Nothing
inst/HaDeX/ui.R
In HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data
source("data-work.R")
options(spinner.color="#715D91")
ui <- fluidPage(theme = "HaDeX_theme.css",
#titlePanel("HaDeX"), #: analysis of data from hydrogen deuterium exchange-mass spectrometry"),
title = "HaDeX",
useShinyjs(),
tags$head(includeScript("ga.js"),
tags$link(rel="stylesheet",
href="mobile_version.css",
media="screen and (max-width: 600px)"),
tags$script(type="text/javascript",
src="detect-element-resize.js")),
tags$div(
class = "site-backbone",
tags$div(
class = "logo-panel",
img(src = "mock_logo.png", class = "logo")
),
tabsetPanel(type = "pills",
tabPanel("Start",
h3("Welcome to HaDeX!"),
h4("Thank you for using our tool."),
#h4("For any additional information, please see the documnetation available online.", a(href = "https://hadexversum.github.io/HaDeX/", "Check it out!")),
h4("Questions/feature requests/commercial applications: hadex@ibb.waw.pl"),
includeMarkdown("readmes/about.md"),
img(class='funding-icons',
src='funding_icons.png'),
br()
),
tabPanel("Input data",
br(),
h4("Upload your file. Otherwise you will see example data."),
h4("Currently HaDeX is limited to `cluster` files from DynamX 3.0 and 2.0"),
h4("Accepted file extensions: .csv, .xsl, .xslx. "),
h4("Supplied file should containt at least two repetitions of the measurement fot the uncertainty to be calculated."),
h4("If supplied file contains modificated peptides, maximal exchange control cannot be applied."),
#
fluidRow(
column(3,
fileInput(
inputId = "data_file",
label = "Choose file:",
multiple = FALSE,
accept = c(".csv", ".xlsx", ".xls"),
placeholder = "No file selected")),
column(4,
h5("File status:"),
tags$div(
class = "file-status-message",
withSpinner(textOutput("data_file_info"))
))
),
#
h4("Please be aware that loading data (including example file) may take a while. Be patient."),
h4("In order for program to behave correctly, please make sure supplied file fulfills following requirements:"),
tags$button("Show requirements",
class = "collapse-button",
style = "width: unset",
`data-toggle`="collapse",
`data-target`="#reqs"),
tags$div(
id = "reqs",
style = "width: min-content",
class = "hideable",
tableOutput("file_req")),
h3("Settings"),
h4("Values chosen here are propagated into all of the tables for coherent results."),
fluidRow(
column(2,
selectInput_h(inputId = "chosen_protein",
label = "Choose protein: ",
choices = c("db_CD160")),
selectInput_h(inputId = "chosen_control",
label = "Choose maximal exchange control for chosen protein: ",
choices = c("db_CD160 | CD160 | 1440")),
numericInput_h(inputId = "deut_concentration",
label = "Choose D20 concentration [%]: ",
value = 100,
min = 0, max = 100, step = 1),
numericInput_h(inputId = "sequence_start_shift",
label = "Move sequence start:",
value = 1,
step = 1),
numericInput_h(inputId = "sequence_length",
label = "Correct sequence length:",
value = 300,
step = 1),
# h5("If C-terminal of is not covered by peptides,
# enter its correct position."),
textOutput("sequence_length_exp_info")
)
),
br(),
br(),
br()
),
tabPanel("Woods plot",
br(),
sidebarPanel(
class = "scrollable",
h3("Select parameters for the plot."),
fluidRow(checkboxInput_h(inputId = "theory",
label = "Theoretical calculations",
value = FALSE)),
radioButtons_h(inputId = "calc_type",
label = "Choose values type:",
choices = c("relative", "absolute"),
selected = "relative"),
h4("Comparison plot parameters:"),
h5("Choose time parameters:"),
splitLayout(
div(id = "in_time_part",
selectInput_h(inputId = "in_time",
label = "IN",
choices = c("0", "1", "5", "25", "1440"))
),
selectInput_h(inputId = "chosen_time",
label = "CHOSEN",
choices = c("0", "1", "5", "25", "1440")),
div(id = "out_time_part",
selectInput_h(inputId = "out_time",
label = "OUT",
choices = c("0", "1", "5", "25", "1440"))
)
),
##
fluidRow(
column(6,
h5("Choose states for comparison:"),
checkboxGroupInput_h(inputId = "compare_states",
label = "",
choices = c("CD160", "CD160VEM"),
selected = c("CD160", "CD160VEM")),
class = "states-to-compare-column"),
column(6,
