deril2605 authored on 25/04/2024 17:28:43
| ... | ... |
@@ -411,18 +411,20 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 411 | 411 |
|
| 412 | 412 |
} else if(loadpage_input()$DDA_DIA=="TMT"){
|
| 413 | 413 |
tryCatch({
|
| 414 |
- plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult, |
|
| 415 |
- type=input$typeplot, |
|
| 416 |
- sig=input$sig, |
|
| 417 |
- FCcutoff=input$FC, |
|
| 418 |
- logBase.pvalue=input$logp, |
|
| 419 |
- ProteinName=input$pname, |
|
| 420 |
- numProtein=input$nump, |
|
| 421 |
- clustering=input$cluster, |
|
| 422 |
- which.Comparison=input$whichComp, |
|
| 423 |
- which.Protein = input$whichProt, |
|
| 424 |
- address=path1(), |
|
| 425 |
- savePDF=pdf) |
|
| 414 |
+ # makes use of MSstats groupComparisonPlots function |
|
| 415 |
+ plot1 = groupComparisonPlots(data=data_comparison()$ComparisonResult, |
|
| 416 |
+ type=input$typeplot, |
|
| 417 |
+ sig=input$sig, |
|
| 418 |
+ FCcutoff=input$FC, |
|
| 419 |
+ logBase.pvalue=as.numeric(input$logp), |
|
| 420 |
+ ProteinName=input$pname, |
|
| 421 |
+ numProtein=input$nump, |
|
| 422 |
+ clustering=input$cluster, |
|
| 423 |
+ which.Comparison=input$whichComp, |
|
| 424 |
+ which.Protein = input$whichProt, |
|
| 425 |
+ height = input$height, |
|
| 426 |
+ address="Ex_", |
|
| 427 |
+ isPlotly = TRUE)[[1]] |
|
| 426 | 428 |
remove_modal_spinner() |
| 427 | 429 |
}, |
| 428 | 430 |
error = function(e){
|
| ... | ... |
@@ -715,8 +717,8 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 715 | 717 |
|
| 716 | 718 |
observeEvent(input$viewresults, {
|
| 717 | 719 |
ns <- session$ns |
| 718 |
- # TMT and PTM plotly plots are still under development |
|
| 719 |
- if ((loadpage_input()$DDA_DIA == "TMT") || (loadpage_input()$BIO == "PTM")) {
|
|
| 720 |
+ # PTM plotly plots are still under development |
|
| 721 |
+ if (loadpage_input()$BIO == "PTM") {
|
|
| 720 | 722 |
output$comp_plots = renderPlot({
|
| 721 | 723 |
group_comparison(FALSE, FALSE) |
| 722 | 724 |
}) |
deril2605 authored on 29/02/2024 23:46:24
deril2605 authored on 29/02/2024 23:32:57
| ... | ... |
@@ -14,24 +14,9 @@ |
| 14 | 14 |
#' |
| 15 | 15 |
#' @return list object with user selected options and matrix build |
| 16 | 16 |
#' |
| 17 |
-#' @export |
|
| 18 | 17 |
#' @examples |
| 19 |
-#' \dontrun{
|
|
| 20 |
-#' library(shiny) |
|
| 18 |
+#' NA |
|
| 21 | 19 |
#' |
| 22 |
-#' # Define UI for app that calls the Expdes Server |
|
| 23 |
-#' ui <- fluidPage( |
|
| 24 |
-#' # UI elements for Expdes Server inputs |
|
| 25 |
-#' ) |
|
| 26 |
-#' |
|
| 27 |
-#' # Define server logic required to call Expdes Server |
|
| 28 |
-#' server <- function(input, output, session) {
|
|
| 29 |
-#' callModule(statmodelServer, "statmodel", parent_session = session) |
|
| 30 |
-#' } |
|
| 31 |
-#' |
|
| 32 |
-#' # Run the application |
|
| 33 |
-#' shinyApp(ui = ui, server = server) |
|
| 34 |
-#' } |
|
| 35 | 20 |
statmodelServer <- function(input, output, session,parent_session, loadpage_input, qc_input,get_data,preprocess_data) {
|
| 36 | 21 |
######### UI ######### |
| 37 | 22 |
|
deril2605 authored on 18/02/2024 17:05:13
| ... | ... |
@@ -15,6 +15,23 @@ |
| 15 | 15 |
#' @return list object with user selected options and matrix build |
| 16 | 16 |
#' |
| 17 | 17 |
#' @export |
| 18 |
+#' @examples |
|
| 19 |
+#' \dontrun{
|
|
| 20 |
+#' library(shiny) |
|
| 21 |
+#' |
|
| 22 |
+#' # Define UI for app that calls the Expdes Server |
|
| 23 |
+#' ui <- fluidPage( |
|
| 24 |
+#' # UI elements for Expdes Server inputs |
|
| 25 |
+#' ) |
|
| 26 |
+#' |
|
| 27 |
+#' # Define server logic required to call Expdes Server |
|
| 28 |
+#' server <- function(input, output, session) {
|
|
| 29 |
+#' callModule(statmodelServer, "statmodel", parent_session = session) |
|
| 30 |
+#' } |
|
| 31 |
+#' |
|
| 32 |
+#' # Run the application |
|
| 33 |
+#' shinyApp(ui = ui, server = server) |
|
| 34 |
+#' } |
|
| 18 | 35 |
statmodelServer <- function(input, output, session,parent_session, loadpage_input, qc_input,get_data,preprocess_data) {
|
| 19 | 36 |
######### UI ######### |
| 20 | 37 |
|
| ... | ... |
@@ -329,7 +346,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 329 | 346 |
codes = paste(codes, "groupComparisonPlots(data=model$ComparisonResult, |
| 330 | 347 |
type=\"Enter VolcanoPlot, Heatmap, or ComparisonPlot\", |
| 331 | 348 |
which.Comparison=\"all\", |
| 332 |
- which.Protein=\"all\", |
|
| 349 |
+ which.Protein=\"all\",isPlotly=FALSE, |
|
| 333 | 350 |
address=\"\")\n", sep="") |
| 334 | 351 |
} |
| 335 | 352 |
|
deril2605 authored on 28/01/2024 04:54:27
| ... | ... |
@@ -448,6 +448,8 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 448 | 448 |
height = input$height, |
| 449 | 449 |
address="Ex_", |
| 450 | 450 |
isPlotly = TRUE)[[1]] |
| 451 |
+ remove_modal_spinner() |
|
| 452 |
+ return(plot1) |
|
| 451 | 453 |
}, error = function(e){
|
| 452 | 454 |
remove_modal_spinner() |
| 453 | 455 |
message("An error occurred: ", conditionMessage(e))
|
| ... | ... |
@@ -455,7 +457,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 455 | 457 |
) |
| 456 | 458 |
} |
| 457 | 459 |
|
| 458 |
- remove_modal_spinner() |
|
| 460 |
+ |
|
| 459 | 461 |
|
| 460 | 462 |
if(saveFile1) {
|
| 461 | 463 |
return(id_address1) |
| ... | ... |
@@ -710,10 +712,22 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 710 | 712 |
|
| 711 | 713 |
observeEvent(input$viewresults, {
|
| 712 | 714 |
ns <- session$ns |
| 715 |
+ # TMT and PTM plotly plots are still under development |
|
| 716 |
+ if ((loadpage_input()$DDA_DIA == "TMT") || (loadpage_input()$BIO == "PTM")) {
|
|
| 717 |
+ output$comp_plots = renderPlot({
|
|
| 718 |
+ group_comparison(FALSE, FALSE) |
|
| 719 |
+ }) |
|
| 720 |
+ op <- plotOutput(ns("comp_plots"))
|
|
| 721 |
+ } else {
|
|
| 722 |
+ output$comp_plots = renderPlotly({
|
|
| 723 |
+ group_comparison(FALSE, FALSE) |
|
| 724 |
+ }) |
|
| 725 |
+ op <- plotlyOutput(ns("comp_plots"), height = input$height)
|
|
| 726 |
+ } |
|
| 713 | 727 |
insertUI( |
| 714 | 728 |
selector = paste0("#", ns("comparison_plots")),
|
| 715 | 729 |
ui=tags$div( |
| 716 |
- plotlyOutput(ns("comp_plots"), height = input$height),
|
|
| 730 |
+ op, |
|
| 717 | 731 |
conditionalPanel(condition = "input['statmodel-typeplot'] == 'VolcanoPlot' && input['loadpage-DDA_DIA']!='TMT'", |
| 718 | 732 |
h5("Click on plot for details"),
|
| 719 | 733 |
verbatimTextOutput(ns("info2"))),
|
| ... | ... |
@@ -723,12 +737,6 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 723 | 737 |
) |
| 724 | 738 |
} |
| 725 | 739 |
) |
| 726 |
- |
|
| 727 |
- observe({output$comp_plots = renderPlotly({
|
|
| 728 |
- group_comparison(FALSE, FALSE) |
|
| 729 |
- } |
|
| 730 |
- ) |
|
| 731 |
- }) |
|
| 732 | 740 |
|
| 733 | 741 |
plotset = reactive({
|
| 734 | 742 |
|
deril2605 authored on 28/01/2024 01:37:13
| ... | ... |
@@ -429,23 +429,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 429 | 429 |
|
| 430 | 430 |
|
| 431 | 431 |
} else{
|
| 432 |
- # tryCatch({
|
|
| 433 |
- print("lets seee comppp")
|
|
| 434 |
- print(input$whichComp) |
|
| 435 |
- print(input$whichProt) |
|
| 436 |
- print("lets seee comppp")
|
|
| 437 |
- # plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult, |
|
| 438 |
- # type=input$typeplot, |
|
| 439 |
- # sig=input$sig, |
|
| 440 |
- # FCcutoff=input$FC, |
|
| 441 |
- # logBase.pvalue=input$logp, |
|
| 442 |
- # ProteinName=input$pname, |
|
| 443 |
- # numProtein=input$nump, |
|
| 444 |
- # clustering=input$cluster, |
|
| 445 |
- # which.Comparison=input$whichComp, |
|
| 446 |
- # which.Protein = input$whichProt, |
|
| 447 |
- # address=path1(), |
|
| 448 |
- # savePDF=pdf) |
|
| 432 |
+ tryCatch({
|
|
| 449 | 433 |
if(toupper(input$typeplot) == "VOLCANOPLOT" && input$whichComp == "all") {
|
| 450 | 434 |
remove_modal_spinner() |
| 451 | 435 |
stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' ) |
| ... | ... |
@@ -464,11 +448,11 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 464 | 448 |
height = input$height, |
| 465 | 449 |
address="Ex_", |
| 466 | 450 |
isPlotly = TRUE)[[1]] |
| 467 |
- # }, error = function(e){
|
|
| 468 |
- # remove_modal_spinner() |
|
| 469 |
- # message("An error occurred: ", conditionMessage(e))
|
|
| 470 |
- # stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' )} |
|
| 471 |
- # ) |
|
| 451 |
+ }, error = function(e){
|
|
| 452 |
+ remove_modal_spinner() |
|
| 453 |
+ message("An error occurred: ", conditionMessage(e))
|
|
| 454 |
+ stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' )} |
|
| 455 |
+ ) |
|
| 472 | 456 |
} |
| 473 | 457 |
|
| 474 | 458 |
remove_modal_spinner() |
| ... | ... |
@@ -482,8 +466,8 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 482 | 466 |
|
| 483 | 467 |
} |
| 484 | 468 |
|
| 469 |
+ # On Heatmap page to display the num of proteins, bound the input range |
|
| 485 | 470 |
observe({
|
| 486 |
- # Check if the input is NA or not a number |
|
| 487 | 471 |
if(is.na(input$nump) || !is.numeric(input$nump) || input$nump <= 0) {
|
| 488 | 472 |
# Reset to default value or handle the error as needed |
| 489 | 473 |
updateNumericInput(session, "nump", value = 100) |
| ... | ... |
@@ -525,21 +509,11 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 525 | 509 |
|
| 526 | 510 |
########## output ########## |
| 527 | 511 |
|
| 528 |
- # |
|
| 529 | 512 |
output$plotresults = downloadHandler( |
| 530 | 513 |
filename = function() {
|
| 531 | 514 |
paste("SummaryPlot-", Sys.Date(), ".zip", sep="")
|
| 532 | 515 |
}, |
| 533 | 516 |
content = function(file) {
|
| 534 |
- # pdf(file) |
|
| 535 |
- # group_comparison(TRUE, TRUE) |
|
| 536 |
- # dev.off() |
|
| 537 |
- # doc = .get.plotly.plot.html(list(group_comparison(FALSE, FALSE)),800,600) |
|
| 538 |
- # print(doc) |
|
| 539 |
- # writeLines(doc, file) |
|
| 540 |
- # print(file) |
|
| 541 |
- # .save.plotly.plot.html(list(group_comparison(FALSE, FALSE)),"",file,800,600) |
|
| 542 |
- # group_comparison(FALSE, FALSE) |
|
| 543 | 517 |
files <- list.files(getwd(), pattern = "^Ex_", full.names = TRUE) |
| 544 | 518 |
file_info <- file.info(files) |
| 545 | 519 |
latest_file <- files[which.max(file_info$mtime)] |
| ... | ... |
@@ -547,22 +521,6 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 547 | 521 |
file.copy(latest_file, file) |
| 548 | 522 |
} |
| 549 | 523 |
) |
