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fix(volcano plot): Upgrade PTM volcano plots to be interactive via plotly #200

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Merged
tonywu1999 merged 4 commits into from
Apr 24, 2026
Merged

fix(volcano plot): Upgrade PTM volcano plots to be interactive via plotly #200

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0714102
trying out plotly for groupcomparisonplotsPTM
tonywu1999 Apr 24, 2026
4915cac
extra fix for plotting purposes
tonywu1999 Apr 24, 2026
658686b
simplify code
tonywu1999 Apr 24, 2026
fb05737
add comment
tonywu1999 Apr 24, 2026
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9 changes: 1 addition & 8 deletions R/module-statmodel-server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -447,14 +447,7 @@ statmodelServer = function(id, parent_session, loadpage_input, qc_input,
req(input[[NAMESPACE_STATMODEL$visualization_view_results]])
ns = session$ns

if (loadpage_input()$BIO == "PTM") {
output_plot = renderPlot({
create_group_comparison_plot(
input, loadpage_input(), data_comparison()
)
})

} else if (input[[NAMESPACE_STATMODEL$visualization_plot_type]] ==
if (input[[NAMESPACE_STATMODEL$visualization_plot_type]] ==
CONSTANTS_STATMODEL$plot_type_response_curve) {
if (app_template() == TEMPLATES$protein_turnover) {
req(turnover_ratios())
Expand Down
10 changes: 8 additions & 2 deletions R/statmodel-server-visualization.R
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Expand Up @@ -83,16 +83,21 @@ create_group_comparison_plot = function(input, loadpage_input, data_comparison)
stop('** Cannot generate multiple plots in a screen. Please refine selection or save to a pdf. **')
}
if (loadpage_input$BIO == "PTM") {
plot_result = groupComparisonPlotsPTM(
result = groupComparisonPlotsPTM(
data_comparison,
input[[NAMESPACE_STATMODEL$visualization_plot_type]],
sig = input[[NAMESPACE_STATMODEL$visualization_volcano_significance_cutoff]],
FCcutoff = fold_change_cutoff,
logBase.pvalue = as.integer(input[[NAMESPACE_STATMODEL$visualization_logp_base]]),
ProteinName = TRUE,
which.Comparison = input[[NAMESPACE_STATMODEL$visualization_which_comparison]],
address = FALSE
address = FALSE,
isPlotly = TRUE
)
# groupComparisonPlotsPTM returns `result` as a list where element 3 is
# the adjusted-peptide plot and element 1 is the unadjusted fallback;
# prefer the adjusted plot (result[[3]]) when available.
plot_result = if (length(result) >= 3) result[[3]] else result[[1]]
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} else if (loadpage_input$DDA_DIA == "TMT") {
plot_result = groupComparisonPlots(
data = data_comparison$ComparisonResult,
Expand Down Expand Up @@ -131,6 +136,7 @@ create_group_comparison_plot = function(input, loadpage_input, data_comparison)
}, error = function(e) {
remove_modal_spinner()
showNotification(conditionMessage(e), type = "error", duration = 8)
NULL
})
}
#' Get filename for plot download based on plot type
Expand Down
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