helper(tags$button("Adjust colors",
class = "collapse-button",
`data-toggle`="collapse",
`data-target`="#colorss"),
content = "adjust_colors", type = "markdown", buttonLabel = "Okay",
easyClose = TRUE, colour = "#F8F1FF"),
tags$div(
class = "hideable",
id = "colorss",
uiOutput("states_colors")
),
class = "states-colors-column"
)
),
##
h4("Woods plot parameters:"),
splitLayout(
selectInput_h(inputId = "state_first",
label = "State 1",
choices = c("CD160", "CD160VEM")),
selectInput_h(inputId = "state_second",
label = "State 2",
choices = c("CD160", "CD160VEM"))
),
splitLayout(
selectInput_h(inputId = "confidence_limit",
label = "Confidence limit 1:",
choices = c("20%" = 0.2, "50%" = 0.5, "80%" = 0.8, "90%" = 0.9, "95%" = 0.95, "98%" = 0.98, "99%" = 0.99, "99.9%" = 0.999),
selected = 0.98),
selectInput_h(inputId = "confidence_limit_2",
label = "Confidence limit 2:",
choices = c("20%" = 0.2, "50%" = 0.5, "80%" = 0.8, "90%" = 0.9, "95%" = 0.95, "98%" = 0.98, "99%" = 0.99, "99.9%" = 0.999),
selected = 0.99)
),
##
h4("Zoom:"),
sliderInput(inputId = 'comp_plot_y_range',
label = 'Choose y range for comparison plot:',
min = -200,
max = 200,
value = c(0, 120),
step = 10,
width = "100%"),
sliderInput(inputId = 'woods_plot_y_range',
label = 'Choose y range for Woods plot:',
min = -200,
max = 200,
value = c(-50, 50),
step = 10),
sliderInput(inputId = 'plot_x_range',
label = 'Choose x range for both plots:',
min = 0,
max = 300,
value = c(0, 300) #,
# ticks = seq(0, 300, 1) # fix for new shiny
),
##
tags$button("Adjust labels",
class = "collapse-button",
`data-toggle`="collapse",
`data-target`="#labs"),
tags$div(
class = "hideable",
id = "labs",
textInput(inputId = "comparison_plot_title",
label = "Comparison plot title:",
value = ""),
textInput(inputId = "comparison_plot_x_label",
label = "Comparison plot axis x label:",
value = "Position in sequence"),
textInput(inputId = "comparison_plot_y_label",
label = "Comparison plot axis y label:",
value = ""),
textInput(inputId = "woods_plot_title",
label = "Woods plot title:",
value = ""),
textInput(inputId = "woods_plot_x_label",
label = "Woods plot axis x label:",
value = "Position in sequence"),
textInput(inputId = "woods_plot_y_label",
label = "Woods plot axis y label:",
value = "")
)
),
mainPanel(
class = "scrollable",
tabsetPanel(
tabPanel("Comparison plot",
br(),
plotOutput_h("comparisonPlot", hover = hoverOpts("comparisonPlot_hover", delay = 10, delayType = "debounce")),
downloadButton("comparisonPlot_download_button",
"Save chart (.svg)")),
tabPanel("Data",
br(),
DT::dataTableOutput("comparisonPlot_data"))),
uiOutput("comparisonPlot_debug"),
br(),
tabsetPanel(
tabPanel("Woods plot",
br(),
div(style = "position:relative",
plotOutput_h("differentialPlot", hover = hoverOpts("differentialPlot_hover", delay = 10, delayType = "debounce")),
uiOutput("differentialPlot_debug")),
downloadButton("differentialPlot_download_button",
"Save chart (.svg)")),
tabPanel("Data",
br(),
DT::dataTableOutput("differentialPlot_data")))
)
),
tabPanel("Coverage",
br(),
sidebarPanel(
class = "scrollable",
radioButtons(
inputId = 'chosen_state',
label = 'Choose state:',
choices = c('CD160', 'CD160_HVEM'),
selected = 'CD160'
),
sliderInput(
inputId = 'plot_range',
label = 'Choose range:',
min = 1,
max = 300,
value = c(1, 300) #,
# ticks = seq(1, 300, 1) fix for shiny
)
),
mainPanel(
class = "scrollable",
tabsetPanel(
tabPanel("Peptide Coverage",
br(),
withSpinner(plotOutput("stateOverlap", hover = hoverOpts("stateOverlap_hover", delay = 10, delayType = "debounce"))),
uiOutput("stateOverlap_debug"),
downloadButton("stateOverlap_download_button",
"Save chart (.svg)")),
tabPanel("Data",
br(),
DT::dataTableOutput("stateOverlap_data"))
),
br(),
tabsetPanel(
tabPanel("Position Frequency",
br(),
div(style = "position:relative;",
withSpinner(plotOutput("stateOverlapDist", hover = hoverOpts("stateOverlapDist_hover", delay = 10, delayType = "debounce"))),
uiOutput("stateOverlapDist_debug")),
downloadButton("stateOverlapDist_download_button",
"Save chart (.svg)")
),
tabPanel("Data",
br(),
DT::dataTableOutput("stateOverlapDist_data"))
