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ui.R
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ui.R
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# Header #####
header <- dashboardHeader(title = "My PhD project")
# Body #####
body <- dashboardBody(tabItems
(
# Add tab items for breast cancer, PDAC and OSCC
# Breast Cancer - general tab
tabItem(tabName = "breast_cancer_project"),
# Breast Cancer - exploratory analysis #####
tabItem(
tabName = "breast_cancer_exploratory",
h2("Exploratory analysis plots and tables"),
fluidRow(
# Histogram plot ##
box(
id = "Histogram_breast",
title = "Histogram",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = 7,
height = 400,
plotlyOutput("breast_histogram")
),
# Histogram tuning
box(
id = "Histogram_tuning_breast",
title = "Histogram tuning",
status = "warning",
solidHeader = TRUE,
collapsible = TRUE,
width = 5,
height = 400,
shinyjs::useShinyjs(),
# Select variable to plot
div(
id = "div_histvar_select_breast",
style = "display:inline-block; width: 32%; margin-left: 7.5%; margin-right: 5%",
selectInput(
"histvar_select_breast",
"Select variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
"IC10",
"Mammaprint_risk",
"Mammaprint_score",
"rorS_risk",
"rorS_score",
"Location",
"Menopause.status",
"ER.status",
"Year",
"Platform",
"Platform_comp",
"Treatment",
"Response"
)
),
selected = "pam50"
)
),
# Select type of histogram (probability, percentage, classic)
div(
id = "div_hist_type_breast",
style = "display:inline-block; width: 38%; margin-left: 5%; margin-right: 5%",
selectInput(
"hist_type_breast",
"Select type of histogram",
choices = list(
classic = "classic",
probability = "probability",
percent = "percentage"
),
selected = "classic"
)
),
# div for checkbox input and select-all button
div(
id = "div_checkbox_selectall_group_breast_hist",
style = "width: 100%;",
# Select the datasets that you want to include in the plot
div(
id = "div_hist_dataset_checkbox",
style = "display: inline-block; width: 55%; margin-left: 7.5%;",
checkboxGroupInput(
"hist_dataset_checkbox",
"Select studies",
selected = unique(breast_cancer_full_pheno$Dataset),
choices = unique(breast_cancer_full_pheno$Dataset),
inline = TRUE
)
),
# add "select all" button for the datasets to choose from
div(
id = "div_select_all_hist_breast",
style = "display: inline-block; margin: 5% 5% 0% 5%; width: 25%; position: absolute;",
actionButton(
"select_all_hist_breast",
"Select/De-select All",
style = "background-color: #F8ECBB; font-weight: bold; border-radius: 10px;",
icon = icon("check", style = "margin-right: 5px; vertical-align: middle;")
)
)
),
# Select colors for fill and outline of the bins
div(
id = "div_hist_fill_breast",
style = "display:inline-block; margin-top: 0%; margin-left: 7.5%; margin-right: 2.5%; width: 25%;",
colourpicker::colourInput(
"hist_fill_breast",
"Bin fill color",
value = "#1194B1",
allowTransparent = TRUE
)
),
div(
id = "div_hist_color_breast",
style = "display:inline-block; margin-left: 2.5%; margin-right: 2.5%; width: 25%",
colourpicker::colourInput(
"hist_color_breast",
"Bin outline color",
value = "#000000",
allowTransparent = TRUE
)
),
# Select number of bins
div(
id = "div_hist_breast_bins",
style = "display:inline-block; margin-left: 2.5%; margin-right: 5%; width: 25%",
numericInput(
"hist_breast_bins",
"Select # of bins",
value = 10,
min = 0,
max = Inf,
width = "150px"
)
),
# div for action buttons
div(
id = "div_action_buttons_hist_breast",
style = "display: flex; width: 100%; align-content: center; justify-content: center",
# Button to trigger plot generation/update
div(
id = "div_draw_breast_hist",
# style = "display: flex; margin-right: 3%; margin-top: 3%;",
tags$head(
tags$link(rel = "stylesheet", type = "text/css",
href = "rgb_button_css.css")
),
actionButton(
inputId = "draw_breast_hist",
label = "Draw!",
icon = icon("paintbrush", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'rgb-button')
),
# Button to reset inputs to default
div(
id = "div_default_breast_hist",
style = "padding-top: 0.5%; padding-left: 6.5%;",
tags$head(
tags$link(rel = "stylesheet", type = "text/css",
href = "default_button.css")
),
actionButton(
inputId = "reset_input_breast_hist",
label = "Default parameters",
icon = icon("repeat", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'default-button')
),
# Add an info button (pop up with shinyalert())
div(
id = "div_info_breast_hist",
style = "padding-left: 6.5%;",
# style = "display: inline-flex; margin-left: 3%; margin-top: 3%;",
tags$head(
tags$link(rel = "stylesheet", type = "text/css",
href = "info_button.css")
),
actionButton(
inputId = "hist_breast_info",
label = "Info",
icon = icon("circle-info", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'info-button')
)
)
),
bsModal(
"histogram_breast_info",
"Information",
"hist_breast_info",
