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ui.R
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#
# This is the user-interface definition of a Shiny web application. You can
# run the application by clicking 'Run App' above.
#
# Find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com/
#
library(shiny)
library(shinyjs)
library(shinyBS)
library(ggplot2)
library(ggrepel)
library(PhosMap)
library(plotly)
library(colourpicker)
library(ggseqlogo)
library(pheatmap)
library(survminer)
library(survival)
library(zip)
library(stringr)
library(dplyr)
library(DT)
library(png)
library(svglite)
library(ggplotify)
library(shinyWidgets)
library(bslib)
library(PhosMap)
library(qpdf)
library(uwot)
library(pcaMethods)
library(rrcovNA)
library(impute)
library(e1071)
library(heatmaply)
library(ggdendro)
library(data.table)
library(tidyr)
library(FactoMineR)
library(factoextra)
ui <- renderUI(
fluidPage(
shinyjs::useShinyjs(),
useSweetAlert(),
tags$head(
HTML("<title>PhosMap</title>"),
HTML('
<script type="text/javascript" src="popper.js"></script>
<script> window.start.init({Palette:"palette1"})</script>
'),
tags$style(type = "text/css", "
body {padding-top: 70px;}
#loadmessage {
position: fixed;
top: -20px;
left: 0px;
width: 100%;
height:100%;
padding: 300px 0px 5px 0px;
text-align: center;
font-weight: bold;
font-size: 40px;
color: #000000;
background-color: #D6D9E4;
opacity:0.7;
z-index: 1050;
}
.manual_iframe {
width: 100%;
height: 100vh;
}
",
HTML("
.navbar-nav {float: right; font-size: 16px}
.warning {border-left: 8px solid;}
.tooltitle {text-align:center;}
.toolsubtitle {text-align:center;}
.downloadbutton {}
.viewbutton {}
.runbutton {color: #fff; background-color: #5DA61E; border-color: #ffacae;}
.loadfiledescription {text-align:left;margin-top:15px;margin-left:10px;margin-right:300px;font-size:190%;}
.analysisbutton {color: #fff; background-color: #7650E6; border-color: #ffacae; width:200px; height:40px; }
.plotbutton{color: #fff; background-color:#da5151; border-color: #ffacae; width:150px; height:40px; }
.warningbutton {color: #fff; background-color: #F01616; border-color: #ffacae;}
.runbuttondiv {text-align: right;}
.dropdown:hover .dropdown-menu {
display: block;
margin-top: 0;
}
#limmastatic{height:70vh !important;}
#limmainter{height:70vh !important;}
#samstatic{height:70vh !important;}
#saminter{height:70vh !important;}
#anovastatic{height:70vh !important;}
#anovainter{height:70vh !important;}
#timecourse{height:70vh !important;}
#kaptimecourseplot{height:70vh !important;}
#kapstep2plot{height:70vh !important;}
#kseastep2plot{height:80vh !important;}
#kseastep2plotmid{height:120vh !important;}
#kseastep2plotmini{height:150vh !important;}
#kseastep2plotxs{height:210vh !important;}
#resultnav {float: left;}
#resultnavdroppro {float: left;}
#mascotdemodropproresultnav {float: left;}
#usermascotnoproresultnav {float: left;}
#usermascotresultnav {float: left;}
#usermascotdropproresultnav {float: left;}
#demomaxresultnav {float: left;}
#demomaxdropproresultnav {float: left;}
#demomaxtmtresultnav {float: left;}
#usermaxtmtresultnav {float: left;}
#demodiannresultnav {float: left;}
#userdiannresultnav {float: left;}
#demosnresultnav {float: left;}
#usersnresultnav {float: left;}
#usermaxnoproresultnav {float: left;}
#usermaxresultnav {float: left;}
#usermaxdropproresultnav {float: left;}
#kapresultnav {float: left;}
")
)
),
conditionalPanel(
condition = "$('html').hasClass('shiny-busy')",
div(h2(strong("PhosMap Calculating..."), img(src = "rmd_loader.gif"), id = "loadmessage"))
),
navbarPage(
div("",img(src = "logo.svg", height = "60px", width = "115px", style = "padding-bottom:10px; padding-right:10px; margin-top: -12px")),
inverse = T,
id = "navbarpage",
position = "fixed-top",
tabPanel(
"Home",
icon = icon("house"),
column(
2,
radioGroupButtons(
inputId = "homenotice",
label = "",
choices = c("Log",
"Notice", "Intro"),
justified = TRUE,
selected = "Intro",
checkIcon = list(
yes = icon("face-smile"))
),
conditionalPanel(
condition = "input.homenotice == 'Log'",
panel(
"",
heading = "Update Log",
status = "warning",
h4("PhosMap 1.2.0 was released in December 2023."),
h5("Key features: "),
h5("- Support the processing of dia and tmt data."),
h5("- Introduce a sample quality checker to filter files for obtaining high-quality data."),
h4("PhosMap 1.1.0 was released in August 2023."),
h5("Key features: Introduce a quality inspector to facilitate iterative preprocessing for obtaining high-quality data."),
h4("PhosMap 1.0.0 was released in July 2023.")