)
)
),
tabPanel("Sequence data",
h3('Protein name'),
h4(textOutput("protein_name"), class = "monospaced"),
h3('Reconstructed sequence'),
htmlOutput("sequenceName", container = tags[["span"]], class = "monospaced"),
br(),
wellPanel(
sidebarLayout(
sidebarPanel(
fluidRow(
column(6,
tableOutput("protein_stats"),
br(),
checkboxGroupInput(
inputId = "hydro_prop",
label = "Hydro-",
choices = c(
"Hydrophilic" = "philic",
"Hydrophobic" = "phobic"),
selected = c("philic", "phobic"))
),
column(6,
br()
)
)
),
mainPanel(withSpinner(plotOutput("aminoDist", hover = hoverOpts("aminoDist_hover", delay = 10, delayType = "debounce"))),
uiOutput("aminoDist_debug"),
downloadButton("aminoDist_download_button",
"Save chart (.svg)"),
p("Source: Kyte, J., and Doolittle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol 157, 105–132."))
)
)
),
tabPanel("Uptake curves",
br(),
sidebarPanel(
class = "scrollable",
h3("Select parameters for the plot."),
checkboxInput_h(inputId = "kin_theory",
label = "Theoretical calculations",
value = FALSE),
radioButtons_h(inputId = "kin_calc_type",
label = "Choose values type:",
choices = c("relative", "absolute"),
selected = "relative"),
div(id = "kin_time_part",
h5("Choose time parameters:"),
splitLayout(
div(id = "kin_in_time_part",
selectInput_h(inputId = "kin_in_time",
label = "IN",
choices = c("0", "1", "5", "25", "1440"))
),
div(id = "kin_out_time_part",
selectInput_h(inputId = "kin_out_time",
label = "OUT",
choices = c("0", "1", "5", "25", "1440")))
)),
h5("Choose peptide:"),
dataTableOutput_h("peptide_list_data"), ## !!
actionButton(inputId = "reset_peptide_list",
label = "Reset chosen peptides"),
br(),
br(),
br(),
sliderInput(inputId = 'kin_plot_y_range',
label = 'Choose y range for the plot:',
min = -50,
max = 200,
value = c(-10, 100),
step = 10),
tags$button("Adjust labels",
class = "collapse-button",
`data-toggle`="collapse",
`data-target`="#kin-labs"),
tags$div(
class = "hideable",
id = "kin-labs",
textInput(inputId = "kin_plot_title",
label = "Uptake curve title:",
value = "Uptake curve for chosen peptides"),
textInput(inputId = "kin_plot_x_label",
label = "Uptake curve axis x label:",
value = "Time point [min]"),
textInput(inputId = "kin_plot_y_label",
label = "Uptake curve axis y label:",
value = "Deuteration")
)
),
mainPanel(
tabsetPanel(
tabPanel(
"Uptake curve",
br(),
plotOutput_h("kinetic_plot_chosen_peptides", hover = hoverOpts("kinetic_plot_chosen_peptides_hover", delay = 10, delayType = "debounce"), height = 600),
uiOutput("kinetic_plot_chosen_peptides_debug"),
downloadButton("kineticPlot_download_button",
"Save chart (.svg)")),
tabPanel("Data",
br(),
DT::dataTableOutput("kin_plot_data"))
)
)
),
#
tabPanel("Quality control",
br(),
sidebarPanel(
h3("Select parameters for the plot."),
h5("The plot can be rendered only for relative experimental values."),
selectInput_h(inputId = "qc_in_time",
label = "Choose in time: ",
choices = c("0", "1", "5", "25", "1440")),
selectInput_h(inputId = "qc_chosen_time",
label = "Choose time: ",
choices = c("0", "1", "5", "25", "1440")),
selectInput_h(inputId = "qc_state_first",
label = "State 1",
choices = c("CD160", "CD160VEM")),
selectInput_h(inputId = "qc_state_second",
label = "State 2",
choices = c("CD160", "CD160VEM"))
),
mainPanel(
tabsetPanel(
tabPanel("Quality control plot",
br(),
plotOutput_h("quality_control_plot", hover = hoverOpts("quality_control_plot_hover", delay = 10, delayType = "debounce"), height = 600),
uiOutput("quality_control_plot_debug"),
downloadButton("quality_control_plot_download_button",
"Save chart (.svg)"),
br(),
h4("This function plots the change in the uncertainty of deuteration levels as a function of incubation time. The uncertainty is averaged over all peptides available at a given time point in a selected state. This chart has a double function: firstly, it allows checking if the measurement uncertainty is decreasing over time (which is the expected behaviour) and the second one helps to plan the appropriate incubation length for the tested protein (whether we obtain the desired data reliability values).")