| 550 |
- # |
|
| 551 |
- # observeEvent(input$plotresults, {
|
|
| 552 |
- # # print("IN DOWNLOADDD 111")
|
|
| 553 |
- # # tryCatch({
|
|
| 554 |
- # MSstats::.save.plotly.plot.html(list(group_comparison(FALSE, FALSE)),"",paste("SummaryPlot-", Sys.Date(), sep=""),800,600)
|
|
| 555 |
- # print("IN DOWNLOADDD 222")
|
|
| 556 |
- # showNotification("File downloaded successfully in your local directory")
|
|
| 557 |
- # print("IN DOWNLOADDD 333")
|
|
| 558 |
- # # }, |
|
| 559 |
- # # error=function(cond) {
|
|
| 560 |
- # # showNotification("File download failed", type='error')
|
|
| 561 |
- # # message(cond) |
|
| 562 |
- # # stop("why")
|
|
| 563 |
- # # }) |
|
| 564 |
- # print("IN DOWNLOADDD 444")
|
|
| 565 |
- # }) |
|
| 566 | 524 |
|
| 567 | 525 |
# download comparison data |
| 568 | 526 |
|
Deril Raju authored on 28/01/2024 01:22:01
• GitHub committed on 28/01/2024 01:22:01
deril2605 authored on 17/01/2024 13:48:39
| ... | ... |
@@ -474,6 +474,14 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 474 | 474 |
} |
| 475 | 475 |
|
| 476 | 476 |
} |
| 477 |
+ |
|
| 478 |
+ observe({
|
|
| 479 |
+ # Check if the input is NA or not a number |
|
| 480 |
+ if(is.na(input$nump) || !is.numeric(input$nump) || input$nump <= 0) {
|
|
| 481 |
+ # Reset to default value or handle the error as needed |
|
| 482 |
+ updateNumericInput(session, "nump", value = 100) |
|
| 483 |
+ } |
|
| 484 |
+ }) |
|
| 477 | 485 |
|
| 478 | 486 |
# model assumptions plots |
| 479 | 487 |
|
deril2605 authored on 11/01/2024 16:11:43
| ... | ... |
@@ -509,6 +509,45 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 509 | 509 |
|
| 510 | 510 |
|
| 511 | 511 |
########## output ########## |
| 512 |
+ |
|
| 513 |
+ # |
|
| 514 |
+ output$plotresults = downloadHandler( |
|
| 515 |
+ filename = function() {
|
|
| 516 |
+ paste("SummaryPlot-", Sys.Date(), ".zip", sep="")
|
|
| 517 |
+ }, |
|
| 518 |
+ content = function(file) {
|
|
| 519 |
+ # pdf(file) |
|
| 520 |
+ # group_comparison(TRUE, TRUE) |
|
| 521 |
+ # dev.off() |
|
| 522 |
+ # doc = .get.plotly.plot.html(list(group_comparison(FALSE, FALSE)),800,600) |
|
| 523 |
+ # print(doc) |
|
| 524 |
+ # writeLines(doc, file) |
|
| 525 |
+ # print(file) |
|
| 526 |
+ # .save.plotly.plot.html(list(group_comparison(FALSE, FALSE)),"",file,800,600) |
|
| 527 |
+ # group_comparison(FALSE, FALSE) |
|
| 528 |
+ files <- list.files(getwd(), pattern = "^Ex_", full.names = TRUE) |
|
| 529 |
+ file_info <- file.info(files) |
|
| 530 |
+ latest_file <- files[which.max(file_info$mtime)] |
|
| 531 |
+ print(latest_file) |
|
| 532 |
+ file.copy(latest_file, file) |
|
| 533 |
+ } |
|
| 534 |
+ ) |
|
| 535 |
+ # |
|
| 536 |
+ # observeEvent(input$plotresults, {
|
|
| 537 |
+ # # print("IN DOWNLOADDD 111")
|
|
| 538 |
+ # # tryCatch({
|
|
| 539 |
+ # MSstats::.save.plotly.plot.html(list(group_comparison(FALSE, FALSE)),"",paste("SummaryPlot-", Sys.Date(), sep=""),800,600)
|
|
| 540 |
+ # print("IN DOWNLOADDD 222")
|
|
| 541 |
+ # showNotification("File downloaded successfully in your local directory")
|
|
| 542 |
+ # print("IN DOWNLOADDD 333")
|
|
| 543 |
+ # # }, |
|
| 544 |
+ # # error=function(cond) {
|
|
| 545 |
+ # # showNotification("File download failed", type='error')
|
|
| 546 |
+ # # message(cond) |
|
| 547 |
+ # # stop("why")
|
|
| 548 |
+ # # }) |
|
| 549 |
+ # print("IN DOWNLOADDD 444")
|
|
| 550 |
+ # }) |
|
| 512 | 551 |
|
| 513 | 552 |
# download comparison data |
| 514 | 553 |
|
| ... | ... |
@@ -873,16 +912,6 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 873 | 912 |
) |
| 874 | 913 |
|
| 875 | 914 |
|
| 876 |
- output$plotresults = downloadHandler( |
|
| 877 |
- filename = function() {
|
|
| 878 |
- paste("SummaryPlot-", Sys.Date(), ".pdf", sep="")
|
|
| 879 |
- }, |
|
| 880 |
- content = function(file) {
|
|
| 881 |
- pdf(file) |
|
| 882 |
- group_comparison(TRUE, TRUE) |
|
| 883 |
- dev.off() |
|
| 884 |
- } |
|
| 885 |
- ) |
|
| 886 | 915 |
|
| 887 | 916 |
observeEvent(input$calculate,{
|
| 888 | 917 |
enable("Design")
|
deril2605 authored on 09/12/2023 20:46:05
| ... | ... |
@@ -422,24 +422,46 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 422 | 422 |
|
| 423 | 423 |
|
| 424 | 424 |
} else{
|
| 425 |
- tryCatch({
|
|
| 426 |
- plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult, |
|
| 427 |
- type=input$typeplot, |
|
| 428 |
- sig=input$sig, |
|
| 429 |
- FCcutoff=input$FC, |
|
| 430 |
- logBase.pvalue=input$logp, |
|
| 431 |
- ProteinName=input$pname, |
|
| 432 |
- numProtein=input$nump, |
|
| 433 |
- clustering=input$cluster, |
|
| 434 |
- which.Comparison=input$whichComp, |
|
| 435 |
- which.Protein = input$whichProt, |
|
| 436 |
- address=path1(), |
|
| 437 |
- savePDF=pdf) |
|
| 438 |
- }, error = function(e){
|
|
| 425 |
+ # tryCatch({
|
|
| 426 |
+ print("lets seee comppp")
|
|
| 427 |
+ print(input$whichComp) |
|
| 428 |
+ print(input$whichProt) |
|
| 429 |
+ print("lets seee comppp")
|
|
| 430 |
+ # plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult, |
|
| 431 |
+ # type=input$typeplot, |
|
| 432 |
+ # sig=input$sig, |
|
| 433 |
+ # FCcutoff=input$FC, |
|
| 434 |
+ # logBase.pvalue=input$logp, |
|
| 435 |
+ # ProteinName=input$pname, |
|
| 436 |
+ # numProtein=input$nump, |
|
| 437 |
+ # clustering=input$cluster, |
|
| 438 |
+ # which.Comparison=input$whichComp, |
|
| 439 |
+ # which.Protein = input$whichProt, |
|
| 440 |
+ # address=path1(), |
|
| 441 |
+ # savePDF=pdf) |
|
| 442 |
+ if(toupper(input$typeplot) == "VOLCANOPLOT" && input$whichComp == "all") {
|
|
| 439 | 443 |
remove_modal_spinner() |
| 440 |
- message("An error occurred: ", conditionMessage(e))
|
|
| 441 |
- stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' )} |
|
| 442 |
- ) |
|
| 444 |
+ stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' ) |
|
| 445 |
+ } |
|
| 446 |
+ |
|
| 447 |
+ plot1 = groupComparisonPlots(data=data_comparison()$ComparisonResult, |
|
| 448 |
+ type=input$typeplot, |
|
| 449 |
+ sig=input$sig, |
|
| 450 |
+ FCcutoff=input$FC, |
|
| 451 |
+ logBase.pvalue=as.numeric(input$logp), |
|
| 452 |
+ ProteinName=input$pname, |
|
| 453 |
+ numProtein=input$nump, |
|
| 454 |
+ clustering=input$cluster, |
|
| 455 |
+ which.Comparison=input$whichComp, |
|
| 456 |
+ which.Protein = input$whichProt, |
|
| 457 |
+ height = input$height, |
|
| 458 |
+ address="Ex_", |
|
| 459 |
+ isPlotly = TRUE)[[1]] |
|
| 460 |
+ # }, error = function(e){
|
|
| 461 |
+ # remove_modal_spinner() |
|
| 462 |
+ # message("An error occurred: ", conditionMessage(e))
|
|
| 463 |
+ # stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' )} |
|
| 464 |
+ # ) |
|
| 443 | 465 |
} |
| 444 | 466 |
|
| 445 | 467 |
remove_modal_spinner() |
| ... | ... |
@@ -679,7 +701,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 679 | 701 |
insertUI( |
| 680 | 702 |
selector = paste0("#", ns("comparison_plots")),
|
| 681 | 703 |
ui=tags$div( |
| 682 |
- plotlyOutput(ns("comp_plots"), height = "100%"),
|
|
| 704 |
+ plotlyOutput(ns("comp_plots"), height = input$height),
|
|
| 683 | 705 |
conditionalPanel(condition = "input['statmodel-typeplot'] == 'VolcanoPlot' && input['loadpage-DDA_DIA']!='TMT'", |
| 684 | 706 |
h5("Click on plot for details"),
|
| 685 | 707 |
verbatimTextOutput(ns("info2"))),
|
devonjkohler authored on 06/11/2023 21:01:22
| ... | ... |
@@ -365,9 +365,15 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 365 | 365 |
data_comp$ComparisonResult$adj.pvalue < input$signif, ] |
| 366 | 366 |
|
| 367 | 367 |
} else {
|
| 368 |
- significant = with(data_comparison(), round_df(ComparisonResult[ |
|
| 369 |
- ComparisonResult$adj.pvalue < input$signif, ])) |
|
| 370 |
- |
|
| 368 |
+ # significant = with(data_comparison(), round_df(ComparisonResult[ |
|
| 369 |
+ # ComparisonResult$adj.pvalue < input$signif & |
|
| 370 |
+ # !is.na(ComparisonResult$Protein), ])) |
|
| 371 |
+ # print(significant) |
|
| 372 |
+ |
|
| 373 |
+ data_comp = data_comparison() |
|
| 374 |
+ significant = data_comp$ComparisonResult[ |
|
| 375 |
+ which(data_comp$ComparisonResult$adj.pvalue < input$signif), ] |
|
| 376 |
+ print(significant) |
|
| 371 | 377 |
} |
| 372 | 378 |
return(significant) |
| 373 | 379 |
}) |
devonjkohler authored on 20/10/2023 14:47:13
deril2605 authored on 27/09/2023 22:21:24
devonjkohler authored on 08/09/2023 14:59:22
| ... | ... |
@@ -346,13 +346,14 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 346 | 346 |
|
| 347 | 347 |
SignificantProteins = eventReactive(input$calculate,{
|
| 348 | 348 |
if (loadpage_input()$BIO == "PTM"){
|
| 349 |
+ |
|
| 349 | 350 |
data_comp = data_comparison() |
| 350 | 351 |
sig_unadj = data_comp$PTM.Model[ |
| 351 |
- data_comp$PTM.Model$adj.pvalue < input$signif] |
|
| 352 |
+ data_comp$PTM.Model$adj.pvalue < input$signif,] |
|
| 352 | 353 |
sig_prot = data_comp$PROTEIN.Model[ |
| 353 |
- data_comp$PROTEIN.Model$adj.pvalue < input$signif] |
|
| 354 |
+ data_comp$PROTEIN.Model$adj.pvalue < input$signif,] |
|
| 354 | 355 |
sig_adj = data_comp$ADJUSTED.Model[ |
| 355 |
- data_comp$ADJUSTED.Model$adj.pvalue < input$signif] |
|
| 356 |
+ data_comp$ADJUSTED.Model$adj.pvalue < input$signif,] |
|
| 356 | 357 |
significant = list(PTM.Model=sig_unadj, |
| 357 | 358 |
PROTEIN.Model=sig_prot, |
| 358 | 359 |
ADJUSTED.Model=sig_adj) |
vasumathi298 authored on 09/08/2023 06:33:38
| ... | ... |
@@ -436,6 +436,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 436 | 436 |
savePDF=pdf) |
| 437 | 437 |
}, error = function(e){
|
| 438 | 438 |
remove_modal_spinner() |
| 439 |
+ message("An error occurred: ", conditionMessage(e))
|
|
| 439 | 440 |
stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' )} |
| 440 | 441 |
) |
| 441 | 442 |
} |
| ... | ... |
@@ -677,7 +678,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 677 | 678 |
insertUI( |
| 678 | 679 |
selector = paste0("#", ns("comparison_plots")),
|
| 679 | 680 |
ui=tags$div( |
| 680 |
- plotOutput(ns("comp_plots"), height = "100%", click = "click1"),
|
|
| 681 |
+ plotlyOutput(ns("comp_plots"), height = "100%"),
|
|
| 681 | 682 |
conditionalPanel(condition = "input['statmodel-typeplot'] == 'VolcanoPlot' && input['loadpage-DDA_DIA']!='TMT'", |
| 682 | 683 |
h5("Click on plot for details"),
|
| 683 | 684 |
verbatimTextOutput(ns("info2"))),
|
| ... | ... |
@@ -688,8 +689,9 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 688 | 689 |