)
),
conditionalPanel(
condition = "input.homenotice == 'Notice'",
panel(
"",
heading = "Notice",
status = "info",
HTML("The server currently operates on a single-thread and utilizes low-level hardware.
To enhance performance and unlock the full potential of PhosMap,
we recommend users consider analyzing their data using the server that is specifically designed for <b>small data sets</b>.
It is advisable to evaluate the possibility of upgrading to higher-level hardware,
considering the potential computational cost associated with the data, to fully maximize the capabilities of PhosMap."),
actionButton("viewinstall", "Tutorial video", icon("video")),
HTML(
"
<table id='help'>
<tr>
<th>Version</th>
<th>Preprocessing</th>
<th>Analysis<br>[Except MEA]</th>
<th>MEA</th>
</tr>
<tr>
<td>Online</td>
<td>✔ </td>
<td>✔</td>
<td>✖</td>
</tr>
<tr>
<td>Local</td>
<td>✔</td>
<td>✔</td>
<td>✔</td>
</tr>
</table>
<style>
#help th {
font-size: 12px;
font-weight: bold;
text-align: center;
background-color: #f2f2f2;
border: 1px solid black;
}
#help td {
font-size: 10px;
text-align: center;
padding: 10px;
border: 1px solid black;
}
</style>
"
)
)
),
conditionalPanel(
condition = "input.homenotice == 'Intro'",
panel(
"",
heading = "Introduction",
status = "success",
HTML("<p>PhosMap supports multiple function modules for full landscape of
phosphoproteomics data analyses including quality control, phosphosite
mapping, dimension reduction analysis, time course analysis, kinase
activity analysis and survival analysis. Various of publication ready
figures and tables could be generated via PhosMap. </p>
<p>- For users without bioinformatics skills, <b>web server</b> can be
used for analysis when the data volume is small. For larger data volumes,
<a href='https://github.com/liuzan-info/PhosMap' target='_blank'>a local version</a> of PhosMap can be utilized.
<p>- For users with bioinformatics skills, a downloadable <b><a href='https://github.com/liuzan-info/PhosMap' target='_blank'>R package</a></b>
is provided for more flexible analysis.
<p>Furthermore, our data flow is standardized, ensuring its strong scalability.
Therefore, if users have other analysis requirements, they are welcome to submit PR or issue on <a href='https://github.com/liuzan-info/PhosMap' target='_blank'>GitHub</a>.</p>"),
# HTML("<b>Related links:</b><br><p>R package:<a href='https://github.com/ecnuzdd/PhosMap'>https://github.com/ecnuzdd/PhosMap</a></p>
# <p>docker image:<a href='https://hub.docker.com/r/liuzandh/phosmap'>https://hub.docker.com/r/liuzandh/phosmap</a></p>
# <p>source code:<a href='https://github.com/liuzan-info/PhosMap'>https://github.com/liuzan-info/PhosMap</a></p>
# ")
)
)
),
column(
10,
h3(style = "text-align: center;", "PhosMap: An Ensemble Bioinformatic Platform to Empower One-stop Interactive Analysis of Quantitative Phosphoproteomics"),
div(style = "text-align:center;", img(src = "main.svg", height = "700px", width = "900px", style = "")),
),
column(
12,
br(),
hr(),
h5(style = "text-align: center;","This website is free and open to all users and there is no login requirement.")