),
tabPanel("Data",
br(),
DT::dataTableOutput("quality_control_plot_data"))
)
)
),
tabPanel("Summary",
br(),
fluidRow(
withSpinner(DT::dataTableOutput("summary_table"))
),
includeMarkdown("./readmes/summary.md")
),
tabPanel("Report",
br(),
sidebarPanel(width = 8,
h4("Choose items for report:"),
fluidRow(
column(6,
checkboxInput(inputId = "export_overlap_dist",
label = "Position Frequency",
value = TRUE),
checkboxInput(inputId = "export_overlap_graph",
label = "Peptide Coverage",
value = TRUE),
checkboxInput(inputId = "export_comparison_plot",
label = "Comparison Plot",
value = TRUE),
checkboxInput(inputId = "export_theo_comparison_plot",
label = "Theoretical Comparison Plot",
value = TRUE),
checkboxInput(inputId = "export_woods_plot",
label = "Woods Plot",
value = TRUE),
checkboxInput(inputId = "export_theo_woods_plot",
label = "Theoretical Woods Plot",
value = TRUE),
checkboxInput(inputId = "export_kin_plot",
label = "Uptake Curve",
value = FALSE),
checkboxInput(inputId = "export_theo_kin_plot",
label = "Theoretical Uptake Curve",
value = FALSE),
checkboxInput(inputId = "export_quality_control_plot",
label = "Quality Control Plot",
value = FALSE)),
column(6,
checkboxInput(inputId = "export_overlap_dist_data",
label = "Position Frequency Data"),
checkboxInput(inputId = "export_overlap_graph_data",
label = "Peptide Coverage Data"),
checkboxInput(inputId = "export_comparison_plot_data",
label = "Comparison Plot Data"),
checkboxInput(inputId = "export_theo_comparison_plot_data",
label = "Theoretical Comparison Plot Data"),
checkboxInput(inputId = "export_woods_plot_data",
label = "Woods Plot Data"),
checkboxInput(inputId = "export_theo_woods_plot_data",
label = "Theoretical Woods Plot Data"),
checkboxInput(input = "export_kin_plot_data",
label = "Uptake Curve Data"),
checkboxInput(inputId = "export_theo_kin_plot_data",
label = "Theoretical Uptake Curve Data"),
checkboxInput(inputId = "export_quality_control_plot_data",
label = "Quality Control Plot Data"))),
br(),
h5("Elements chosen for report have the same parameters as chosen in panel e.g. axis range and title. Adjust parameters for plots as needed in the report."),
br(),
downloadButton(outputId = "export_action",
label = " Create report!",
icon = icon("fas fa-download"))
)
)
)
),
tags$div(
class = "mobile-site-backbone",
tags$div(
class = "logo-panel",
img(src = "mock_logo.png", class = "logo")
),
tags$div(
class = "mobile-information",
h3("Welcome to HaDeX website!"),
h4("For better user experience please use device with wider screen (at least 900px)."),
img(src='funding_icons.png', height = 100)
)
),
tags$script(type="text/javascript",
src="resize-logo-panel.js")
)
#tags$div(class = "logo-container",
# tags$img(source = "www/mock_logo.png"))
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source("data-work.R")
options(spinner.color="#715D91")
ui <- fluidPage(theme = "HaDeX_theme.css",
#titlePanel("HaDeX"), #: analysis of data from hydrogen deuterium exchange-mass spectrometry"),
title = "HaDeX",
useShinyjs(),
tags$head(includeScript("ga.js"),
tags$link(rel="stylesheet",
href="mobile_version.css",
media="screen and (max-width: 600px)"),
tags$script(type="text/javascript",
src="detect-element-resize.js")),
tags$div(
class = "site-backbone",
tags$div(
class = "logo-panel",
img(src = "mock_logo.png", class = "logo")
),
tabsetPanel(type = "pills",
tabPanel("Start",
h3("Welcome to HaDeX!"),
h4("Thank you for using our tool."),
#h4("For any additional information, please see the documnetation available online.", a(href = "https://hadexversum.github.io/HaDeX/", "Check it out!")),
h4("Questions/feature requests/commercial applications: hadex@ibb.waw.pl"),
includeMarkdown("readmes/about.md"),
img(class='funding-icons',