} |
| 689 | 690 |
) |
| 690 | 691 |
|
| 691 |
- observe({output$comp_plots = renderPlot({
|
|
| 692 |
- group_comparison(FALSE, FALSE)}, height = input$height |
|
| 692 |
+ observe({output$comp_plots = renderPlotly({
|
|
| 693 |
+ group_comparison(FALSE, FALSE) |
|
| 694 |
+ } |
|
| 693 | 695 |
) |
| 694 | 696 |
}) |
| 695 | 697 |
|
| ... | ... |
@@ -847,6 +849,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 847 | 849 |
} |
| 848 | 850 |
) |
| 849 | 851 |
|
| 852 |
+ |
|
| 850 | 853 |
output$plotresults = downloadHandler( |
| 851 | 854 |
filename = function() {
|
| 852 | 855 |
paste("SummaryPlot-", Sys.Date(), ".pdf", sep="")
|
vasumathi298 authored on 17/07/2023 05:28:00
| ... | ... |
@@ -20,9 +20,9 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 20 | 20 |
# choices of groups for contrast matrix |
| 21 | 21 |
|
| 22 | 22 |
choices = reactive({
|
| 23 |
- if (loadpage_input()$BIO == "PTM" & (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil')){
|
|
| 23 |
+ if (loadpage_input()$BIO == "PTM" & ((loadpage_input()$BIO == "PTM" & loadpage_input()$DDA_DIA == "TMT") | loadpage_input()$filetype=='phil')){
|
|
| 24 | 24 |
levels(preprocess_data()$PTM$ProteinLevelData$Condition) |
| 25 |
- } else if(loadpage_input()$BIO == "PTM" & loadpage_input()$PTMTMT == "No"){
|
|
| 25 |
+ } else if(loadpage_input()$BIO == "PTM" & (loadpage_input()$BIO == "PTM" & loadpage_input()$DDA_DIA != "TMT")){
|
|
| 26 | 26 |
levels(preprocess_data()$PTM$ProteinLevelData$GROUP) |
| 27 | 27 |
} else if(loadpage_input()$DDA_DIA=="TMT"){
|
| 28 | 28 |
levels(preprocess_data()$ProteinLevelData$Condition) |
| ... | ... |
@@ -303,7 +303,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 303 | 303 |
remove_empty_channel = TRUE |
| 304 | 304 |
)\n", sep = "") |
| 305 | 305 |
} else if (loadpage_input()$BIO == "PTM"){
|
| 306 |
- if (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil'){
|
|
| 306 |
+ if ((loadpage_input()$BIO == "PTM" & loadpage_input()$DDA_DIA == "TMT") | loadpage_input()$filetype=='phil'){
|
|
| 307 | 307 |
dt = "TMT" |
| 308 | 308 |
} else {
|
| 309 | 309 |
dt = "LabelFree" |
vasumathi298 authored on 13/07/2023 07:24:51
| ... | ... |
@@ -20,9 +20,9 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 20 | 20 |
# choices of groups for contrast matrix |
| 21 | 21 |
|
| 22 | 22 |
choices = reactive({
|
| 23 |
- if (loadpage_input()$DDA_DIA == "PTM" & (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil')){
|
|
| 23 |
+ if (loadpage_input()$BIO == "PTM" & (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil')){
|
|
| 24 | 24 |
levels(preprocess_data()$PTM$ProteinLevelData$Condition) |
| 25 |
- } else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
|
|
| 25 |
+ } else if(loadpage_input()$BIO == "PTM" & loadpage_input()$PTMTMT == "No"){
|
|
| 26 | 26 |
levels(preprocess_data()$PTM$ProteinLevelData$GROUP) |
| 27 | 27 |
} else if(loadpage_input()$DDA_DIA=="TMT"){
|
| 28 | 28 |
levels(preprocess_data()$ProteinLevelData$Condition) |
| ... | ... |
@@ -39,7 +39,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 39 | 39 |
|
| 40 | 40 |
|
| 41 | 41 |
observe({
|
| 42 |
- if(loadpage_input()$DDA_DIA == "TMT" | loadpage_input()$DDA_DIA == "PTM"){
|
|
| 42 |
+ if(loadpage_input()$DDA_DIA == "TMT" | loadpage_input()$BIO == "PTM"){
|
|
| 43 | 43 |
hide("Design")
|
| 44 | 44 |
} |
| 45 | 45 |
else{
|
| ... | ... |
@@ -302,7 +302,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 302 | 302 |
remove_norm_channel = TRUE, |
| 303 | 303 |
remove_empty_channel = TRUE |
| 304 | 304 |
)\n", sep = "") |
| 305 |
- } else if (loadpage_input()$DDA_DIA == "PTM"){
|
|
| 305 |
+ } else if (loadpage_input()$BIO == "PTM"){
|
|
| 306 | 306 |
if (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil'){
|
| 307 | 307 |
dt = "TMT" |
| 308 | 308 |
} else {
|
| ... | ... |
@@ -318,7 +318,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 318 | 318 |
codes = paste(codes, "\n# Model-based comparison\n", sep = "") |
| 319 | 319 |
codes = paste(codes,"model = MSstats::groupComparison(contrast.matrix, summarized)\n", sep = "") |
| 320 | 320 |
} |
| 321 |
- if (loadpage_input()$DDA_DIA == "PTM"){
|
|
| 321 |
+ if (loadpage_input()$BIO == "PTM"){
|
|
| 322 | 322 |
codes = paste(codes, "groupComparisonPlotsPTM(data=model, |
| 323 | 323 |
type=\"Enter VolcanoPlot, Heatmap, or ComparisonPlot\", |
| 324 | 324 |
which.Comparison=\"all\", |
| ... | ... |
@@ -345,7 +345,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 345 | 345 |
} |
| 346 | 346 |
|
| 347 | 347 |
SignificantProteins = eventReactive(input$calculate,{
|
| 348 |
- if (loadpage_input()$DDA_DIA == "PTM"){
|
|
| 348 |
+ if (loadpage_input()$BIO == "PTM"){
|
|
| 349 | 349 |
data_comp = data_comparison() |
| 350 | 350 |
sig_unadj = data_comp$PTM.Model[ |
| 351 | 351 |
data_comp$PTM.Model$adj.pvalue < input$signif] |
| ... | ... |
@@ -387,7 +387,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 387 | 387 |
return(path1_id) |
| 388 | 388 |
} |
| 389 | 389 |
|
| 390 |
- if (loadpage_input()$DDA_DIA=="PTM"){
|
|
| 390 |
+ if (loadpage_input()$BIO=="PTM"){
|
|
| 391 | 391 |
plot1 = groupComparisonPlotsPTM(data_comparison(), |
| 392 | 392 |
input$typeplot, |
| 393 | 393 |
sig=input$sig, |
devonjkohler authored on 12/06/2023 11:30:47
| ... | ... |
@@ -20,7 +20,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 20 | 20 |
# choices of groups for contrast matrix |
| 21 | 21 |
|
| 22 | 22 |
choices = reactive({
|
| 23 |
- if (loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "Yes"){
|
|
| 23 |
+ if (loadpage_input()$DDA_DIA == "PTM" & (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil')){
|
|
| 24 | 24 |
levels(preprocess_data()$PTM$ProteinLevelData$Condition) |
| 25 | 25 |
} else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
|
| 26 | 26 |
levels(preprocess_data()$PTM$ProteinLevelData$GROUP) |
| ... | ... |
@@ -303,7 +303,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 303 | 303 |
remove_empty_channel = TRUE |
| 304 | 304 |
)\n", sep = "") |
| 305 | 305 |
} else if (loadpage_input()$DDA_DIA == "PTM"){
|
| 306 |
- if (loadpage_input()$PTMTMT == "Yes"){
|
|
| 306 |
+ if (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil'){
|
|
| 307 | 307 |
dt = "TMT" |
| 308 | 308 |
} else {
|
| 309 | 309 |
dt = "LabelFree" |
| ... | ... |
@@ -412,7 +412,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 412 | 412 |
which.Protein = input$whichProt, |
| 413 | 413 |
address=path1(), |
| 414 | 414 |
savePDF=pdf) |
| 415 |
- # remove_modal_spinner() |
|
| 415 |
+ remove_modal_spinner() |
|
| 416 | 416 |
}, |
| 417 | 417 |
error = function(e){
|
| 418 | 418 |
remove_modal_spinner() |
devonjkohler authored on 22/05/2023 17:26:14
| ... | ... |
@@ -421,7 +421,8 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 421 | 421 |
|
| 422 | 422 |
|
| 423 | 423 |
} else{
|
| 424 |
- tryCatch({plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult,
|
|
| 424 |
+ tryCatch({
|
|
| 425 |
+ plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult, |
|
| 425 | 426 |
type=input$typeplot, |
| 426 | 427 |
sig=input$sig, |
| 427 | 428 |
FCcutoff=input$FC, |
| ... | ... |
@@ -437,7 +438,6 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 437 | 438 |
remove_modal_spinner() |
| 438 | 439 |
stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' )} |
| 439 | 440 |
) |
| 440 |
- |
|
| 441 | 441 |
} |
| 442 | 442 |
|
| 443 | 443 |
remove_modal_spinner() |
deril2605 authored on 14/04/2023 19:26:52
| ... | ... |
@@ -9,6 +9,8 @@ |
| 9 | 9 |
#' @param parent_session session of the main calling module |
| 10 | 10 |
#' @param loadpage_input input object from loadpage UI |
| 11 | 11 |
#' @param qc_input input object from QC UI |
| 12 |
+#' @param get_data stored function that returns the data from loadpage |
|
| 13 |
+#' @param preprocess_data stored function that returns preprocessed data |
|
| 12 | 14 |
#' |
| 13 | 15 |
#' @return list object with user selected options and matrix build |
| 14 | 16 |
#' |
deril2605 authored on 14/04/2023 17:22:55
| ... | ... |
@@ -12,21 +12,21 @@ |
| 12 | 12 |
#' |
| 13 | 13 |
#' @return list object with user selected options and matrix build |
| 14 | 14 |
#' |
| 15 |
-statmodelServer <- function(input, output, session,parent_session, loadpage_input, qc_input) {
|
|
| 15 |
+statmodelServer <- function(input, output, session,parent_session, loadpage_input, qc_input,get_data,preprocess_data) {
|
|
| 16 | 16 |
######### UI ######### |
| 17 | 17 |
|
| 18 | 18 |
# choices of groups for contrast matrix |
| 19 | 19 |
|
| 20 | 20 |
choices = reactive({
|
| 21 | 21 |
if (loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "Yes"){
|
| 22 |
- levels(preprocessData(qc_input(),loadpage_input())$PTM$ProteinLevelData$Condition) |
|
| 22 |
+ levels(preprocess_data()$PTM$ProteinLevelData$Condition) |
|
| 23 | 23 |
} else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
|
| 24 |
- levels(preprocessData(qc_input(),loadpage_input())$PTM$ProteinLevelData$GROUP) |
|
| 24 |
+ levels(preprocess_data()$PTM$ProteinLevelData$GROUP) |
|
| 25 | 25 |
} else if(loadpage_input()$DDA_DIA=="TMT"){
|
| 26 |
- levels(preprocessData(qc_input(),loadpage_input())$ProteinLevelData$Condition) |
|
| 26 |
+ levels(preprocess_data()$ProteinLevelData$Condition) |
|
| 27 | 27 |
} |
| 28 | 28 |
else{
|
| 29 |
- levels(preprocessData(qc_input(),loadpage_input())$ProteinLevelData$GROUP) |
|
| 29 |
+ levels(preprocess_data()$ProteinLevelData$GROUP) |
|
| 30 | 30 |
} |
| 31 | 31 |
|
| 32 | 32 |
}) |
| ... | ... |
@@ -94,13 +94,13 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 94 | 94 |
output$WhichProt = renderUI ({
|
| 95 | 95 |
ns <- session$ns |
| 96 | 96 |
selectInput(ns("whichProt"),
|
| 97 |
- label = h4("which protein to plot"), unique(getData(loadpage_input())[[1]]))
|
|
| 97 |
+ label = h4("which protein to plot"), unique(get_data()[[1]]))
|
|
| 98 | 98 |
}) |
| 99 | 99 |
|
| 100 | 100 |
output$WhichProt1 = renderUI ({
|
| 101 | 101 |
ns <- session$ns |
| 102 | 102 |
selectizeInput(ns("whichProt1"),
|
| 103 |
- label = h4("which protein to plot"), c("", unique(getData(loadpage_input())[[1]])))
|
|
| 103 |
+ label = h4("which protein to plot"), c("", unique(get_data()[[1]])))
|
|
| 104 | 104 |
}) |
| 105 | 105 |
|
| 106 | 106 |
|
| ... | ... |