)
),
tabPanel(
"Import Data",
icon = icon("upload", class = "fa-solid fa-upload"),
sidebarLayout(
sidebarPanel(
width = 3,
fluidRow(
column(4, h3("Import Data")),
column(6, actionButton("samplequalityinspector", "Sample Quality Control", icon = icon("magnifying-glass"))),
column(2, tags$div(title = "If pre-processed data is available, click this button to proceed directly to the analysis module and upload the data for analysis.",
actionButton("pre2analysis", NULL, icon = icon("paper-plane"))
))
),
wellPanel(
prettySwitch(
inputId = "loaddatatype",
label = "Load example data",
fill = TRUE,
status = "success",
value = TRUE
),
radioButtons("mstech", "MS-based Technique:",
choiceNames = list(
"label-free DDA",
"labeled DDA[TMT]",
"DIA"
),
choiceValues = list(
1,
2,
3
),
inline = TRUE
),
conditionalPanel(
condition = "input.mstech == 1",
radioGroupButtons(
inputId = "softwaretype",
label = "Searching Software:",
choices = list("MaxQuant" = 1, "Firmiana" = 2),
# direction = "vertical",
individual = TRUE,
selected = 1,
checkIcon = list(
yes = tags$i(class = "fa fa-circle",
style = "color: steelblue"),
no = tags$i(class = "fa fa-circle-o",
style = "color: steelblue")),
)
),
conditionalPanel(
condition = "input.mstech == 2",
radioGroupButtons(
inputId = "lddasoftwaretype",
label = "Searching Software:",
choices = list("MaxQuant" = 1),
selected = 1,
checkIcon = list(
yes = tags$i(class = "fa fa-circle",
style = "color: steelblue"),
no = tags$i(class = "fa fa-circle-o",
style = "color: steelblue")),
)
),
conditionalPanel(
condition = "input.mstech == 3",
radioGroupButtons(
inputId = "diasoftwaretype",
label = "Searching Software:",
choices = list("Spectronaut" = 1, "DIANN" = 2),
individual = TRUE,
selected = 1,
checkIcon = list(
yes = tags$i(class = "fa fa-circle",
style = "color: steelblue"),
no = tags$i(class = "fa fa-circle-o",
style = "color: steelblue")),
)
)
),
# label-free dda
conditionalPanel(
condition = "input.loaddatatype == true & input.mstech == 1",
h4("1. Experimental design file: "),
actionButton("viewbt1", "view", icon("eye"), class = "viewbutton"),
hr(style = "border-style: dashed;border-color: grey;")
),
# mascot
conditionalPanel(
condition = "input.loaddatatype == true & input.softwaretype == 2 & input.mstech == 1",
h4("2. Mascot xml file: "),
selectInput("mascotdemoxmlid", NULL, choices = c("Exp027015_F1_R1", "Exp027016_F1_R1", "Exp027017_F1_R1", "Exp027031_F1_R1", "Exp027032_F1_R1", "Exp027033_F1_R1", "Exp027046_F1_R1", "Exp027047_F1_R1", "Exp027048_F1_R1")),
hr(style = "border-style: dashed;border-color: grey;"),
# hr(),
h4("3. Phosphoproteomics peptide file: "),
selectInput("mascotdemopeptidefileid", NULL, choices = c("Exp027015_peptide", "Exp027016_peptide", "Exp027017_peptide", "Exp027031_peptide", "Exp027032_peptide", "Exp027033_peptide", "Exp027046_peptide", "Exp027047_peptide", "Exp027048_peptide")),
hr(style = "border-style: dashed;border-color: grey;"),
h4("4. Proteomics data[optional]"),
br(style = "line-height:1px;"),
h4("4.1 Proteomics experimental design file: "),
actionButton("viewbt5", "view", icon("eye"), class = "viewbutton"),
h4("4.2 Profiling file: "),
selectInput("mascotdemoproid", NULL, choices = c("Exp026982_gene", "Exp026983_gene", "Exp026995_gene", "Exp026996_gene", "Exp027008_gene", "Exp027009_gene"))
),
# Maxquant label-free
conditionalPanel(
condition = "input.loaddatatype == true & input.softwaretype == 1 & input.mstech == 1",
h4("2. Phospho (STY)Sites.txt: "),
actionButton("viewdemomaxphosbt", "view", icon("eye"), class = "viewbutton"),
hr(style = "border-style: dashed;border-color: grey;"),
# hr(),
h4("3. Proteomics data[optional]"),
br(),
h4("3.1 Proteomics experimental design file: "),
actionButton("viewdemomaxprodesignbt", "view", icon("eye"), class = "viewbutton"),
h4("3.2 proteinGroups.txt: "),
actionButton("viewdemomaxprobt", "view", icon("eye"), class = "viewbutton"),
),
# Maxquant tmt
conditionalPanel(