src='funding_icons.png'),
br()
),
tabPanel("Input data",
br(),
h4("Upload your file. Otherwise you will see example data."),
h4("Currently HaDeX is limited to `cluster` files from DynamX 3.0 and 2.0"),
h4("Accepted file extensions: .csv, .xsl, .xslx. "),
h4("Supplied file should containt at least two repetitions of the measurement fot the uncertainty to be calculated."),
h4("If supplied file contains modificated peptides, maximal exchange control cannot be applied."),
#
fluidRow(
column(3,
fileInput(
inputId = "data_file",
label = "Choose file:",
multiple = FALSE,
accept = c(".csv", ".xlsx", ".xls"),
placeholder = "No file selected")),
column(4,
h5("File status:"),
tags$div(
class = "file-status-message",
withSpinner(textOutput("data_file_info"))
))
),
#
h4("Please be aware that loading data (including example file) may take a while. Be patient."),
h4("In order for program to behave correctly, please make sure supplied file fulfills following requirements:"),
tags$button("Show requirements",
class = "collapse-button",
style = "width: unset",
`data-toggle`="collapse",
`data-target`="#reqs"),
tags$div(
id = "reqs",
style = "width: min-content",
class = "hideable",
tableOutput("file_req")),
h3("Settings"),
h4("Values chosen here are propagated into all of the tables for coherent results."),
fluidRow(
column(2,
selectInput_h(inputId = "chosen_protein",
label = "Choose protein: ",
choices = c("db_CD160")),
selectInput_h(inputId = "chosen_control",
label = "Choose maximal exchange control for chosen protein: ",
choices = c("db_CD160 | CD160 | 1440")),
numericInput_h(inputId = "deut_concentration",
label = "Choose D20 concentration [%]: ",
value = 100,
min = 0, max = 100, step = 1),
numericInput_h(inputId = "sequence_start_shift",
label = "Move sequence start:",
value = 1,
step = 1),
numericInput_h(inputId = "sequence_length",
label = "Correct sequence length:",
value = 300,
step = 1),
# h5("If C-terminal of is not covered by peptides,
# enter its correct position."),
textOutput("sequence_length_exp_info")
)
),
br(),
br(),
br()
),
tabPanel("Woods plot",
br(),
sidebarPanel(
class = "scrollable",
h3("Select parameters for the plot."),
fluidRow(checkboxInput_h(inputId = "theory",
label = "Theoretical calculations",
value = FALSE)),
radioButtons_h(inputId = "calc_type",
label = "Choose values type:",
choices = c("relative", "absolute"),
selected = "relative"),
h4("Comparison plot parameters:"),
h5("Choose time parameters:"),
splitLayout(
div(id = "in_time_part",
selectInput_h(inputId = "in_time",
label = "IN",
choices = c("0", "1", "5", "25", "1440"))
),
selectInput_h(inputId = "chosen_time",
label = "CHOSEN",
choices = c("0", "1", "5", "25", "1440")),
div(id = "out_time_part",
selectInput_h(inputId = "out_time",
label = "OUT",
choices = c("0", "1", "5", "25", "1440"))
)
),
##
fluidRow(
column(6,
h5("Choose states for comparison:"),
checkboxGroupInput_h(inputId = "compare_states",
label = "",
choices = c("CD160", "CD160VEM"),
selected = c("CD160", "CD160VEM")),
class = "states-to-compare-column"),
column(6,
helper(tags$button("Adjust colors",
class = "collapse-button",
`data-toggle`="collapse",
`data-target`="#colorss"),
content = "adjust_colors", type = "markdown", buttonLabel = "Okay",
easyClose = TRUE, colour = "#F8F1FF"),
tags$div(
class = "hideable",
id = "colorss",
uiOutput("states_colors")
),
class = "states-colors-column"
)
),
##
h4("Woods plot parameters:"),
splitLayout(
selectInput_h(inputId = "state_first",
label = "State 1",
choices = c("CD160", "CD160VEM")),
selectInput_h(inputId = "state_second",
label = "State 2",
choices = c("CD160", "CD160VEM"))
),
splitLayout(
selectInput_h(inputId = "confidence_limit",
label = "Confidence limit 1:",