@@ -272,7 +272,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 272 | 272 |
input |
| 273 | 273 |
}) |
| 274 | 274 |
matrix = matrix_build() |
| 275 |
- dataComparison(statmodel_input(),qc_input(),loadpage_input(),matrix) |
|
| 275 |
+ dataComparison(statmodel_input(),qc_input(),loadpage_input(),matrix,preprocess_data()) |
|
| 276 | 276 |
}) |
| 277 | 277 |
|
| 278 | 278 |
data_comparison_code = eventReactive(input$calculate, {
|
| ... | ... |
@@ -866,7 +866,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 866 | 866 |
return( |
| 867 | 867 |
list( |
| 868 | 868 |
input = input, |
| 869 |
- matrix = matrix_build |
|
| 869 |
+ dataComparison = data_comparison |
|
| 870 | 870 |
) |
| 871 | 871 |
) |
| 872 | 872 |
} |
| 873 | 873 |
\ No newline at end of file |
deril2605 authored on 14/04/2023 16:15:36
devonjkohler authored on 13/04/2023 18:27:48
| ... | ... |
@@ -856,34 +856,13 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 856 | 856 |
} |
| 857 | 857 |
) |
| 858 | 858 |
|
| 859 |
-# observeEvent(input$plotresults, {
|
|
| 860 |
-# insertUI( |
|
| 861 |
-# selector = "#comparison_plots", |
|
| 862 |
-# ui=tags$div( |
|
| 863 |
-# if (input$typeplot == "VolcanoPlot") {
|
|
| 864 |
-# js = paste("window.open('", group_comparison(TRUE, TRUE), "VolcanoPlot.pdf')", sep="")
|
|
| 865 |
-# print(js) |
|
| 866 |
-# runjs(js); |
|
| 867 |
-# } |
|
| 868 |
-# else if (input$typeplot == "Heatmap") {
|
|
| 869 |
-# js = paste("window.open('", group_comparison(TRUE, TRUE), "Heatmap.pdf')", sep="")
|
|
| 870 |
-# runjs(js); |
|
| 871 |
-# } |
|
| 872 |
-# else if (input$typeplot == "ComparisonPlot") {
|
|
| 873 |
-# js = paste("window.open('", group_comparison(TRUE, TRUE), "ComparisonPlot.pdf')", sep="")
|
|
| 874 |
-# runjs(js); |
|
| 875 |
-# } |
|
| 876 |
-# ) |
|
| 877 |
-# ) |
|
| 878 |
-# }) |
|
| 879 |
- |
|
| 880 | 859 |
observeEvent(input$calculate,{
|
| 881 | 860 |
enable("Design")
|
| 882 | 861 |
enable("typeplot")
|
| 883 | 862 |
enable("WhichComp")
|
| 884 | 863 |
enable("download_code")
|
| 885 | 864 |
}) |
| 886 |
- |
|
| 865 |
+ |
|
| 887 | 866 |
return( |
| 888 | 867 |
list( |
| 889 | 868 |
ip = input, |
Deril Raju authored on 11/04/2023 14:38:11
| ... | ... |
@@ -254,11 +254,6 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 254 | 254 |
} |
| 255 | 255 |
} |
| 256 | 256 |
enable("calculate")
|
| 257 |
- print("THIS IS THE MATRIX")
|
|
| 258 |
- print(contrast$matrix) |
|
| 259 |
- print(class(contrast$matrix)) |
|
| 260 |
- print(typeof(contrast$matrix)) |
|
| 261 |
- print("THIS IS THE MATRIX")
|
|
| 262 | 257 |
return(contrast$matrix) |
| 263 | 258 |
}) |
| 264 | 259 |
|
Deril Raju authored on 31/03/2023 20:04:32
| ... | ... |
@@ -1,3 +1,17 @@ |
| 1 |
+#' Statmodel Server module for stat inference |
|
| 2 |
+#' |
|
| 3 |
+#' This function sets up the Statmodel server to process data based on user |
|
| 4 |
+#' selected inputs |
|
| 5 |
+#' |
|
| 6 |
+#' @param input input object to capture different ui element values |
|
| 7 |
+#' @param output to render and create elements |
|
| 8 |
+#' @param session session current module |
|
| 9 |
+#' @param parent_session session of the main calling module |
|
| 10 |
+#' @param loadpage_input input object from loadpage UI |
|
| 11 |
+#' @param qc_input input object from QC UI |
|
| 12 |
+#' |
|
| 13 |
+#' @return list object with user selected options and matrix build |
|
| 14 |
+#' |
|
| 1 | 15 |
statmodelServer <- function(input, output, session,parent_session, loadpage_input, qc_input) {
|
| 2 | 16 |
######### UI ######### |
| 3 | 17 |
|
Deril Raju authored on 24/03/2023 15:08:06
| ... | ... |
@@ -1,11 +1,4 @@ |
| 1 |
-statmodelServer <- function(input, output, session,parent_session, loadpage_inputs, qc_inputs) {
|
|
| 2 |
- |
|
| 3 |
- loadpage_input <- reactive({
|
|
| 4 |
- loadpage_inputs |
|
| 5 |
- }) |
|
| 6 |
- qc_input <- reactive({
|
|
| 7 |
- qc_inputs |
|
| 8 |
- }) |
|
| 1 |
+statmodelServer <- function(input, output, session,parent_session, loadpage_input, qc_input) {
|
|
| 9 | 2 |
######### UI ######### |
| 10 | 3 |
|
| 11 | 4 |
# choices of groups for contrast matrix |
Deril Raju authored on 24/03/2023 06:06:40
| ... | ... |
@@ -12,14 +12,14 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 12 | 12 |
|
| 13 | 13 |
choices = reactive({
|
| 14 | 14 |
if (loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "Yes"){
|
| 15 |
- levels(preprocessData(qc_input,loadpage_input)$PTM$ProteinLevelData$Condition) |
|
| 15 |
+ levels(preprocessData(qc_input(),loadpage_input())$PTM$ProteinLevelData$Condition) |
|
| 16 | 16 |
} else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
|
| 17 |
- levels(preprocessData(qc_input,loadpage_input)$PTM$ProteinLevelData$GROUP) |
|
| 17 |
+ levels(preprocessData(qc_input(),loadpage_input())$PTM$ProteinLevelData$GROUP) |
|
| 18 | 18 |
} else if(loadpage_input()$DDA_DIA=="TMT"){
|
| 19 |
- levels(preprocessData(qc_input,loadpage_input)$ProteinLevelData$Condition) |
|
| 19 |
+ levels(preprocessData(qc_input(),loadpage_input())$ProteinLevelData$Condition) |
|
| 20 | 20 |
} |
| 21 | 21 |
else{
|
| 22 |
- levels(preprocessData(qc_input,loadpage_input)$ProteinLevelData$GROUP) |
|
| 22 |
+ levels(preprocessData(qc_input(),loadpage_input())$ProteinLevelData$GROUP) |
|
| 23 | 23 |
} |
| 24 | 24 |
|
| 25 | 25 |
}) |
| ... | ... |
@@ -270,12 +270,12 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 270 | 270 |
input |
| 271 | 271 |
}) |
| 272 | 272 |
matrix = matrix_build() |
| 273 |
- dataComparison(statmodel_input,qc_input,loadpage_input,matrix) |
|
| 273 |
+ dataComparison(statmodel_input(),qc_input(),loadpage_input(),matrix) |
|
| 274 | 274 |
}) |
| 275 | 275 |
|
| 276 | 276 |
data_comparison_code = eventReactive(input$calculate, {
|
| 277 | 277 |
|
| 278 |
- codes = preprocessDataCode(qc_input,loadpage_input) |
|
| 278 |
+ codes = preprocessDataCode(qc_input(),loadpage_input()) |
|
| 279 | 279 |
comp.mat = matrix_build() |
| 280 | 280 |
|
| 281 | 281 |
codes = paste(codes, "\n# Create the contrast matrix\n", sep = "") |
Deril Raju authored on 11/03/2023 18:15:56
| ... | ... |
@@ -395,20 +395,24 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 395 | 395 |
|
| 396 | 396 |
|
| 397 | 397 |
} else if(loadpage_input()$DDA_DIA=="TMT"){
|
| 398 |
- tryCatch({plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult,
|
|
| 399 |
- type=input$typeplot, |
|
| 400 |
- sig=input$sig, |
|
| 401 |
- FCcutoff=input$FC, |
|
| 402 |
- logBase.pvalue=input$logp, |
|
| 403 |
- ProteinName=input$pname, |
|
| 404 |
- numProtein=input$nump, |
|
| 405 |
- clustering=input$cluster, |
|
| 406 |
- which.Comparison=input$whichComp, |
|
| 407 |
- which.Protein = input$whichProt, |
|
| 408 |
- address=path1(), |
|
| 409 |
- savePDF=pdf)}, |
|
| 410 |
- error = function(e){remove_modal_spinner()
|
|
| 411 |
- print("All plots cannot be shown in browser. Please select and individual comparison or download pdf.")}
|
|
| 398 |
+ tryCatch({
|
|
| 399 |
+ plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult, |
|
| 400 |
+ type=input$typeplot, |
|
| 401 |
+ sig=input$sig, |
|
| 402 |
+ FCcutoff=input$FC, |
|
| 403 |
+ logBase.pvalue=input$logp, |
|
| 404 |
+ ProteinName=input$pname, |
|
| 405 |
+ numProtein=input$nump, |
|
| 406 |
+ clustering=input$cluster, |
|
| 407 |
+ which.Comparison=input$whichComp, |
|
| 408 |
+ which.Protein = input$whichProt, |
|
| 409 |
+ address=path1(), |
|
| 410 |
+ savePDF=pdf) |
|
| 411 |
+ # remove_modal_spinner() |
|
| 412 |
+ }, |
|
| 413 |
+ error = function(e){
|
|
| 414 |
+ remove_modal_spinner() |
|
| 415 |
+ stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf. **' )} |
|
| 412 | 416 |
) |
| 413 | 417 |
|
| 414 | 418 |
|
| ... | ... |
@@ -419,14 +423,15 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 419 | 423 |
FCcutoff=input$FC, |
| 420 | 424 |
logBase.pvalue=input$logp, |
| 421 | 425 |
ProteinName=input$pname, |
| 422 |
- numProtein=input$nump, |
|
| 423 |
- clustering=input$cluster, |
|
| 426 |
+ numProtein=input$nump, |
|
| 427 |
+ clustering=input$cluster, |
|
| 424 | 428 |
which.Comparison=input$whichComp, |
| 425 | 429 |
which.Protein = input$whichProt, |
| 426 | 430 |
address=path1(), |
| 427 |
- savePDF=pdf)}, |
|
| 428 |
- error = function(e){remove_modal_spinner()
|
|
| 429 |
- print("All plots cannot be shown in browser. Please select and individual comparison or download pdf.")}
|
|
| 431 |
+ savePDF=pdf) |
|
| 432 |
+ }, error = function(e){
|
|
| 433 |
+ remove_modal_spinner() |
|
| 434 |
+ stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' )} |
|
| 430 | 435 |
) |
| 431 | 436 |
|
| 432 | 437 |
} |
Deril Raju authored on 08/03/2023 18:56:13
| ... | ... |
@@ -247,6 +247,11 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 247 | 247 |
} |
| 248 | 248 |
} |
| 249 | 249 |
enable("calculate")
|
| 250 |
+ print("THIS IS THE MATRIX")
|
|
| 251 |
+ print(contrast$matrix) |
|
| 252 |
+ print(class(contrast$matrix)) |
|
| 253 |
+ print(typeof(contrast$matrix)) |
|
| 254 |
+ print("THIS IS THE MATRIX")
|
|
| 250 | 255 |
return(contrast$matrix) |
| 251 | 256 |
}) |
| 252 | 257 |
|
Deril Raju authored on 22/02/2023 22:14:00
| ... | ... |
@@ -267,36 +267,6 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 267 | 267 |
matrix = matrix_build() |
| 268 | 268 |
dataComparison(statmodel_input,qc_input,loadpage_input,matrix) |
| 269 | 269 |
}) |
| 270 |
- |
|
| 271 |
- # data_comparison = eventReactive(input$calculate, {
|
|
| 272 |
- # input_data = preprocessData(qc_input,loadpage_input) |
|
| 273 |
- # contrast.matrix = matrix_build() |
|
| 274 |
- # if (loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "Yes"){
|
|
| 275 |
- # model_ptm = MSstatsShiny::tmt_model(input_data$PTM, input, contrast.matrix) |
|
| 276 |
- # model_protein = MSstatsShiny::tmt_model(input_data$PROTEIN, input, contrast.matrix) |
|
| 277 |
- # model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult, |
|
| 278 |
- # model_protein$ComparisonResult) |
|
| 279 |
- # model = list('PTM.Model' = model_ptm$ComparisonResult,
|
|
| 280 |
- # 'PROTEIN.Model' = model_protein$ComparisonResult, |
|
| 281 |
- # 'ADJUSTED.Model' = model_adj) |
|
| 282 |
- # |
|
| 283 |
- # } else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
|
|
| 284 |
- # model_ptm = MSstatsShiny::lf_model(input_data$PTM, contrast.matrix) |
|
| 285 |