condition = "input.loaddatatype == true & input.lddasoftwaretype == 1 & input.mstech == 2",
h4("1. Experimental design file: "),
actionButton("viedemomaxtmtphosbt1", "view", icon("eye"), class = "viewbutton"),
hr(style = "border-style: dashed;border-color: grey;"),
h4("2. Phospho (STY)Sites.txt: "),
actionButton("viewdemomaxtmtphosbt2", "view", icon("eye"), class = "viewbutton"),
),
# dia
conditionalPanel(
condition = "input.loaddatatype == true & input.mstech == 3",
h4("1. Experimental design file: "),
actionButton("dianndemoviewbt1", "view", icon("eye"), class = "viewbutton"),
hr(style = "border-style: dashed;border-color: grey;")
),
# SN
conditionalPanel(
condition = "input.loaddatatype == true & input.diasoftwaretype == 1 & input.mstech == 3",
h4("2. Report.xls: "),
actionButton("sndemoviewbt2", "view", icon("eye"), class = "viewbutton"),
),
# diann
conditionalPanel(
condition = "input.loaddatatype == true & input.diasoftwaretype == 2 & input.mstech == 3",
h4("2. report.tsv: "),
actionButton("dianndemoviewbt2", "view", icon("eye"), class = "viewbutton"),
),
## user data
# shared phosphoproteomics design file
conditionalPanel(
condition = "input.loaddatatype == false",
h4("1. Experimental design file: "),
downloadButton("userdesigndl", "Download Template", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("userdesigninstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("updesign", NULL, accept = ".txt"),
hidden(
div(
id = "hiddenview1",
actionButton("viewbt4", "view", icon("eye"))
)
),
hr(style = "border-style: dashed;border-color: grey;")
),
# mascot
conditionalPanel(
condition = "input.loaddatatype == false & input.softwaretype == 2 & input.mstech == 1",
h4("2. Mascot xml file: "),
downloadButton("usermascotxmldl", "Download Demo", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("usermascotxmlinstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("upmascot", NULL, accept = "application/zip"),
uiOutput("masui"),
hr(style = "border-style: dashed;border-color: grey;"),
h4("3. Phosphoproteomics peptide file: "),
downloadButton("usermascotpepdl", "Download Demo", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("usermascotpepinstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("uppeptide", NULL, accept = "application/zip"),
uiOutput("pepui"),
hr(style = "border-style: dashed;border-color: grey;"),
h4("4. Proteomics data[optional]"),
br(),
h4("4.1 Proteomics experimental design file: "),
downloadButton("userpromascotdesigndl", "Download Template", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("userpromascotdesigninstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("upprodesign", NULL, accept = ".txt"),
uiOutput("prodesignui"),
hidden(
div(
id = "prohiddenview",
actionButton("proviewbt", "view", icon("eye"))
)
),
h4("4.2 Profiling file: "),
downloadButton("usermascotprodl", "Download Demo", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("usermascotprofilinginstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("upprogene", NULL, accept = "application/zip"),
uiOutput("progeneui"),
),
# Maxquant
conditionalPanel(
condition = "input.loaddatatype == false & input.softwaretype == 1 & input.mstech == 1",
h4("2. Phospho (STY)Sites.txt: "),
downloadButton("userphosmaxdl", "Download Demo", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("userphosmaxinstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("upusermaxphos", NULL, accept = ".txt"),
hidden(
div(
id = "hidviewusermaxphosbt",
actionButton("viewusermaxphosbt", "view", icon("eye"), class = "viewbutton")
),
div(
id = "hidviewusermaxphosbtwarning",
actionButton("viewusermaxphosbtwarning", "error...", icon("triangle-exclamation"), class = "warningbutton")
)
),
hr(style = "border-style: dashed;border-color: grey;"),
h4("3. Proteomics data[optional]"),
br(),
h4("3.1 Proteomics experimental design file: "),
downloadButton("userprodesigndl", "Download Template", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("userprodesigninstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("upusermaxprodesign", NULL, accept = ".txt"),