choices = c("20%" = 0.2, "50%" = 0.5, "80%" = 0.8, "90%" = 0.9, "95%" = 0.95, "98%" = 0.98, "99%" = 0.99, "99.9%" = 0.999),
selected = 0.98),
selectInput_h(inputId = "confidence_limit_2",
label = "Confidence limit 2:",
choices = c("20%" = 0.2, "50%" = 0.5, "80%" = 0.8, "90%" = 0.9, "95%" = 0.95, "98%" = 0.98, "99%" = 0.99, "99.9%" = 0.999),
selected = 0.99)
),
##
h4("Zoom:"),
sliderInput(inputId = 'comp_plot_y_range',
label = 'Choose y range for comparison plot:',
min = -200,
max = 200,
value = c(0, 120),
step = 10,
width = "100%"),
sliderInput(inputId = 'woods_plot_y_range',
label = 'Choose y range for Woods plot:',
min = -200,
max = 200,
value = c(-50, 50),
step = 10),
sliderInput(inputId = 'plot_x_range',
label = 'Choose x range for both plots:',
min = 0,
max = 300,
value = c(0, 300) #,
# ticks = seq(0, 300, 1) # fix for new shiny
),
##
tags$button("Adjust labels",
class = "collapse-button",
`data-toggle`="collapse",
`data-target`="#labs"),
tags$div(
class = "hideable",
id = "labs",
textInput(inputId = "comparison_plot_title",
label = "Comparison plot title:",
value = ""),
textInput(inputId = "comparison_plot_x_label",
label = "Comparison plot axis x label:",
value = "Position in sequence"),
textInput(inputId = "comparison_plot_y_label",
label = "Comparison plot axis y label:",
value = ""),
textInput(inputId = "woods_plot_title",
label = "Woods plot title:",
value = ""),
textInput(inputId = "woods_plot_x_label",
label = "Woods plot axis x label:",
value = "Position in sequence"),
textInput(inputId = "woods_plot_y_label",
label = "Woods plot axis y label:",
value = "")
)
),
mainPanel(
class = "scrollable",
tabsetPanel(
tabPanel("Comparison plot",
br(),
plotOutput_h("comparisonPlot", hover = hoverOpts("comparisonPlot_hover", delay = 10, delayType = "debounce")),
downloadButton("comparisonPlot_download_button",
"Save chart (.svg)")),
tabPanel("Data",
br(),
DT::dataTableOutput("comparisonPlot_data"))),
uiOutput("comparisonPlot_debug"),
br(),
tabsetPanel(
tabPanel("Woods plot",
br(),
div(style = "position:relative",
plotOutput_h("differentialPlot", hover = hoverOpts("differentialPlot_hover", delay = 10, delayType = "debounce")),
uiOutput("differentialPlot_debug")),
downloadButton("differentialPlot_download_button",
"Save chart (.svg)")),
tabPanel("Data",
br(),
DT::dataTableOutput("differentialPlot_data")))
)
),
tabPanel("Coverage",
br(),
sidebarPanel(
class = "scrollable",
radioButtons(
inputId = 'chosen_state',
label = 'Choose state:',
choices = c('CD160', 'CD160_HVEM'),
selected = 'CD160'
),
sliderInput(
inputId = 'plot_range',
label = 'Choose range:',
min = 1,
max = 300,
value = c(1, 300) #,
# ticks = seq(1, 300, 1) fix for shiny
)
),
mainPanel(
class = "scrollable",
tabsetPanel(
tabPanel("Peptide Coverage",
br(),
withSpinner(plotOutput("stateOverlap", hover = hoverOpts("stateOverlap_hover", delay = 10, delayType = "debounce"))),
uiOutput("stateOverlap_debug"),
downloadButton("stateOverlap_download_button",
"Save chart (.svg)")),
tabPanel("Data",
br(),
DT::dataTableOutput("stateOverlap_data"))
),
br(),
tabsetPanel(
tabPanel("Position Frequency",
br(),
div(style = "position:relative;",
withSpinner(plotOutput("stateOverlapDist", hover = hoverOpts("stateOverlapDist_hover", delay = 10, delayType = "debounce"))),
uiOutput("stateOverlapDist_debug")),
downloadButton("stateOverlapDist_download_button",
"Save chart (.svg)")
),
tabPanel("Data",
br(),
DT::dataTableOutput("stateOverlapDist_data"))
)
)
),
tabPanel("Sequence data",
h3('Protein name'),
h4(textOutput("protein_name"), class = "monospaced"),
h3('Reconstructed sequence'),
htmlOutput("sequenceName", container = tags[["span"]], class = "monospaced"),
br(),
wellPanel(
sidebarLayout(
sidebarPanel(
fluidRow(
column(6,
tableOutput("protein_stats"),
br(),
checkboxGroupInput(