- # model_protein = MSstatsShiny::lf_model(input_data$PROTEIN, contrast.matrix) |
|
| 286 |
- # model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult, |
|
| 287 |
- # model_protein$ComparisonResult) |
|
| 288 |
- # model = list('PTM.Model' = model_ptm$ComparisonResult,
|
|
| 289 |
- # 'PROTEIN.Model' = model_protein$ComparisonResult, |
|
| 290 |
- # 'ADJUSTED.Model' = model_adj) |
|
| 291 |
- # |
|
| 292 |
- # } else if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 293 |
- # model = MSstatsShiny::tmt_model(input_data, input, contrast.matrix) |
|
| 294 |
- # } |
|
| 295 |
- # else{
|
|
| 296 |
- # model = MSstatsShiny::lf_model(input_data, contrast.matrix) |
|
| 297 |
- # } |
|
| 298 |
- # return(model) |
|
| 299 |
- # }) |
|
| 300 | 270 |
|
| 301 | 271 |
data_comparison_code = eventReactive(input$calculate, {
|
| 302 | 272 |
|
| ... | ... |
@@ -420,7 +390,6 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 420 | 390 |
|
| 421 | 391 |
|
| 422 | 392 |
} else if(loadpage_input()$DDA_DIA=="TMT"){
|
| 423 |
- |
|
| 424 | 393 |
tryCatch({plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult,
|
| 425 | 394 |
type=input$typeplot, |
| 426 | 395 |
sig=input$sig, |
| ... | ... |
@@ -439,7 +408,6 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 439 | 408 |
|
| 440 | 409 |
|
| 441 | 410 |
} else{
|
| 442 |
- |
|
| 443 | 411 |
tryCatch({plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult,
|
| 444 | 412 |
type=input$typeplot, |
| 445 | 413 |
sig=input$sig, |
Deril Raju authored on 15/02/2023 20:13:56
| ... | ... |
@@ -136,6 +136,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 136 | 136 |
)} |
| 137 | 137 |
}) |
| 138 | 138 |
|
| 139 |
+ |
|
| 139 | 140 |
matrix_build = eventReactive(input$submit | input$submit1 | input$submit2 | input$submit3, {
|
| 140 | 141 |
req(input$def_comp) |
| 141 | 142 |
req(loadpage_input()$DDA_DIA) |
| ... | ... |
@@ -258,35 +259,44 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 258 | 259 |
}) |
| 259 | 260 |
|
| 260 | 261 |
# Run Models |
| 261 |
- data_comparison = eventReactive(input$calculate, {
|
|
| 262 |
- input_data = preprocessData(qc_input,loadpage_input) |
|
| 263 |
- contrast.matrix = matrix_build() |
|
| 264 |
- if (loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "Yes"){
|
|
| 265 |
- model_ptm = MSstatsShiny::tmt_model(input_data$PTM, input, contrast.matrix) |
|
| 266 |
- model_protein = MSstatsShiny::tmt_model(input_data$PROTEIN, input, contrast.matrix) |
|
| 267 |
- model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult, |
|
| 268 |
- model_protein$ComparisonResult) |
|
| 269 |
- model = list('PTM.Model' = model_ptm$ComparisonResult,
|
|
| 270 |
- 'PROTEIN.Model' = model_protein$ComparisonResult, |
|
| 271 |
- 'ADJUSTED.Model' = model_adj) |
|
| 272 |
- |
|
| 273 |
- } else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
|
|
| 274 |
- model_ptm = MSstatsShiny::lf_model(input_data$PTM, contrast.matrix) |
|
| 275 |
- model_protein = MSstatsShiny::lf_model(input_data$PROTEIN, contrast.matrix) |
|
| 276 |
- model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult, |
|
| 277 |
- model_protein$ComparisonResult) |
|
| 278 |
- model = list('PTM.Model' = model_ptm$ComparisonResult,
|
|
| 279 |
- 'PROTEIN.Model' = model_protein$ComparisonResult, |
|
| 280 |
- 'ADJUSTED.Model' = model_adj) |
|
| 281 |
- |
|
| 282 |
- } else if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 283 |
- model = MSstatsShiny::tmt_model(input_data, input, contrast.matrix) |
|
| 284 |
- } |
|
| 285 |
- else{
|
|
| 286 |
- model = MSstatsShiny::lf_model(input_data, contrast.matrix) |
|
| 287 |
- } |
|
| 288 |
- return(model) |
|
| 262 |
+ |
|
| 263 |
+ data_comparison <- eventReactive(input$calculate,{
|
|
| 264 |
+ statmodel_input <- reactive({
|
|
| 265 |
+ input |
|
| 266 |
+ }) |
|
| 267 |
+ matrix = matrix_build() |
|
| 268 |
+ dataComparison(statmodel_input,qc_input,loadpage_input,matrix) |
|
| 289 | 269 |
}) |
| 270 |
+ |
|
| 271 |
+ # data_comparison = eventReactive(input$calculate, {
|
|
| 272 |
+ # input_data = preprocessData(qc_input,loadpage_input) |
|
| 273 |
+ # contrast.matrix = matrix_build() |
|
| 274 |
+ # if (loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "Yes"){
|
|
| 275 |
+ # model_ptm = MSstatsShiny::tmt_model(input_data$PTM, input, contrast.matrix) |
|
| 276 |
+ # model_protein = MSstatsShiny::tmt_model(input_data$PROTEIN, input, contrast.matrix) |
|
| 277 |
+ # model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult, |
|
| 278 |
+ # model_protein$ComparisonResult) |
|
| 279 |
+ # model = list('PTM.Model' = model_ptm$ComparisonResult,
|
|
| 280 |
+ # 'PROTEIN.Model' = model_protein$ComparisonResult, |
|
| 281 |
+ # 'ADJUSTED.Model' = model_adj) |
|
| 282 |
+ # |
|
| 283 |
+ # } else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
|
|
| 284 |
+ # model_ptm = MSstatsShiny::lf_model(input_data$PTM, contrast.matrix) |
|
| 285 |
+ # model_protein = MSstatsShiny::lf_model(input_data$PROTEIN, contrast.matrix) |
|
| 286 |
+ # model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult, |
|
| 287 |
+ # model_protein$ComparisonResult) |
|
| 288 |
+ # model = list('PTM.Model' = model_ptm$ComparisonResult,
|
|
| 289 |
+ # 'PROTEIN.Model' = model_protein$ComparisonResult, |
|
| 290 |
+ # 'ADJUSTED.Model' = model_adj) |
|
| 291 |
+ # |
|
| 292 |
+ # } else if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 293 |
+ # model = MSstatsShiny::tmt_model(input_data, input, contrast.matrix) |
|
| 294 |
+ # } |
|
| 295 |
+ # else{
|
|
| 296 |
+ # model = MSstatsShiny::lf_model(input_data, contrast.matrix) |
|
| 297 |
+ # } |
|
| 298 |
+ # return(model) |
|
| 299 |
+ # }) |
|
| 290 | 300 |
|
| 291 | 301 |
data_comparison_code = eventReactive(input$calculate, {
|
| 292 | 302 |
|
| ... | ... |
@@ -695,7 +705,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 695 | 705 |
) |
| 696 | 706 |
} |
| 697 | 707 |
) |
| 698 |
- # |
|
| 708 |
+ |
|
| 699 | 709 |
observe({output$comp_plots = renderPlot({
|
| 700 | 710 |
group_comparison(FALSE, FALSE)}, height = input$height |
| 701 | 711 |
) |
| ... | ... |
@@ -894,5 +904,10 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu |
| 894 | 904 |
enable("download_code")
|
| 895 | 905 |
}) |
| 896 | 906 |
|
| 897 |
- |
|
| 907 |
+ return( |
|
| 908 |
+ list( |
|
| 909 |
+ ip = input, |
|
| 910 |
+ matrix = matrix_build |
|
| 911 |
+ ) |
|
| 912 |
+ ) |
|
| 898 | 913 |
} |
| 899 | 914 |
\ No newline at end of file |
Deril Raju authored on 14/02/2023 21:22:19
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,898 @@ |
| 1 |
+statmodelServer <- function(input, output, session,parent_session, loadpage_inputs, qc_inputs) {
|
|
| 2 |
+ |
|
| 3 |
+ loadpage_input <- reactive({
|
|
| 4 |
+ loadpage_inputs |
|
| 5 |
+ }) |
|
| 6 |
+ qc_input <- reactive({
|
|
| 7 |
+ qc_inputs |
|
| 8 |
+ }) |
|
| 9 |
+ ######### UI ######### |
|
| 10 |
+ |
|
| 11 |
+ # choices of groups for contrast matrix |
|
| 12 |
+ |
|
| 13 |
+ choices = reactive({
|
|
| 14 |
+ if (loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "Yes"){
|
|
| 15 |
+ levels(preprocessData(qc_input,loadpage_input)$PTM$ProteinLevelData$Condition) |
|
| 16 |
+ } else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
|
|
| 17 |
+ levels(preprocessData(qc_input,loadpage_input)$PTM$ProteinLevelData$GROUP) |
|
| 18 |
+ } else if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 19 |
+ levels(preprocessData(qc_input,loadpage_input)$ProteinLevelData$Condition) |
|
| 20 |
+ } |
|
| 21 |
+ else{
|
|
| 22 |
+ levels(preprocessData(qc_input,loadpage_input)$ProteinLevelData$GROUP) |
|
| 23 |
+ } |
|
| 24 |
+ |
|
| 25 |
+ }) |
|
| 26 |
+ row = reactive({rep(0, length(choices()))})
|
|
| 27 |
+ contrast = reactiveValues() |
|
| 28 |
+ comp_list = reactiveValues() |
|
| 29 |
+ significant = reactiveValues() |
|
| 30 |
+ |
|
| 31 |
+ |
|
| 32 |
+ observe({
|
|
| 33 |
+ if(loadpage_input()$DDA_DIA == "TMT" | loadpage_input()$DDA_DIA == "PTM"){
|
|
| 34 |
+ hide("Design")
|
|
| 35 |
+ } |
|
| 36 |
+ else{
|
|
| 37 |
+ shinyjs::show("Design")
|
|
| 38 |
+ } |
|
| 39 |
+ }) |
|
| 40 |
+ |
|
| 41 |
+ output$choice1 = renderUI({
|
|
| 42 |
+ ns <- session$ns |
|
| 43 |
+ selectInput(ns("group1"), "Group 1", choices())
|
|
| 44 |
+ }) |
|
| 45 |
+ |
|
| 46 |
+ output$choice2 = renderUI({
|
|
| 47 |
+ ns <- session$ns |
|
| 48 |
+ selectInput(ns("group2"), "Group 2", choices())
|
|
| 49 |
+ }) |
|
| 50 |
+ |
|
| 51 |
+ output$choice3 = renderUI({
|
|
| 52 |
+ ns <- session$ns |
|
| 53 |
+ selectInput(ns("group3"), "", choices())
|
|
| 54 |
+ }) |
|
| 55 |
+ |
|
| 56 |
+ output$comp_name = renderUI({
|
|
| 57 |
+ ns <- session$ns |
|
| 58 |
+ textInput(ns("comp_name"), label = "Comparison Name", value = "")
|
|
| 59 |
+ }) |
|
| 60 |
+ |
|
| 61 |
+ output$weights = renderUI({
|
|
| 62 |
+ ns <- session$ns |
|
| 63 |
+ lapply(1:length(choices()), function(i) {
|
|
| 64 |
+ list( |
|
| 65 |
+ numericInput(ns(paste0("weight", i)), label = choices()[i], value=0))
|
|
| 66 |
+ }) |
|
| 67 |
+ }) |
|
| 68 |
+ |
|
| 69 |
+ # rownames for matrix |
|
| 70 |
+ |
|
| 71 |
+ Rownames = eventReactive(input$submit | input$submit1 | input$submit2 | input$submit3, {
|
|
| 72 |
+ req(input$def_comp) |
|
| 73 |
+ req(loadpage_input()$DDA_DIA) |
|
| 74 |
+ tryCatch({
|
|
| 75 |
+ rownames(matrix_build())}, |
|
| 76 |
+ error=function(e){})
|
|
| 77 |
+ }) |
|
| 78 |
+ |
|
| 79 |
+ # choices of comparisons/proteins to plot |
|
| 80 |
+ |
|
| 81 |
+ output$WhichComp = renderUI ({
|
|
| 82 |
+ ns <- session$ns |
|
| 83 |
+ selectInput(ns("whichComp"),
|
|
| 84 |
+ label = h5("Select comparison to plot"), c("all", Rownames()), selected = "all")
|
|
| 85 |
+ }) |
|
| 86 |
+ |
|
| 87 |
+ output$WhichProt = renderUI ({
|
|
| 88 |
+ ns <- session$ns |
|
| 89 |
+ selectInput(ns("whichProt"),
|
|
| 90 |
+ label = h4("which protein to plot"), unique(getData(loadpage_input())[[1]]))
|
|
| 91 |
+ }) |
|
| 92 |
+ |
|
| 93 |
+ output$WhichProt1 = renderUI ({
|
|
| 94 |
+ ns <- session$ns |
|
| 95 |
+ selectizeInput(ns("whichProt1"),
|
|
| 96 |
+ label = h4("which protein to plot"), c("", unique(getData(loadpage_input())[[1]])))
|
|
| 97 |
+ }) |
|
| 98 |
+ |
|
| 99 |
+ |
|
| 100 |
+ ########## functions ######## |
|
| 101 |
+ |
|
| 102 |
+ # build matrix |
|
| 103 |
+ |
|
| 104 |
+ observeEvent(input$def_comp, {