hidden(
div(
id = "hidviewusermaxprodesignbt",
actionButton("viewusermaxprodesignbt", "view", icon("eye"), class = "viewbutton")
)
),
h4("3.2 proteinGroups.txt: "),
downloadButton("userpromaxdl", "Download Demo", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("userpromaxinstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("upusermaxpro", NULL, accept = ".txt"),
hidden(
div(
id = "hidviewusermaxprobt",
actionButton("viewusermaxprobt", "view", icon("eye"), class = "viewbutton")
),
div(
id = "hidviewusermaxprobtwarning",
actionButton("viewusermaxprobtwarning", "error...", icon("triangle-exclamation"), class = "warningbutton")
)
)
),
# Maxquant tmt
conditionalPanel(
condition = "input.loaddatatype == false & input.lddasoftwaretype == 1 & input.mstech == 2",
h4("2. Phospho (STY)Sites.txt: "),
downloadButton("userphosmaxtmtdl", "Download Demo", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("userphosmaxtmtinstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("upusermaxtmtphos", NULL, accept = ".txt"),
hidden(
div(
id = "hidviewusermaxtmtphosbt",
actionButton("viewusermaxtmtphosbt", "view", icon("eye"), class = "viewbutton")
),
div(
id = "hidviewusermaxtmtphosbtwarning",
actionButton("viewusermaxtmtphosbtwarning", "error...", icon("triangle-exclamation"), class = "warningbutton")
)
)
),
# SN
conditionalPanel(
condition = "input.loaddatatype == false & input.diasoftwaretype == 1 & input.mstech == 3",
h4("2. Report.xls: "),
downloadButton("userphossndl", "Download Demo", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("userphossninstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("upusersnphos", NULL, accept = ".xls"),
hidden(
div(
id = "hidviewusersnphosbt",
actionButton("viewusersnphosbt", "view", icon("eye"), class = "viewbutton")
),
div(
id = "hidviewusersnphosbtwarning",
actionButton("viewusersnphosbtwarning", "error...", icon("triangle-exclamation"), class = "warningbutton")
)
)
),
# diann
conditionalPanel(
condition = "input.loaddatatype == false & input.diasoftwaretype == 2 & input.mstech == 3",
h4("2. report.tsv: "),
downloadButton("userphosdianndl", "Download Demo", icon = NULL,
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
actionButton("userphosdianninstruction", "View Upload Instructions",
style = "padding: 2px 5px; font-size: 12px; line-height: 1;"),
fileInput("upuserdiannphos", NULL, accept = ".tsv"),
hidden(
div(
id = "hidviewuserdiannphosbt",
actionButton("viewuserdiannphosbt", "view", icon("eye"), class = "viewbutton")
),
div(
id = "hidviewuserdiannphosbtwarning",
actionButton("viewuserdiannphosbtwarning", "error...", icon("triangle-exclamation"), class = "warningbutton")
)
)
)
),
mainPanel(
width = 9,
hr(),
# tabsetPanel(
# tabPanel(
# "Data Overview",
conditionalPanel(
condition = "input.loaddatatype == true",
htmlOutput("html"),
dataTableOutput("viewedfile")
),
conditionalPanel(
condition = "input.loaddatatype == false",
htmlOutput("html2"),
dataTableOutput("viewedfile2"),
)
)
)
),
tabPanel(
"Preprocessing",
icon = icon("arrows-spin"),
fluidRow(
column(4, NULL),
column(4, h2(style = "text-align: center;", "Preprocessing")),
column(2, actionButton("qualityinspector", "Quality Inspector", icon = icon("magnifying-glass"))),
column(2, actionButton("maxpre2analysis", "Go to analysis tools", icon = icon("paper-plane"))),
conditionalPanel( # label-free dda + mascot
condition = "input.softwaretype == 2 & input.mstech == 1",
column(
12,
conditionalPanel(
condition = "input.loaddatatype == true",
progressBar(id = "preprobar", value = 0, status = "success")
),
conditionalPanel(
condition = "input.loaddatatype == false",
progressBar(id = "userpreprobar", value = 0, status = "success")
),
),
column(
3,
panel(
heading = "Step1: Parser",
status = "primary",
h5("no parameter"),
conditionalPanel(
condition = "input.loaddatatype == true",
div(