inputId = "hydro_prop",
label = "Hydro-",
choices = c(
"Hydrophilic" = "philic",
"Hydrophobic" = "phobic"),
selected = c("philic", "phobic"))
),
column(6,
br()
)
)
),
mainPanel(withSpinner(plotOutput("aminoDist", hover = hoverOpts("aminoDist_hover", delay = 10, delayType = "debounce"))),
uiOutput("aminoDist_debug"),
downloadButton("aminoDist_download_button",
"Save chart (.svg)"),
p("Source: Kyte, J., and Doolittle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol 157, 105–132."))
)
)
),
tabPanel("Uptake curves",
br(),
sidebarPanel(
class = "scrollable",
h3("Select parameters for the plot."),
checkboxInput_h(inputId = "kin_theory",
label = "Theoretical calculations",
value = FALSE),
radioButtons_h(inputId = "kin_calc_type",
label = "Choose values type:",
choices = c("relative", "absolute"),
selected = "relative"),
div(id = "kin_time_part",
h5("Choose time parameters:"),
splitLayout(
div(id = "kin_in_time_part",
selectInput_h(inputId = "kin_in_time",
label = "IN",
choices = c("0", "1", "5", "25", "1440"))
),
div(id = "kin_out_time_part",
selectInput_h(inputId = "kin_out_time",
label = "OUT",
choices = c("0", "1", "5", "25", "1440")))
)),
h5("Choose peptide:"),
dataTableOutput_h("peptide_list_data"), ## !!
actionButton(inputId = "reset_peptide_list",
label = "Reset chosen peptides"),
br(),
br(),
br(),
sliderInput(inputId = 'kin_plot_y_range',
label = 'Choose y range for the plot:',
min = -50,
max = 200,
value = c(-10, 100),
step = 10),
tags$button("Adjust labels",
class = "collapse-button",
`data-toggle`="collapse",
`data-target`="#kin-labs"),
tags$div(
class = "hideable",
id = "kin-labs",
textInput(inputId = "kin_plot_title",
label = "Uptake curve title:",
value = "Uptake curve for chosen peptides"),
textInput(inputId = "kin_plot_x_label",
label = "Uptake curve axis x label:",
value = "Time point [min]"),
textInput(inputId = "kin_plot_y_label",
label = "Uptake curve axis y label:",
value = "Deuteration")
)
),
mainPanel(
tabsetPanel(
tabPanel(
"Uptake curve",
br(),
plotOutput_h("kinetic_plot_chosen_peptides", hover = hoverOpts("kinetic_plot_chosen_peptides_hover", delay = 10, delayType = "debounce"), height = 600),
uiOutput("kinetic_plot_chosen_peptides_debug"),
downloadButton("kineticPlot_download_button",
"Save chart (.svg)")),
tabPanel("Data",
br(),
DT::dataTableOutput("kin_plot_data"))
)
)
),
#
tabPanel("Quality control",
br(),
sidebarPanel(
h3("Select parameters for the plot."),
h5("The plot can be rendered only for relative experimental values."),
selectInput_h(inputId = "qc_in_time",
label = "Choose in time: ",
choices = c("0", "1", "5", "25", "1440")),
selectInput_h(inputId = "qc_chosen_time",
label = "Choose time: ",
choices = c("0", "1", "5", "25", "1440")),
selectInput_h(inputId = "qc_state_first",
label = "State 1",
choices = c("CD160", "CD160VEM")),
selectInput_h(inputId = "qc_state_second",
label = "State 2",
choices = c("CD160", "CD160VEM"))
),
mainPanel(
tabsetPanel(
tabPanel("Quality control plot",
br(),
plotOutput_h("quality_control_plot", hover = hoverOpts("quality_control_plot_hover", delay = 10, delayType = "debounce"), height = 600),
uiOutput("quality_control_plot_debug"),
downloadButton("quality_control_plot_download_button",
"Save chart (.svg)"),
br(),
h4("This function plots the change in the uncertainty of deuteration levels as a function of incubation time. The uncertainty is averaged over all peptides available at a given time point in a selected state. This chart has a double function: firstly, it allows checking if the measurement uncertainty is decreasing over time (which is the expected behaviour) and the second one helps to plan the appropriate incubation length for the tested protein (whether we obtain the desired data reliability values).")