|
|
| 105 |
+ contrast$matrix = NULL |
|
| 106 |
+ comp_list$dList = NULL |
|
| 107 |
+ }) |
|
| 108 |
+ |
|
| 109 |
+ observeEvent(loadpage_input()$proceed1, {
|
|
| 110 |
+ contrast$matrix = NULL |
|
| 111 |
+ comp_list$dList = NULL |
|
| 112 |
+ significant$result = NULL |
|
| 113 |
+ }) |
|
| 114 |
+ |
|
| 115 |
+ |
|
| 116 |
+ |
|
| 117 |
+ ## Check contrast matrix was created correctly |
|
| 118 |
+ check_cond = eventReactive(input$submit | input$submit1 | input$submit2 | input$submit3, {
|
|
| 119 |
+ req(input$def_comp) |
|
| 120 |
+ req(loadpage_input()$DDA_DIA) |
|
| 121 |
+ if(input$def_comp == "custom") {
|
|
| 122 |
+ validate( |
|
| 123 |
+ need(input$group1 != input$group2, "Please select different groups") |
|
| 124 |
+ )} |
|
| 125 |
+ |
|
| 126 |
+ else if(input$def_comp == "custom_np") {
|
|
| 127 |
+ |
|
| 128 |
+ wt_sum = 0 |
|
| 129 |
+ for (index in 1:length(choices())){
|
|
| 130 |
+ wt_sum = wt_sum + input[[paste0("weight", index)]]
|
|
| 131 |
+ } |
|
| 132 |
+ |
|
| 133 |
+ validate( |
|
| 134 |
+ need( wt_sum == 0, |
|
| 135 |
+ "The contrast weights should sum up to 0") |
|
| 136 |
+ )} |
|
| 137 |
+ }) |
|
| 138 |
+ |
|
| 139 |
+ matrix_build = eventReactive(input$submit | input$submit1 | input$submit2 | input$submit3, {
|
|
| 140 |
+ req(input$def_comp) |
|
| 141 |
+ req(loadpage_input()$DDA_DIA) |
|
| 142 |
+ if(input$def_comp == "custom") {
|
|
| 143 |
+ if(input$group1 == input$group2){
|
|
| 144 |
+ return(contrast$matrix) |
|
| 145 |
+ } |
|
| 146 |
+ index1 = reactive({which(choices() == input$group1)})
|
|
| 147 |
+ index2 = reactive({which(choices() == input$group2)})
|
|
| 148 |
+ comp_list$dList = unique(c(isolate(comp_list$dList), paste(input$group1, "vs", |
|
| 149 |
+ input$group2, sep = " "))) |
|
| 150 |
+ contrast$row = matrix(row(), nrow=1) |
|
| 151 |
+ contrast$row[index1()] = 1 |
|
| 152 |
+ contrast$row[index2()] = -1 |
|
| 153 |
+ if (is.null(contrast$matrix)) {
|
|
| 154 |
+ contrast$matrix = contrast$row |
|
| 155 |
+ } |
|
| 156 |
+ else {
|
|
| 157 |
+ contrast$matrix = rbind(contrast$matrix, contrast$row) |
|
| 158 |
+ contrast$matrix = rbind(contrast$matrix[!duplicated(contrast$matrix),]) |
|
| 159 |
+ } |
|
| 160 |
+ rownames(contrast$matrix) = comp_list$dList |
|
| 161 |
+ colnames(contrast$matrix) = choices() |
|
| 162 |
+ } |
|
| 163 |
+ |
|
| 164 |
+ else if(input$def_comp == "custom_np") {
|
|
| 165 |
+ |
|
| 166 |
+ wt_sum = 0 |
|
| 167 |
+ for (index in 1:length(choices())){
|
|
| 168 |
+ wt_sum = wt_sum + input[[paste0("weight", index)]]
|
|
| 169 |
+ } |
|
| 170 |
+ |
|
| 171 |
+ if(wt_sum != 0){
|
|
| 172 |
+ return(contrast$matrix) |
|
| 173 |
+ } |
|
| 174 |
+ |
|
| 175 |
+ comp_list$dList = unique(c(isolate(comp_list$dList), input$comp_name)) |
|
| 176 |
+ contrast$row = matrix(row(), nrow=1) |
|
| 177 |
+ |
|
| 178 |
+ for (index in 1:length(choices())){
|
|
| 179 |
+ contrast$row[index] = input[[paste0("weight", index)]]
|
|
| 180 |
+ } |
|
| 181 |
+ |
|
| 182 |
+ if (is.null(contrast$matrix)) {
|
|
| 183 |
+ contrast$matrix = contrast$row |
|
| 184 |
+ } else {
|
|
| 185 |
+ contrast$matrix = rbind(contrast$matrix, contrast$row) |
|
| 186 |
+ contrast$matrix = rbind(contrast$matrix[!duplicated(contrast$matrix),]) |
|
| 187 |
+ } |
|
| 188 |
+ rownames(contrast$matrix) = comp_list$dList |
|
| 189 |
+ colnames(contrast$matrix) = choices() |
|
| 190 |
+ } |
|
| 191 |
+ |
|
| 192 |
+ else if (input$def_comp == "all_one") {
|
|
| 193 |
+ for (index in 1:length(choices())) {
|
|
| 194 |
+ index3 = reactive({which(choices() == input$group3)})
|
|
| 195 |
+ if(index == index3()) next |
|
| 196 |
+ if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 197 |
+ comp_list$dList = c(isolate(comp_list$dList), |
|
| 198 |
+ paste(choices()[index], " vs ", |
|
| 199 |
+ input$group3, sep = "")) |
|
| 200 |
+ } else{
|
|
| 201 |
+ comp_list$dList = c(isolate(comp_list$dList), |
|
| 202 |
+ paste(choices()[index], " vs ", |
|
| 203 |
+ input$group3, sep = "")) |
|
| 204 |
+ } |
|
| 205 |
+ |
|
| 206 |
+ contrast$row = matrix(row(), nrow=1) |
|
| 207 |
+ contrast$row[index] = 1 |
|
| 208 |
+ contrast$row[index3()] = -1 |
|
| 209 |
+ if (is.null(contrast$matrix)) {
|
|
| 210 |
+ contrast$matrix = contrast$row |
|
| 211 |
+ } else {
|
|
| 212 |
+ contrast$matrix = rbind(contrast$matrix, contrast$row) |
|
| 213 |
+ } |
|
| 214 |
+ rownames(contrast$matrix) = comp_list$dList |
|
| 215 |
+ colnames(contrast$matrix) = choices() |
|
| 216 |
+ } |
|
| 217 |
+ } |
|
| 218 |
+ else if (input$def_comp == "all_pair") {
|
|
| 219 |
+ contrast$matrix = NULL |
|
| 220 |
+ for (index in 1:length(choices())) {
|
|
| 221 |
+ for (index1 in 1:length(choices())) {
|
|
| 222 |
+ if (index == index1) next |
|
| 223 |
+ if (index < index1) {
|
|
| 224 |
+ if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 225 |
+ comp_list$dList = c(isolate(comp_list$dList), |
|
| 226 |
+ paste(choices()[index], " vs ", |
|
| 227 |
+ choices()[index1], sep = "")) |
|
| 228 |
+ } else{
|
|
| 229 |
+ comp_list$dList = c(isolate(comp_list$dList), |
|
| 230 |
+ paste(choices()[index], " vs ", |
|
| 231 |
+ choices()[index1], sep = "")) |
|
| 232 |
+ } |
|
| 233 |
+ contrast$row = matrix(row(), nrow=1) |
|
| 234 |
+ contrast$row[index] = 1 |
|
| 235 |
+ contrast$row[index1] = -1 |
|
| 236 |
+ if (is.null(contrast$matrix)) {
|
|
| 237 |
+ contrast$matrix = contrast$row |
|
| 238 |
+ } else {
|
|
| 239 |
+ contrast$matrix = rbind(contrast$matrix, contrast$row) |
|
| 240 |
+ contrast$matrix = rbind(contrast$matrix[!duplicated(contrast$matrix),]) |
|
| 241 |
+ } |
|
| 242 |
+ rownames(contrast$matrix) = comp_list$dList |
|
| 243 |
+ colnames(contrast$matrix) = choices() |
|
| 244 |
+ } |
|
| 245 |
+ } |
|
| 246 |
+ } |
|
| 247 |
+ } |
|
| 248 |
+ enable("calculate")
|
|
| 249 |
+ return(contrast$matrix) |
|
| 250 |
+ }) |
|
| 251 |
+ |
|
| 252 |
+ # clear matrix |
|
| 253 |
+ |
|
| 254 |
+ observeEvent({input$clear | input$clear1 | input$clear2 | input$clear3}, {
|
|
| 255 |
+ disable("calculate")
|
|
| 256 |
+ comp_list$dList = NULL |
|
| 257 |
+ contrast$matrix = NULL |
|
| 258 |
+ }) |
|
| 259 |
+ |
|
| 260 |
+ # Run Models |
|
| 261 |
+ data_comparison = eventReactive(input$calculate, {
|
|
| 262 |
+ input_data = preprocessData(qc_input,loadpage_input) |
|
| 263 |
+ contrast.matrix = matrix_build() |
|
| 264 |
+ if (loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "Yes"){
|
|
| 265 |
+ model_ptm = MSstatsShiny::tmt_model(input_data$PTM, input, contrast.matrix) |
|
| 266 |
+ model_protein = MSstatsShiny::tmt_model(input_data$PROTEIN, input, contrast.matrix) |
|
| 267 |
+ model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult, |
|
| 268 |
+ model_protein$ComparisonResult) |
|
| 269 |
+ model = list('PTM.Model' = model_ptm$ComparisonResult,
|
|
| 270 |
+ 'PROTEIN.Model' = model_protein$ComparisonResult, |
|
| 271 |
+ 'ADJUSTED.Model' = model_adj) |
|
| 272 |
+ |
|
| 273 |
+ } else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
|
|
| 274 |
+ model_ptm = MSstatsShiny::lf_model(input_data$PTM, contrast.matrix) |
|
| 275 |
+ model_protein = MSstatsShiny::lf_model(input_data$PROTEIN, contrast.matrix) |
|
| 276 |
+ model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult, |
|
| 277 |
+ model_protein$ComparisonResult) |
|
| 278 |
+ model = list('PTM.Model' = model_ptm$ComparisonResult,
|
|
| 279 |
+ 'PROTEIN.Model' = model_protein$ComparisonResult, |
|
| 280 |
+ 'ADJUSTED.Model' = model_adj) |
|
| 281 |
+ |
|
| 282 |
+ } else if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 283 |
+ model = MSstatsShiny::tmt_model(input_data, input, contrast.matrix) |
|
| 284 |
+ } |
|
| 285 |
+ else{
|
|
| 286 |
+ model = MSstatsShiny::lf_model(input_data, contrast.matrix) |
|
| 287 |
+ } |
|
| 288 |
+ return(model) |
|
| 289 |
+ }) |
|
| 290 |
+ |
|
| 291 |
+ data_comparison_code = eventReactive(input$calculate, {
|
|
| 292 |
+ |
|
| 293 |
+ codes = preprocessDataCode(qc_input,loadpage_input) |
|
| 294 |
+ comp.mat = matrix_build() |
|
| 295 |
+ |
|
| 296 |
+ codes = paste(codes, "\n# Create the contrast matrix\n", sep = "") |
|
| 297 |
+ codes = paste(codes, "contrast.matrix = NULL\n", sep = "") |
|
| 298 |
+ for(i in 1:nrow(comp.mat)){
|
|
| 299 |
+ codes = paste(codes, "comparison = matrix(c(", toString(comp.mat[i,]),"),nrow=1)\n", sep = "")
|
|
| 300 |
+ codes = paste(codes, "contrast.matrix = rbind(contrast.matrix, comparison)\n", sep = "") |
|
| 301 |
+ |
|
| 302 |
+ } |
|
| 303 |
+ |
|
| 304 |
+ codes = paste(codes, "row.names(contrast.matrix)=c(\"", paste(row.names(comp.mat), collapse='","'),"\")\n", sep = "") |
|
| 305 |
+ codes = paste(codes, "colnames(contrast.matrix)=c(\"", paste(colnames(comp.mat), collapse='","'),"\")\n", sep = "") |
|
| 306 |
+ |
|
| 307 |
+ if(loadpage_input()$DDA_DIA == "TMT"){
|
|
| 308 |
+ codes = paste(codes, "\n# Model-based comparison\n", sep = "") |
|
| 309 |
+ codes = paste(codes,"model = MSstatsTMT::groupComparisonTMT(summarized, |
|
| 310 |
+ contrast.matrix = contrast.matrix, |
|
| 311 |
+ moderated = ", input$moderated,",\t\t\t\t |
|
| 312 |
+ adj.method = \"BH\", |
|
| 313 |
+ remove_norm_channel = TRUE, |
|
| 314 |
+ remove_empty_channel = TRUE |
|
| 315 |
+ )\n", sep = "") |
|
| 316 |
+ } else if (loadpage_input()$DDA_DIA == "PTM"){
|
|
| 317 |
+ if (loadpage_input()$PTMTMT == "Yes"){
|
|
| 318 |
+ dt = "TMT" |
|
| 319 |
+ } else {
|
|
| 320 |
+ dt = "LabelFree" |
|
| 321 |
+ } |
|
| 322 |
+ codes = paste(codes, "\n# Model-based comparison\n", sep = "") |
|
| 323 |
+ codes = paste(codes,"model = MSstatsPTM::groupComparisonPTM(summarized, '", |
|
| 324 |
+ dt, "', \t\t\t\t |
|
| 325 |
+ contrast.matrix = contrast.matrix)\n", sep = "") |
|
| 326 |
+ } |
|
| 327 |
+ else{
|
|
| 328 |
+ |
|
| 329 |
+ codes = paste(codes, "\n# Model-based comparison\n", sep = "") |
|
| 330 |
+ codes = paste(codes,"model = MSstats::groupComparison(contrast.matrix, summarized)\n", sep = "") |
|
| 331 |
+ } |
|
| 332 |
+ if (loadpage_input()$DDA_DIA == "PTM"){
|
|
| 333 |
+ codes = paste(codes, "groupComparisonPlotsPTM(data=model, |
|
| 334 |
+ type=\"Enter VolcanoPlot, Heatmap, or ComparisonPlot\", |
|
| 335 |
+ which.Comparison=\"all\", |
|
| 336 |
+ which.PTM=\"all\", |
|
| 337 |
+ address=\"\")\n", sep="") |
|
| 338 |
+ } else {
|
|
| 339 |