class = "runbuttondiv",
actionButton(
"parserbt01",
"",
icon("play"),
class = "runbutton"
)
)
),
conditionalPanel(
condition = "input.loaddatatype == false",
div(
class = "runbuttondiv",
actionButton(
"parserbt11",
"",
icon("play"),
class = "runbutton"
)
)
)
),
panel(
heading = "Step2: p-site Quality Control & Merging",
status = "warning",
numericInput(
"qcscore",
"minimum score:",
20,
max = 100,
min = 0,
step = 0.5
),
bsTooltip(
"qcscore",
"the minimum score of credible peptides",
placement = "right",
options = list(container = "body")
),
numericInput(
"qcfdr",
"minimum FDR:",
0.01,
max = 0.02,
min = 0,
step = 0.002
),
bsTooltip(
"qcfdr",
"the minimum FDR of credible peptides",
placement = "right",
options = list(container = "body")
),
conditionalPanel(
condition = "input.loaddatatype == true",
div(
class = "runbuttondiv",
actionButton(
"mergingbt0",
"",
icon("play"),
class = "runbutton"
)
)
),
conditionalPanel(
condition = "input.loaddatatype == false",
div(
class = "runbuttondiv",
actionButton(
"mergingbt1",
"",
icon("play"),
class = "runbutton"
)
)
)
),
panel(
heading = "Step3: Mapping",
status = "danger",
selectInput("species", "species:", choices = c("human", "mouse", "rattus")),
selectInput("idtype", "id type", choices = c("RefSeq_Protein_GI", "RefSeq_Protein_Accession", "Uniprot_Protein_Accession", "GeneID")),
selectInput("fastatype", "fasta type", choices = c("refseq", "uniprot")),
conditionalPanel(
condition = "input.loaddatatype == true",
div(
class = "runbuttondiv",
actionButton(
"mappingbt01",
"",
icon("play"),
class = "runbutton"
)
)
),
conditionalPanel(
condition = "input.loaddatatype == false",
div(
class = "runbuttondiv",
actionButton(
"mappingbt11",
"",
icon("play"),
class = "runbutton"
)
)
)
)
),
column(
3,
panel(
heading = "Step4: Filtering & Normalization & Imputation",
footer = "This step also filters modification types, remaining only 'S/T/Y'",
status = "info",
conditionalPanel(
condition = "input.loaddatatype == true",
numericInput("masphosNAthre", label = "minimum detection frequency: ", value = 1, min = 0),
),
bsTooltip(
"masphosNAthre",
# "xxxx",
"minimum detection frequency for per locus, equivalents to the number of samples minus the number of ‘0’ value",
placement = "right",
options = list(container = "body")
),
conditionalPanel(
condition = "input.loaddatatype == false",
numericInput("usermasphosNAthre", label = "minimum detection frequency: ", value = 1, min = 0),
),
bsTooltip(
"usermasphosNAthre",
"minimum detection frequency for per locus, equivalents to the number of samples minus the number of ‘0’ value",
placement = "right",
options = list(container = "body")
),
selectInput("mascotnormmethod", label = "normalization method: ", choices = c("global", "median")),
column(12,
prettyToggle(
inputId = "democountbygroup",
label_on = "impute by group",
icon_on = icon("check"),
status_on = "info",
status_off = "warning",
label_off = "impute globally ",
icon_off = icon("xmark"),
value = FALSE
)
),
selectInput(
"mascotimputemethod",
label = "imputation method: ",
choices = list(
"globally"= c("0", "minimum", "minimum/10", "impseq", "impseqrob", "colmedian"),
"globally_or_bygroup" = c("bpca", "lls", "knnmethod", "rowmedian")
),
selected = "minimum/10"
),
# selectInput("mascotimputemethod", label = "imputation method: ", choices = c("0", "minimum", "minimum/10", "bpca", "lls", "impseq", "impseqrob", "knnmethod", "colmedian", "rowmedian"), selected = "minimum/10"),
numericInputIcon(
inputId = "top",
label = "top",
value = 100,
step = 1,
max = 100,
min = 1,
icon = list(NULL, icon("percent"))
),
bsTooltip(
"top",
"compute row maximum each psites, sort row maximum in decreasing order and keep top N (percentage).",
placement = "right",
options = list(container = "body")
),
conditionalPanel(
condition = "input.loaddatatype == true",
div(
class = "runbuttondiv",
actionButton(
"normalizationbt01",
"",
icon("play"),
class = "runbutton"
)
)
),
conditionalPanel(