),
tabPanel("Data",
br(),
DT::dataTableOutput("quality_control_plot_data"))
)
)
),
tabPanel("Summary",
br(),
fluidRow(
withSpinner(DT::dataTableOutput("summary_table"))
),
includeMarkdown("./readmes/summary.md")
),
tabPanel("Report",
br(),
sidebarPanel(width = 8,
h4("Choose items for report:"),
fluidRow(
column(6,
checkboxInput(inputId = "export_overlap_dist",
label = "Position Frequency",
value = TRUE),
checkboxInput(inputId = "export_overlap_graph",
label = "Peptide Coverage",
value = TRUE),
checkboxInput(inputId = "export_comparison_plot",
label = "Comparison Plot",
value = TRUE),
checkboxInput(inputId = "export_theo_comparison_plot",
label = "Theoretical Comparison Plot",
value = TRUE),
checkboxInput(inputId = "export_woods_plot",
label = "Woods Plot",
value = TRUE),
checkboxInput(inputId = "export_theo_woods_plot",
label = "Theoretical Woods Plot",
value = TRUE),
checkboxInput(inputId = "export_kin_plot",
label = "Uptake Curve",
value = FALSE),
checkboxInput(inputId = "export_theo_kin_plot",
label = "Theoretical Uptake Curve",
value = FALSE),
checkboxInput(inputId = "export_quality_control_plot",
label = "Quality Control Plot",
value = FALSE)),
column(6,
checkboxInput(inputId = "export_overlap_dist_data",
label = "Position Frequency Data"),
checkboxInput(inputId = "export_overlap_graph_data",
label = "Peptide Coverage Data"),
checkboxInput(inputId = "export_comparison_plot_data",
label = "Comparison Plot Data"),
checkboxInput(inputId = "export_theo_comparison_plot_data",
label = "Theoretical Comparison Plot Data"),
checkboxInput(inputId = "export_woods_plot_data",
label = "Woods Plot Data"),
checkboxInput(inputId = "export_theo_woods_plot_data",
label = "Theoretical Woods Plot Data"),
checkboxInput(input = "export_kin_plot_data",
label = "Uptake Curve Data"),
checkboxInput(inputId = "export_theo_kin_plot_data",
label = "Theoretical Uptake Curve Data"),
checkboxInput(inputId = "export_quality_control_plot_data",
label = "Quality Control Plot Data"))),
br(),
h5("Elements chosen for report have the same parameters as chosen in panel e.g. axis range and title. Adjust parameters for plots as needed in the report."),
br(),
downloadButton(outputId = "export_action",
label = " Create report!",
icon = icon("fas fa-download"))
)
)
)
),
tags$div(
class = "mobile-site-backbone",
tags$div(
class = "logo-panel",
img(src = "mock_logo.png", class = "logo")
),
tags$div(
class = "mobile-information",
h3("Welcome to HaDeX website!"),
h4("For better user experience please use device with wider screen (at least 900px)."),
img(src='funding_icons.png', height = 100)
)
),
tags$script(type="text/javascript",
src="resize-logo-panel.js")
)
#tags$div(class = "logo-container",
# tags$img(source = "www/mock_logo.png"))
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