleEqual(c("True"), c("2px solid red")))
%>% formatStyle(c("Transcript Pass"), "Transcript Pass", fontWeight = styleEqual(c("False"), c("bold")), border = styleEqual(c("False"), c("2px solid red")))
%>% formatStyle("Best Peptide", fontFamily="monospace")
, server = FALSE)
#capture last selected row so that it still displays data from that row when
Expand Down Expand Up @@ -1474,14 +1515,17 @@ server <- shinyServer(function(input, output, session) {
}
}
incProgress(1)
dtable <- datatable(binding_reformat, options = list(
pageLength = 10,
lengthChange = FALSE,
rowCallback = JS("function(row, data, index, rowId) {",
"if(((rowId+1) % 4) == 3 || ((rowId+1) % 4) == 0) {",
'row.style.backgroundColor = "#E0E0E0";', "}", "}"),
columnDefs = list(list(visible = FALSE, targets = seq(original_length+1, ncol(binding_reformat))))
)) %>% formatStyle("Mutant", fontWeight = styleEqual("MT", "bold"), color = styleEqual("MT", "#E74C3C"))
dtable <- datatable(binding_reformat,
selection = 'none',
options = list(
pageLength = 10,
lengthChange = FALSE,
rowCallback = JS("function(row, data, index, rowId) {",
"if(((rowId+1) % 4) == 3 || ((rowId+1) % 4) == 0) {",
'row.style.backgroundColor = "#E0E0E0";', "}", "}"),
columnDefs = list(list(visible = FALSE, targets = seq(original_length+1, ncol(binding_reformat))))
)
) %>% formatStyle("Mutant", fontWeight = styleEqual("MT", "bold"), color = styleEqual("MT", "#E74C3C"))
for (col_name in colnames(binding_reformat)[3:original_length]) {
scaled_col_name <- paste0("Scaled_", col_name)
if (is.null(input$binding_table_mode) || input$binding_table_mode == 'IC50') {
Expand Down Expand Up @@ -1569,14 +1613,17 @@ server <- shinyServer(function(input, output, session) {
})
}
incProgress(1)
dtable <- datatable(immunogenicity_reformat, options = list(
pageLength = 10,
lengthChange = FALSE,
rowCallback = JS("function(row, data, index, rowId) {",
"if(((rowId+1) % 4) == 3 || ((rowId+1) % 4) == 0) {",
'row.style.backgroundColor = "#E0E0E0";', "}", "}"),
columnDefs = list(list(visible = FALSE, targets = seq(original_length+1, ncol(immunogenicity_reformat))))
)) %>% formatStyle("Mutant", fontWeight = styleEqual("MT", "bold"), color = styleEqual("MT", "#E74C3C"))
dtable <- datatable(immunogenicity_reformat,
selection = 'none',
options = list(
pageLength = 10,
lengthChange = FALSE,
rowCallback = JS("function(row, data, index, rowId) {",
"if(((rowId+1) % 4) == 3 || ((rowId+1) % 4) == 0) {",
'row.style.backgroundColor = "#E0E0E0";', "}", "}"),
columnDefs = list(list(visible = FALSE, targets = seq(original_length+1, ncol(immunogenicity_reformat))))
)
) %>% formatStyle("Mutant", fontWeight = styleEqual("MT", "bold"), color = styleEqual("MT", "#E74C3C"))
for (col_name in colnames(immunogenicity_reformat)[3:original_length]) {
scaled_col_name <- paste0("Scaled_", col_name)
dtable <- dtable %>% formatStyle(col_name, scaled_col_name,
Expand Down Expand Up @@ -1659,14 +1706,17 @@ server <- shinyServer(function(input, output, session) {
})
}
incProgress(1)
dtable <- datatable(presentation_reformat, options = list(
pageLength = 10,
lengthChange = FALSE,
rowCallback = JS("function(row, data, index, rowId) {",
"if(((rowId+1) % 4) == 3 || ((rowId+1) % 4) == 0) {",
'row.style.backgroundColor = "#E0E0E0";', "}", "}"),
columnDefs = list(list(visible = FALSE, targets = seq(original_length+1, ncol(presentation_reformat))))
)) %>% formatStyle("Mutant", fontWeight = styleEqual("MT", "bold"), color = styleEqual("MT", "#E74C3C"))
dtable <- datatable(presentation_reformat,
selection = 'none',
options = list(
pageLength = 10,
lengthChange = FALSE,
rowCallback = JS("function(row, data, index, rowId) {",
"if(((rowId+1) % 4) == 3 || ((rowId+1) % 4) == 0) {",
'row.style.backgroundColor = "#E0E0E0";', "}", "}"),
columnDefs = list(list(visible = FALSE, targets = seq(original_length+1, ncol(presentation_reformat))))
)
) %>% formatStyle("Mutant", fontWeight = styleEqual("MT", "bold"), color = styleEqual("MT", "#E74C3C"))
for (col_name in colnames(presentation_reformat)[3:original_length]) {
scaled_col_name <- paste0("Scaled_", col_name)
dtable <- dtable %>% formatStyle(col_name, scaled_col_name,
Expand Down Expand Up @@ -1864,8 +1914,7 @@ server <- shinyServer(function(input, output, session) {
"Scaled BA", "Scaled binding percentile", "Scaled immunogenicity percentile", "Scaled presentation percentile", "Comments", "Gene of Interest",
"Col RNA Expr", "Col RNA VAF", "Col Allele Expr", "Col RNA Depth", "Col DNA VAF",
"IC50 Pass", "Binding Percentile Pass", "Immunogenicity Percentile Pass", "Presentation Percentile Pass", "Anchor Pass","VAF Clonal Pass", "Allele Expr Pass",
"RNA Expr Fail", "RNA VAF Fail", "RNA Depth Fail", "Prob Pos Pass",
"TSL Fail", "MANE Select Fail", "Canonical Fail")
"RNA Expr Fail", "RNA VAF Fail", "RNA Depth Fail", "Prob Pos Pass")
data <- df$mainTable[, !(colsToDrop)]
col_names <- colnames(data)
evaluations <- data.frame("ID" = row.names(df$evaluations), Evaluation = df$evaluations[, 1])
Expand Down
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