condition = "input.loaddatatype == false",
div(
class = "runbuttondiv",
actionButton(
"normalizationbt11",
"",
icon("play"),
class = "runbutton"
)
)
)
),
conditionalPanel(
condition = "input.loaddatatype == true",
panel(
heading = "Step5: Normalization based on proteomics data",
status = "success",
prettyToggle(
inputId = "useprocheck1",
label_on = "With proteomics data",
icon_on = icon("check"),
status_on = "info",
status_off = "warning",
label_off = "Without proteomics data",
icon_off = icon("xmark"),
value = TRUE
),
conditionalPanel(
condition = "input.useprocheck1 == 1",
wellPanel(
h5("Proteomics data preprocessing parameters", style = "color: grey;"),
numericInput("masuscutoff", label = "US cutoff: ", value = 1),
numericInput("masproNAthre", label = "minimum detection frequency: ", value = 1, min = 0),
bsTooltip(
"masproNAthre",
"minimum detection frequency for per locus, equivalents to the number of samples minus the number of ‘0’ value",
placement = "right",
options = list(container = "body")
),
selectInput("mascotpronormmethod", label = "normalization method: ", choices = c("global", "median")),
selectInput("mascotproimputemethod", label = "imputation method: ", choices = c("0", "minimum", "minimum/10"), selected = "minimum/10")
),
selectInput("mascotcontrol", label = "control label: ", choices = c("0", "6", "48", "no control")),
div(
class = "runbuttondiv",
actionButton(
"normalizationbt02",
"",
icon("play"),
class = "runbutton"
)
)
),
conditionalPanel(
condition = "input.useprocheck1 == 0",
wellPanel(
h5("After 'Step1-Step2-Step3-Step4' have been run, you can click 'Go to analysis tools'", style = "color: grey;")
)
)
)
),
conditionalPanel(
condition = "input.loaddatatype == false",
uiOutput("userusepro")
)
),
column(
6,
conditionalPanel(
condition = "input.loaddatatype == true & input.useprocheck1 == 1",
navbarPage(
title = "Result",
id = "resultnav",
tabPanel(
"Step 1",
value = "demomascotstep1val",
h4("Peptide identification files with psites scores:"),
uiOutput("demomascotparserui")
),
tabPanel(
"Step 2",
value = "demomascotstep2val",
h4("Peptide data frame through phosphorylation sites quality control:"),
uiOutput("mergingui0"),
column(11,dataTableOutput("viewedmerging")),
column(1,downloadBttn(
outputId = "viewedmerging_dl",
label = "",
style = "material-flat",
color = "default",
size = "sm"
))
),
tabPanel(
"Step 3",
value = "demomascotstep3val",
h4("Data frame mapped ID to Gene Symbol:"),
uiOutput("mapping02"),
column(11,dataTableOutput("viewedmapping02")),
column(1,downloadBttn(
outputId = "viewedmapping02_dl",
label = "",
style = "material-flat",
color = "default",
size = "sm"
))
),
tabPanel(
"Step 4",
value = "demomascotstep4val",
h4("PhosMap Matrix:"),
column(11,dataTableOutput("viewednorm01")),
column(1,downloadBttn(
outputId = "viewednorm01_dl",
label = "",
style = "material-flat",
color = "default",
size = "sm"
))
),
tabPanel(
"Step 5",
value = "demomascotstep5val",
h4("PhosMap Matrix:"),
column(11,dataTableOutput("viewednorm02")),
column(1,downloadBttn(
outputId = "viewednorm02_dl",
label = "",
style = "material-flat",
color = "default",
size = "sm"
)),
br(),
h4("Proteomics data frame:"),
column(11,dataTableOutput("viewednorm02pro")),
column(1,downloadBttn(
outputId = "viewednorm02pro_dl",
label = "",
style = "material-flat",
color = "default",
size = "sm"
))
)
)
),
conditionalPanel(
condition = "input.loaddatatype == true & input.useprocheck1 == 0",
navbarPage(
title = "Result",
id = "resultnavdroppro",
tabPanel(
"Step 1",
value = "demomascotdropprostep1val",
h4("Peptide identification files with psites scores:"),
uiOutput("demomascotdropproparserui")
),
tabPanel(
"Step 2",
value = "demomascotdropprostep2val",
h4("Peptide data frame through phosphorylation sites quality control:"),
column(11,dataTableOutput("viewedmergingdroppro")),
column(1,downloadBttn(
outputId = "viewedmergingdroppro_dl",
label = "",
style = "material-flat",
color = "default",
size = "sm"
))
),
tabPanel(