+ codes = paste(codes, "groupComparisonPlots(data=model$ComparisonResult, |
|
| 340 |
+ type=\"Enter VolcanoPlot, Heatmap, or ComparisonPlot\", |
|
| 341 |
+ which.Comparison=\"all\", |
|
| 342 |
+ which.Protein=\"all\", |
|
| 343 |
+ address=\"\")\n", sep="") |
|
| 344 |
+ } |
|
| 345 |
+ |
|
| 346 |
+ return(codes) |
|
| 347 |
+ }) |
|
| 348 |
+ |
|
| 349 |
+ |
|
| 350 |
+ round_df = function(df) {
|
|
| 351 |
+ nums = vapply(df, is.numeric, FUN.VALUE = logical(1)) |
|
| 352 |
+ |
|
| 353 |
+ df[,nums] = round(df[,nums], digits = 4) |
|
| 354 |
+ |
|
| 355 |
+ (df) |
|
| 356 |
+ } |
|
| 357 |
+ |
|
| 358 |
+ SignificantProteins = eventReactive(input$calculate,{
|
|
| 359 |
+ if (loadpage_input()$DDA_DIA == "PTM"){
|
|
| 360 |
+ data_comp = data_comparison() |
|
| 361 |
+ sig_unadj = data_comp$PTM.Model[ |
|
| 362 |
+ data_comp$PTM.Model$adj.pvalue < input$signif] |
|
| 363 |
+ sig_prot = data_comp$PROTEIN.Model[ |
|
| 364 |
+ data_comp$PROTEIN.Model$adj.pvalue < input$signif] |
|
| 365 |
+ sig_adj = data_comp$ADJUSTED.Model[ |
|
| 366 |
+ data_comp$ADJUSTED.Model$adj.pvalue < input$signif] |
|
| 367 |
+ significant = list(PTM.Model=sig_unadj, |
|
| 368 |
+ PROTEIN.Model=sig_prot, |
|
| 369 |
+ ADJUSTED.Model=sig_adj) |
|
| 370 |
+ |
|
| 371 |
+ } else if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 372 |
+ data_comp = data_comparison() |
|
| 373 |
+ significant = data_comp$ComparisonResult[ |
|
| 374 |
+ data_comp$ComparisonResult$adj.pvalue < input$signif, ] |
|
| 375 |
+ |
|
| 376 |
+ } else {
|
|
| 377 |
+ significant = with(data_comparison(), round_df(ComparisonResult[ |
|
| 378 |
+ ComparisonResult$adj.pvalue < input$signif, ])) |
|
| 379 |
+ |
|
| 380 |
+ } |
|
| 381 |
+ return(significant) |
|
| 382 |
+ }) |
|
| 383 |
+ |
|
| 384 |
+ group_comparison = function(saveFile1, pdf) {
|
|
| 385 |
+ |
|
| 386 |
+ show_modal_spinner() |
|
| 387 |
+ |
|
| 388 |
+ id1 = as.character(UUIDgenerate(FALSE)) |
|
| 389 |
+ id_address1 = paste(tempdir(), "\\", id1, sep = "") |
|
| 390 |
+ |
|
| 391 |
+ path1 = function() {
|
|
| 392 |
+ if (saveFile1) {
|
|
| 393 |
+ path1_id = paste(tempdir(), "\\", id1, sep = "") |
|
| 394 |
+ } |
|
| 395 |
+ else {
|
|
| 396 |
+ path1_id = FALSE |
|
| 397 |
+ } |
|
| 398 |
+ return(path1_id) |
|
| 399 |
+ } |
|
| 400 |
+ |
|
| 401 |
+ if (loadpage_input()$DDA_DIA=="PTM"){
|
|
| 402 |
+ plot1 = groupComparisonPlotsPTM(data_comparison(), |
|
| 403 |
+ input$typeplot, |
|
| 404 |
+ sig=input$sig, |
|
| 405 |
+ FCcutoff=input$FC, |
|
| 406 |
+ logBase.pvalue=as.integer(input$logp), |
|
| 407 |
+ ProteinName = input$pname, |
|
| 408 |
+ which.Comparison = input$whichComp, |
|
| 409 |
+ address = FALSE) |
|
| 410 |
+ |
|
| 411 |
+ |
|
| 412 |
+ } else if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 413 |
+ |
|
| 414 |
+ tryCatch({plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult,
|
|
| 415 |
+ type=input$typeplot, |
|
| 416 |
+ sig=input$sig, |
|
| 417 |
+ FCcutoff=input$FC, |
|
| 418 |
+ logBase.pvalue=input$logp, |
|
| 419 |
+ ProteinName=input$pname, |
|
| 420 |
+ numProtein=input$nump, |
|
| 421 |
+ clustering=input$cluster, |
|
| 422 |
+ which.Comparison=input$whichComp, |
|
| 423 |
+ which.Protein = input$whichProt, |
|
| 424 |
+ address=path1(), |
|
| 425 |
+ savePDF=pdf)}, |
|
| 426 |
+ error = function(e){remove_modal_spinner()
|
|
| 427 |
+ print("All plots cannot be shown in browser. Please select and individual comparison or download pdf.")}
|
|
| 428 |
+ ) |
|
| 429 |
+ |
|
| 430 |
+ |
|
| 431 |
+ } else{
|
|
| 432 |
+ |
|
| 433 |
+ tryCatch({plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult,
|
|
| 434 |
+ type=input$typeplot, |
|
| 435 |
+ sig=input$sig, |
|
| 436 |
+ FCcutoff=input$FC, |
|
| 437 |
+ logBase.pvalue=input$logp, |
|
| 438 |
+ ProteinName=input$pname, |
|
| 439 |
+ numProtein=input$nump, |
|
| 440 |
+ clustering=input$cluster, |
|
| 441 |
+ which.Comparison=input$whichComp, |
|
| 442 |
+ which.Protein = input$whichProt, |
|
| 443 |
+ address=path1(), |
|
| 444 |
+ savePDF=pdf)}, |
|
| 445 |
+ error = function(e){remove_modal_spinner()
|
|
| 446 |
+ print("All plots cannot be shown in browser. Please select and individual comparison or download pdf.")}
|
|
| 447 |
+ ) |
|
| 448 |
+ |
|
| 449 |
+ } |
|
| 450 |
+ |
|
| 451 |
+ remove_modal_spinner() |
|
| 452 |
+ |
|
| 453 |
+ if(saveFile1) {
|
|
| 454 |
+ return(id_address1) |
|
| 455 |
+ } |
|
| 456 |
+ else {
|
|
| 457 |
+ return(plot1) |
|
| 458 |
+ } |
|
| 459 |
+ |
|
| 460 |
+ } |
|
| 461 |
+ |
|
| 462 |
+ # model assumptions plots |
|
| 463 |
+ |
|
| 464 |
+ assumptions1 = function(saveFile3, protein) {
|
|
| 465 |
+ if (input$whichProt1 != "") {
|
|
| 466 |
+ id2 = as.character(UUIDgenerate(FALSE)) |
|
| 467 |
+ id_address2 = paste("tmp/",id2, sep = "")
|
|
| 468 |
+ path2 = function(saveFile3) {
|
|
| 469 |
+ if (saveFile3) {
|
|
| 470 |
+ path_id2 = paste("www/", id_address2, sep = "")
|
|
| 471 |
+ } |
|
| 472 |
+ else {
|
|
| 473 |
+ path_id2 = FALSE |
|
| 474 |
+ } |
|
| 475 |
+ return (path_id2) |
|
| 476 |
+ } |
|
| 477 |
+ |
|
| 478 |
+ plots = modelBasedQCPlots(data=data_comparison(), type=input$assum_type, |
|
| 479 |
+ which.Protein = protein, address = path2()) |
|
| 480 |
+ |
|
| 481 |
+ if(saveFile3) {
|
|
| 482 |
+ return(path2()) |
|
| 483 |
+ } |
|
| 484 |
+ else {
|
|
| 485 |
+ return(plots) |
|
| 486 |
+ } |
|
| 487 |
+ } |
|
| 488 |
+ else {
|
|
| 489 |
+ return(NULL) |
|
| 490 |
+ } |
|
| 491 |
+ } |
|
| 492 |
+ |
|
| 493 |
+ |
|
| 494 |
+ |
|
| 495 |
+ ########## output ########## |
|
| 496 |
+ |
|
| 497 |
+ # download comparison data |
|
| 498 |
+ |
|
| 499 |
+ output$compar = downloadHandler( |
|
| 500 |
+ filename = function() {
|
|
| 501 |
+ paste("comparison-", Sys.Date(), ".csv", sep="")
|
|
| 502 |
+ }, |
|
| 503 |
+ content = function(file) {
|
|
| 504 |
+ write.csv(data_comparison()$ComparisonResult, file) |
|
| 505 |
+ }) |
|
| 506 |
+ |
|
| 507 |
+ output$model_QC = downloadHandler( |
|
| 508 |
+ filename = function() {
|
|
| 509 |
+ paste("ModelQC-", Sys.Date(), ".csv", sep="")
|
|
| 510 |
+ }, |
|
| 511 |
+ content = function(file) {
|
|
| 512 |
+ write.csv(data_comparison()$ModelQC, file) |
|
| 513 |
+ }) |
|
| 514 |
+ |
|
| 515 |
+ output$fitted_v = downloadHandler( |
|
| 516 |
+ filename = function() {
|
|
| 517 |
+ paste("model_summary-", Sys.Date(), ".csv", sep="")
|
|
| 518 |
+ }, |
|
| 519 |
+ content = function(file) {
|
|
| 520 |
+ write.csv(capture.output(data_comparison()$fittedmodel), file) |
|
| 521 |
+ }) |
|
| 522 |
+ |
|
| 523 |
+ # matrix |
|
| 524 |
+ |
|
| 525 |
+ output$message = renderText({
|
|
| 526 |
+ check_cond() |
|
| 527 |
+ }) |
|
| 528 |
+ observeEvent(input$calculate, {output$code.button = renderUI({
|
|
| 529 |
+ ns <- session$ns |
|
| 530 |
+ downloadButton(ns("download_code"), "Download analysis code", icon("download"),
|
|
| 531 |
+ style="color: #000000; background-color: #75ba82; border-color: #000000") |
|
| 532 |
+ })}) |
|
| 533 |
+ |
|
| 534 |
+ output$matrix = renderUI({
|
|
| 535 |
+ ns <- session$ns |
|
| 536 |
+ tagList( |
|
| 537 |
+ h2("Comparison matrix"),
|
|
| 538 |
+ br(), |
|
| 539 |
+ textOutput(ns("message")),
|
|
| 540 |
+ br(), |
|
| 541 |
+ if (is.null(contrast$matrix)) {
|
|
| 542 |
+ "" |
|
| 543 |
+ } else {
|
|
| 544 |
+ dataTableOutput(ns("table"))
|
|
| 545 |
+ } |
|
| 546 |
+ ) |
|
| 547 |
+ }) |
|
| 548 |
+ |
|
| 549 |
+ output$table = renderDataTable({
|
|
| 550 |
+ matrix_build() |
|
| 551 |
+ } |
|
| 552 |
+ ) |
|
| 553 |
+ |
|
| 554 |
+ # table of significant proteins |
|
| 555 |
+ output$table_results = renderUI({
|
|
| 556 |
+ ns <- session$ns |
|
| 557 |
+ req(data_comparison()) |
|
| 558 |
+ req(SignificantProteins()) |
|
| 559 |
+ |
|
| 560 |
+ if (is.null(significant)) {
|
|
| 561 |
+ |
|
| 562 |
+ tagList( |
|
| 563 |
+ tags$br()) |
|
| 564 |
+ } else {
|
|
| 565 |
+ tagList( |
|
| 566 |
+ tags$br(), |
|
| 567 |
+ h2("Results"),
|
|
| 568 |
+ h5("There are ",textOutput(ns("number"), inline = TRUE),"significant proteins"),
|
|
| 569 |
+ tags$br(), |
|
| 570 |
+ dataTableOutput(ns("significant")),
|
|
| 571 |
+ downloadButton(ns("download_compar"), "Download all modeling results"),
|
|
| 572 |
+ downloadButton(ns("download_signif"), "Download significant proteins")
|
|
| 573 |
+ |
|
| 574 |
+ ) |
|
| 575 |
+ } |
|
| 576 |
+ }) |
|
| 577 |
+ |
|
| 578 |
+ output$adj_table_results = renderUI({
|
|
| 579 |
+ ns <- session$ns |
|
| 580 |
+ req(data_comparison()) |
|
| 581 |
+ req(SignificantProteins()) |
|
| 582 |
+ significant = SignificantProteins() |
|
| 583 |
+ if (is.null(significant$ADJUSTED.Model)) {
|
|
| 584 |
+ tagList( |
|
| 585 |
+ tags$br()) |
|
| 586 |
+ } else {
|
|
| 587 |
+ tagList( |
|
| 588 |
+ tags$br(), |
|
| 589 |
+ h2("Adjusted PTM Modeling Results"),
|
|
| 590 |
+ h5("There are ",textOutput(ns("number_adj"), inline = TRUE),"significant PTMs"),
|
|
| 591 |
+ tags$br(), |
|
| 592 |
+ dataTableOutput(ns("adj_significant")),
|
|
| 593 |
+ downloadButton(ns("download_compar_adj"), "Download all modeling results"),
|
|
| 594 |
+ downloadButton(ns("download_signif_adj"), "Download significant PTMs")
|
|
| 595 |
+ ) |
|
| 596 |
+ } |
|
| 597 |
+ }) |
|
| 598 |
+ |
|
| 599 |
+ output$unadj_table_results = renderUI({
|
|
| 600 |
+ ns <- session$ns |
|
| 601 |
+ req(data_comparison()) |
|
| 602 |
+ req(SignificantProteins()) |
|
| 603 |
+ significant = SignificantProteins() |
|
| 604 |
+ if (is.null(significant$PTM.Model)) {
|
|
| 605 |
+ tagList( |
|
| 606 |
+ tags$br()) |
|
| 607 |
+ } else {
|
|
| 608 |
+ tagList( |
|
| 609 |
+ tags$br(), |
|
| 610 |
+ h2("Unadjusted PTM Modeling Results"),
|
|
| 611 |
+ h5("There are ",textOutput(ns("number_unadj"), inline = TRUE),"significant PTMs"),
|
|
| 612 |
+ tags$br(), |
|
| 613 |
+ dataTableOutput(ns("unadj_significant")),
|
|
| 614 |
+ downloadButton(ns("download_compar_unadj"), "Download all modeling results"),
|
|
| 615 |
+ downloadButton(ns("download_signif_unadj"), "Download significant PTMs")
|
|
| 616 |
+ ) |
|
| 617 |
+ } |
|
| 618 |
+ }) |
|
| 619 |
+ |
|
| 620 |
+ output$prot_table_results = renderUI({
|
|
| 621 |
+ ns <- session$ns |
|
| 622 |
+ req(data_comparison()) |
|
| 623 |
+ req(SignificantProteins()) |
|
| 624 |
+ significant = SignificantProteins() |
|
| 625 |
+ if (is.null(significant$PTM.Model)) {
|
|
| 626 |
