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MSstatsPTM Plotly plots adaptation for Shiny #94

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MSstatsPTM Plotly plots adaptation for Shiny #94

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b0c06c3
adopt ptm plots
deril2605 Jun 2, 2024
559cfe4
fixes
deril2605 Jun 2, 2024
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42 changes: 27 additions & 15 deletions R/module-qc-server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -170,17 +170,19 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
which.Protein = protein,
originalPlot = original,
summaryPlot = input$summ,
address = file, isPlotly = TRUE
address="Ex_", isPlotly = TRUE
)[[1]]
return(plot)
# return(plot)

} else if (loadpage_input()$BIO == "PTM"){

dataProcessPlotsPTM(preprocess_data(),
plot <- dataProcessPlotsPTM(preprocess_data(),
type=input$type1,
which.PTM = protein,
originalPlot = original,
summaryPlot = input$summ,
address = file)
address="Ex_", isPlotly = TRUE)[[1]]
# return(plot)

} else{
plot <- dataProcessPlots(data = preprocess_data(),
Expand All @@ -194,12 +196,14 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
originalPlot = original,
summaryPlot = input$summ,
save_condition_plot_result = FALSE,
address = file,
address="Ex_",
isPlotly = TRUE

)[[1]]
return(plot)
# return(plot)
}
enable("plotresults_qc")
return(plot)
}
else {
return(NULL)
Expand Down Expand Up @@ -367,17 +371,25 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
# }
# })


### OUTPUT ####
output$plotresults_qc = downloadHandler(
filename = function() {
paste("SummaryPlot-", Sys.Date(), ".zip", sep="")
},
content = function(file) {
files <- list.files(getwd(), pattern = "^Ex_", full.names = TRUE)
file_info <- file.info(files)
latest_file <- files[which.max(file_info$mtime)]
print(latest_file)
file.copy(latest_file, file)
}
)

output$showplot = renderUI({
ns<- session$ns

# PTM plotly plots are still under development
if (loadpage_input()$BIO == "PTM") {
output$theplot = renderPlot(theplot())
op <- plotOutput(ns("theplot"))
} else {
output$theplot = renderPlotly(theplot())
op <- plotlyOutput(ns("theplot"))
}
output$theplot = renderPlotly(theplot())
op <- plotlyOutput(ns("theplot"))

tagList(
op,
Expand Down
6 changes: 4 additions & 2 deletions R/module-qc-ui.R
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Original file line number Diff line number Diff line change
Expand Up @@ -227,16 +227,18 @@ qcUI <- function(id) {
"No feature legend"="NA"))

),

p("Use the camera icon on the top right of the plot to download as PNG"),
uiOutput(ns("Which")),
tags$br()
),
# conditionalPanel(condition="$('html').hasClass('shiny-busy')",
# tags$br(),
# tags$br(),
# tags$h4("Calculation in progress...")),
uiOutput(ns("showplot")),
disabled(downloadButton(ns("plotresults_qc"), "Save plot results as Zip")),
uiOutput(ns("showplot"))
# disabled(downloadButton(ns("saveplot"), "Save this plot"))

),
tabPanel("Download Data",
#verbatimTextOutput('effect'),
Expand Down
50 changes: 29 additions & 21 deletions R/module-statmodel-server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -399,15 +399,31 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu
}

if (loadpage_input()$BIO=="PTM"){
plot1 = groupComparisonPlotsPTM(data_comparison(),
input$typeplot,
sig=input$sig,
FCcutoff=input$FC,
logBase.pvalue=as.integer(input$logp),
ProteinName = input$pname,
which.Comparison = input$whichComp,
address = FALSE)

tryCatch({
if(toupper(input$typeplot) == "COMPARISONPLOT") {
remove_modal_spinner()
stop( 'Comparison Plot is not offered by MSstatsPTM at the moment' )
}
plot = groupComparisonPlotsPTM(data_comparison(),
input$typeplot,
sig=input$sig,
FCcutoff=input$FC,
logBase.pvalue=as.integer(input$logp),
ProteinName = input$pname,
numProtein=input$nump,
which.Comparison = input$whichComp,
address = "Ex_",
isPlotly = TRUE)
if(length(plot) == 3) { # return adjusted if we have it
plot1 = plot[[3]]
} else {
plot1 = plot[[1]]
}
remove_modal_spinner()
},error = function(e){
remove_modal_spinner()
stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf. **' )}
)

} else if(loadpage_input()$DDA_DIA=="TMT"){
tryCatch({
Expand Down Expand Up @@ -717,18 +733,10 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu

observeEvent(input$viewresults, {
ns <- session$ns
# PTM plotly plots are still under development
if (loadpage_input()$BIO == "PTM") {
output$comp_plots = renderPlot({
group_comparison(FALSE, FALSE)
})
op <- plotOutput(ns("comp_plots"))
} else {
output$comp_plots = renderPlotly({
group_comparison(FALSE, FALSE)
})
op <- plotlyOutput(ns("comp_plots"), height = input$height)
}
output$comp_plots = renderPlotly({
group_comparison(FALSE, FALSE)
})
op <- plotlyOutput(ns("comp_plots"), height = input$height)
insertUI(
selector = paste0("#", ns("comparison_plots")),
ui=tags$div(
Expand Down
5 changes: 4 additions & 1 deletion R/module-statmodel-ui.R
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,10 @@ statmodelUI <- function(id) {
Volcano Plot comparison, you must save the results \
as a HTML."),
conditionalPanel(
condition = "input['loadpage-BIO'] !== 'PTM'",
condition = "input['loadpage-BIO'] == 'PTM' && input['statmodel-typeplot'] == 'ComparisonPlot'",
p("Comparison Plot is not offered by MSstatsPTM at the moment")),
conditionalPanel(
condition = "input['loadpage-BIO'] !== 'PTM_'",
actionButton(ns("viewresults"),
"View plot in browser (only for one \
comparison/protein)")),
Expand Down