+ tagList( |
|
| 627 |
+ tags$br()) |
|
| 628 |
+ } else {
|
|
| 629 |
+ tagList( |
|
| 630 |
+ tags$br(), |
|
| 631 |
+ h2("Protein Modeling Results"),
|
|
| 632 |
+ h5("There are ",textOutput(ns("number_prot"), inline = TRUE),"significant proteins"),
|
|
| 633 |
+ tags$br(), |
|
| 634 |
+ dataTableOutput(ns("prot_significant")),
|
|
| 635 |
+ downloadButton(ns("download_compar_prot"), "Download all modeling results"),
|
|
| 636 |
+ downloadButton(ns("download_signif_prot"), "Download significant proteins")
|
|
| 637 |
+ ) |
|
| 638 |
+ } |
|
| 639 |
+ }) |
|
| 640 |
+ |
|
| 641 |
+ output$significant = renderDataTable({
|
|
| 642 |
+ SignificantProteins() |
|
| 643 |
+ } |
|
| 644 |
+ ) |
|
| 645 |
+ |
|
| 646 |
+ output$adj_significant = renderDataTable({
|
|
| 647 |
+ SignificantProteins()$ADJUSTED.Model |
|
| 648 |
+ } |
|
| 649 |
+ ) |
|
| 650 |
+ |
|
| 651 |
+ output$unadj_significant = renderDataTable({
|
|
| 652 |
+ SignificantProteins()$PTM.Model |
|
| 653 |
+ } |
|
| 654 |
+ ) |
|
| 655 |
+ |
|
| 656 |
+ output$prot_significant = renderDataTable({
|
|
| 657 |
+ SignificantProteins()$PROTEIN.Model |
|
| 658 |
+ } |
|
| 659 |
+ ) |
|
| 660 |
+ |
|
| 661 |
+ # number of significant proteins |
|
| 662 |
+ output$number = renderText({
|
|
| 663 |
+ nrow(SignificantProteins()) |
|
| 664 |
+ }) |
|
| 665 |
+ |
|
| 666 |
+ output$number_adj = renderText({
|
|
| 667 |
+ nrow(SignificantProteins()$ADJUSTED.Model) |
|
| 668 |
+ }) |
|
| 669 |
+ |
|
| 670 |
+ output$number_unadj = renderText({
|
|
| 671 |
+ nrow(SignificantProteins()$PTM.Model) |
|
| 672 |
+ }) |
|
| 673 |
+ |
|
| 674 |
+ output$number_prot = renderText({
|
|
| 675 |
+ nrow(SignificantProteins()$PROTEIN.Model) |
|
| 676 |
+ }) |
|
| 677 |
+ |
|
| 678 |
+ # plot in browser |
|
| 679 |
+ observeEvent(input$typeplot, {
|
|
| 680 |
+ updateSelectInput(session, "whichComp", selected = "all") |
|
| 681 |
+ }) |
|
| 682 |
+ |
|
| 683 |
+ observeEvent(input$viewresults, {
|
|
| 684 |
+ ns <- session$ns |
|
| 685 |
+ insertUI( |
|
| 686 |
+ selector = paste0("#", ns("comparison_plots")),
|
|
| 687 |
+ ui=tags$div( |
|
| 688 |
+ plotOutput(ns("comp_plots"), height = "100%", click = "click1"),
|
|
| 689 |
+ conditionalPanel(condition = "input['statmodel-typeplot'] == 'VolcanoPlot' && input['loadpage-DDA_DIA']!='TMT'", |
|
| 690 |
+ h5("Click on plot for details"),
|
|
| 691 |
+ verbatimTextOutput(ns("info2"))),
|
|
| 692 |
+ conditionalPanel(condition = "input['statmodel-typeplot'] == 'Heatmap'", |
|
| 693 |
+ sliderInput(ns("height"), "Plot height", value = 500, min = 200, max = 1300, post = "px"))
|
|
| 694 |
+ ) |
|
| 695 |
+ ) |
|
| 696 |
+ } |
|
| 697 |
+ ) |
|
| 698 |
+ # |
|
| 699 |
+ observe({output$comp_plots = renderPlot({
|
|
| 700 |
+ group_comparison(FALSE, FALSE)}, height = input$height |
|
| 701 |
+ ) |
|
| 702 |
+ }) |
|
| 703 |
+ |
|
| 704 |
+ plotset = reactive({
|
|
| 705 |
+ |
|
| 706 |
+ if(loadpage_input()$DDA_DIA=="TMT"){
|
|
| 707 |
+ data_comp = data_comparison()$ComparisonResult |
|
| 708 |
+ v1 = data_comp[,1] |
|
| 709 |
+ v2 = round(data_comp[,3], 10) |
|
| 710 |
+ v3 = round(data_comp[,8], 10) |
|
| 711 |
+ v4 = data_comp[,2] |
|
| 712 |
+ |
|
| 713 |
+ } else{
|
|
| 714 |
+ v1 = data_comparison()$ComparisonResult[,1] |
|
| 715 |
+ v2 = round(data_comparison()$ComparisonResult[,3], 10) |
|
| 716 |
+ v3 = round(data_comparison()$ComparisonResult[,8], 10) |
|
| 717 |
+ v4 = data_comparison()$ComparisonResult[,2] |
|
| 718 |
+ |
|
| 719 |
+ } |
|
| 720 |
+ |
|
| 721 |
+ if (input$logp == "2") {
|
|
| 722 |
+ v3 = -log2(v3) |
|
| 723 |
+ } |
|
| 724 |
+ else if (input$logp == "10") {
|
|
| 725 |
+ v3 = - log10(v3) |
|
| 726 |
+ } |
|
| 727 |
+ |
|
| 728 |
+ df = data.frame(v1,v2,v3,v4) |
|
| 729 |
+ df = df[df$v4 == input$whichComp,] |
|
| 730 |
+ colnames(df) = c("Protein", "logFC", "logadj.pvalue", "comparison")
|
|
| 731 |
+ return(df) |
|
| 732 |
+ }) |
|
| 733 |
+ |
|
| 734 |
+ output$info2 = renderPrint({
|
|
| 735 |
+ print(nearPoints(plotset(), input$click1, xvar = "logFC", yvar = "logadj.pvalue")) |
|
| 736 |
+ }) |
|
| 737 |
+ |
|
| 738 |
+ # Assumption plots in browser |
|
| 739 |
+ |
|
| 740 |
+ output$verify = renderUI ({
|
|
| 741 |
+ ns <- session$ns |
|
| 742 |
+ tagList( |
|
| 743 |
+ plotOutput(ns("assum_plots"), width = "800px", height = "600px"),
|
|
| 744 |
+ conditionalPanel(condition = "input['statmodel-whichProt1'] != ''", |
|
| 745 |
+ actionButton(ns("saveone1"), "Save this plot"),
|
|
| 746 |
+ bsTooltip(id = ns("saveone1"), title = "Open plot as pdf. Popups must be enabled", placement = "bottom", trigger = "hover"),
|
|
| 747 |
+ actionButton(ns("saveall1"), "Save all plots"),
|
|
| 748 |
+ bsTooltip(id = ns("saveall1"), title = "Open pdf of all plots. Popups must be enabled", placement = "bottom", trigger = "hover")
|
|
| 749 |
+ ) |
|
| 750 |
+ ) |
|
| 751 |
+ }) |
|
| 752 |
+ |
|
| 753 |
+ output$assum_plots = renderPlot({
|
|
| 754 |
+ assumptions1(FALSE, input$whichProt1)}) |
|
| 755 |
+ |
|
| 756 |
+ |
|
| 757 |
+ # downloads |
|
| 758 |
+ observeEvent(input$saveone1, {
|
|
| 759 |
+ path = assumptions1(TRUE, input$whichProt1) |
|
| 760 |
+ if (input$assum_type == "QQPlots") {
|
|
| 761 |
+ js = paste("window.open('", path, "QQPlot.pdf')", sep="")
|
|
| 762 |
+ runjs(js); |
|
| 763 |
+ } |
|
| 764 |
+ else if (input$type == "ResidualPlots") {
|
|
| 765 |
+ js = paste("window.open('", path, "ResidualPlots.pdf')", sep="")
|
|
| 766 |
+ runjs(js); |
|
| 767 |
+ } |
|
| 768 |
+ }) |
|
| 769 |
+ |
|
| 770 |
+ observeEvent(input$saveall1, {
|
|
| 771 |
+ path = assumptions1(TRUE, "all") |
|
| 772 |
+ if (input$assum_type == "QQPlots") {
|
|
| 773 |
+ js = paste("window.open('", path, "QQPlot.pdf')", sep="")
|
|
| 774 |
+ runjs(js); |
|
| 775 |
+ } |
|
| 776 |
+ else if (input$type == "ResidualPlots") {
|
|
| 777 |
+ js = paste("window.open('", path, "ResidualPlots.pdf')", sep="")
|
|
| 778 |
+ runjs(js); |
|
| 779 |
+ } |
|
| 780 |
+ }) |
|
| 781 |
+ |
|
| 782 |
+ |
|
| 783 |
+ output$download_compar = downloadHandler( |
|
| 784 |
+ filename = function() {
|
|
| 785 |
+ paste("test_result-", Sys.Date(), ".csv", sep="")
|
|
| 786 |
+ }, |
|
| 787 |
+ content = function(file) {
|
|
| 788 |
+ write.csv(data_comparison()$ComparisonResult, file) |
|
| 789 |
+ } |
|
| 790 |
+ ) |
|
| 791 |
+ output$download_compar_adj = downloadHandler( |
|
| 792 |
+ filename = function() {
|
|
| 793 |
+ paste("adj_data-", Sys.Date(), ".csv", sep="")
|
|
| 794 |
+ }, |
|
| 795 |
+ content = function(file) {
|
|
| 796 |
+ write.csv(data_comparison()$ADJUSTED.Model, file) |
|
| 797 |
+ } |
|
| 798 |
+ ) |
|
| 799 |
+ output$download_compar_unadj = downloadHandler( |
|
| 800 |
+ filename = function() {
|
|
| 801 |
+ paste("unadj_data-", Sys.Date(), ".csv", sep="")
|
|
| 802 |
+ }, |
|
| 803 |
+ content = function(file) {
|
|
| 804 |
+ write.csv(data_comparison()$PTM.Model, file) |
|
| 805 |
+ } |
|
| 806 |
+ ) |
|
| 807 |
+ output$download_compar_prot = downloadHandler( |
|
| 808 |
+ filename = function() {
|
|
| 809 |
+ paste("prot_data-", Sys.Date(), ".csv", sep="")
|
|
| 810 |
+ }, |
|
| 811 |
+ content = function(file) {
|
|
| 812 |
+ write.csv(data_comparison()$PROTEIN.Model, file) |
|
| 813 |
+ } |
|
| 814 |
+ ) |
|
| 815 |
+ |
|
| 816 |
+ output$download_code = downloadHandler( |
|
| 817 |
+ filename = function() {
|
|
| 818 |
+ paste("mstats-code-", Sys.Date(), ".R", sep="")
|
|
| 819 |
+ }, |
|
| 820 |
+ content = function(file) {
|
|
| 821 |
+ writeLines(paste( |
|
| 822 |
+ data_comparison_code(), sep = ""), file) |
|
| 823 |
+ }) |
|
| 824 |
+ |
|
| 825 |
+ output$download_signif = downloadHandler( |
|
| 826 |
+ filename = function() {
|
|
| 827 |
+ paste("data-", Sys.Date(), ".csv", sep="")
|
|
| 828 |
+ }, |
|
| 829 |
+ content = function(file) {
|
|
| 830 |
+ write.csv(SignificantProteins(), file) |
|
| 831 |
+ } |
|
| 832 |
+ ) |
|
| 833 |
+ output$download_signif_adj = downloadHandler( |
|
| 834 |
+ filename = function() {
|
|
| 835 |
+ paste("adj_data-", Sys.Date(), ".csv", sep="")
|
|
| 836 |
+ }, |
|
| 837 |
+ content = function(file) {
|
|
| 838 |
+ write.csv(SignificantProteins()$ADJUSTED.Model, file) |
|
| 839 |
+ } |
|
| 840 |
+ ) |
|
| 841 |
+ output$download_signif_unadj = downloadHandler( |
|
| 842 |
+ filename = function() {
|
|
| 843 |
+ paste("unadj_data-", Sys.Date(), ".csv", sep="")
|
|
| 844 |
+ }, |
|
| 845 |
+ content = function(file) {
|
|
| 846 |
+ write.csv(SignificantProteins()$PTM.Model, file) |
|
| 847 |
+ } |
|
| 848 |
+ ) |
|
| 849 |
+ output$download_signif_prot = downloadHandler( |
|
| 850 |
+ filename = function() {
|
|
| 851 |
+ paste("prot_data-", Sys.Date(), ".csv", sep="")
|
|
| 852 |
+ }, |
|
| 853 |
+ content = function(file) {
|
|
| 854 |
+ write.csv(SignificantProteins()$PROTEIN.Model, file) |
|
| 855 |
+ } |
|
| 856 |
+ ) |
|
| 857 |
+ |
|
| 858 |
+ output$plotresults = downloadHandler( |
|
| 859 |
+ filename = function() {
|
|
| 860 |
+ paste("SummaryPlot-", Sys.Date(), ".pdf", sep="")
|
|
| 861 |
+ }, |
|
| 862 |
+ content = function(file) {
|
|
| 863 |
+ pdf(file) |
|
| 864 |
+ group_comparison(TRUE, TRUE) |
|
| 865 |
+ dev.off() |
|
| 866 |
+ } |
|
| 867 |
+ ) |
|
| 868 |
+ |
|
| 869 |
+# observeEvent(input$plotresults, {
|
|
| 870 |
+# insertUI( |
|
| 871 |
+# selector = "#comparison_plots", |
|
| 872 |
+# ui=tags$div( |
|
| 873 |
+# if (input$typeplot == "VolcanoPlot") {
|
|
| 874 |
+# js = paste("window.open('", group_comparison(TRUE, TRUE), "VolcanoPlot.pdf')", sep="")
|
|
| 875 |
+# print(js) |
|
| 876 |
+# runjs(js); |
|
| 877 |
+# } |
|
| 878 |
+# else if (input$typeplot == "Heatmap") {
|
|
| 879 |
+# js = paste("window.open('", group_comparison(TRUE, TRUE), "Heatmap.pdf')", sep="")
|
|
| 880 |
+# runjs(js); |
|
| 881 |
+# } |
|
| 882 |
+# else if (input$typeplot == "ComparisonPlot") {
|
|
| 883 |
+# js = paste("window.open('", group_comparison(TRUE, TRUE), "ComparisonPlot.pdf')", sep="")
|
|
| 884 |
+# runjs(js); |
|
| 885 |
+# } |
|
| 886 |
+# ) |
|
| 887 |
+# ) |
|
| 888 |
+# }) |
|
| 889 |
+ |
|
| 890 |
+ observeEvent(input$calculate,{
|
|
| 891 |
+ enable("Design")
|
|
| 892 |
+ enable("typeplot")
|
|
| 893 |
+ enable("WhichComp")
|
|
| 894 |
+ enable("download_code")
|
|
| 895 |
+ }) |
|
| 896 |
+ |
|
| 897 |
+ |
|
| 898 |
+} |
|
| 0 | 899 |
\ No newline at end of file |