fluidRow(htmlOutput("hist_breast_info_text"))
),
# Bar chart ##
box(
id = "Barchart_plot_breast",
title = "Bar chart",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = 7,
height = 400,
plotlyOutput("breast_barchart")
),
# Bar chart tuning
box(
id = "Barchart_plot_tuning_breast",
title = "Bar chart tuning",
status = "warning",
solidHeader = TRUE,
collapsible = TRUE,
width = 5,
height = 400,
shinyjs::useShinyjs(),
# Select main variable to plot
div(
id = "div_barchart_varmain_select_breast",
style = "display:inline-block; width: 27.5%; margin-left: 3%; margin-right: 2.5%",
selectInput(
"barchart_varmain_select_breast",
"Main variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
"IC10",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"ER.status",
"Year",
"Platform",
"Platform_comp",
"Treatment",
"Response"
)
),
selected = "pam50"
)
),
# Select clustering variable (optional)
div(
id = "div_barchart_varclust_select_breast",
style = "display:inline-block; width: 27.5%; margin-left: 2.5%; margin-right: 2.5%",
selectInput(
"barchart_varclust_select_breast",
"Second variable (optional)",
choices = c("None", sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
"IC10",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"ER.status",
"Year",
"Platform",
"Platform_comp",
"Treatment",
"Response"
)
)),
selected = "None"
)
),
# Select type of bar chart (clustered, stacked) - if a second variable is selected
div(
id = "div_barchart_type_breast",
style = "display:inline-block; width: 27.5%; margin-left: 2.5%; margin-right: 3%",
selectInput(
"barchart_type_breast",
"Select type of bar chart",
choices = c("group", "stack"),
selected = "group"
)
),
# div for checkbox input and select-all button
div(
id = "div_checkbox_selectall_group_breast_barchart",
style = "width: 100%;",
# Select the datasets that you want to include in the plot
div(
id = "div_barchart_dataset_checkbox",
style = "display: inline-block; width: 55%; margin-left: 3%;",
checkboxGroupInput(
"barchart_dataset_checkbox",
"Select studies",
selected = unique(breast_cancer_full_pheno$Dataset),
choices = unique(breast_cancer_full_pheno$Dataset),
inline = TRUE
)
),
# add "select all" button for the datasets to choose from
div(
id = "div_select_all_barchart_breast",
style = "display: inline-block; margin: 5% 3% 0% 7%; width: 25%; position: absolute;",
actionButton(
"select_all_barchart_breast",
"Select/De-select All",
style = "background-color: #F8ECBB; font-weight: bold; border-radius: 10px;",
icon = icon("check", style = "margin-right: 5px; vertical-align: middle;")
)
)
),
# div for color and fill selections for barchart
div(
id = "div_fill_color_group_barachart",
style = "display: flex; justify-content: center; align-content:center;",
# Select colors for fill and outline of the bins
div(
id = "div_barchart_fill_breast",
style = "display:inline-block; margin-top: 0%; margin-left: 3%; margin-right: 7.5%; width: 35%;",
colourpicker::colourInput(
"barchart_fill_breast",
"Bin fill color",
value = "#9419B2",
allowTransparent = TRUE
)
),
div(
id = "div_barchart_color_breast",
style = "display:inline-block; margin-left: 7.5%; margin-right: 3%; width: 35%",
colourpicker::colourInput(
"barchart_color_breast",
"Bin outline color",
value = "#000000",
allowTransparent = TRUE
)
)
),
# div for action buttons
div(
id = "div_action_buttons_hist_breast",
style = "display: flex; width: 100%; align-content: center; justify-content: center",
# Button to trigger plot generation/update
div(
id = "div_draw_breast_barchart",
actionButton(
inputId = "draw_breast_barchart",
label = "Draw!",
icon = icon("paintbrush", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'rgb-button')
),
# Button to reset inputs to default
div(
id = "div_default_breast_hist",
actionButton(
inputId = "reset_input_breast_barchart",
label = "Default parameters",
icon = icon("repeat", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'default-button'),
style = "padding-top: 0.5%; padding-left: 6.5%;"
),
# Add an info button (pop up with shinyalert())
div(
id = "div_info_breast_hist",
style = "padding-left: 6.5%;",
actionButton(
inputId = "barchart_breast_info",
label = "Info",
icon = icon("circle-info", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'info-button')
)
)
),
bsModal(
"barchart_breast_information",
"Information",
"barchart_breast_info",
fluidRow(htmlOutput("barchart_breast_info_text"))
)
)
),
# Breast Cancer - sunburst tab #####
tabItem(
tabName = "breast_cancer_sunburst",
h2("Sunburst plots: analytical dataset and consensus subtypes"),
fluidRow(
# tabBox of plotting sunbursts
tabBox(
title = "Sunburst plots",
id = "sunburst_tabs_breast",
height = 700,
width = 7,
selected = "Analytical data sunburst plot",
# Panel for analytical set
tabPanel(
"Analytical data sunburst plot",
title = "Analytical dataset",
plotlyOutput("analytical_sunburst_breast")
),
# Panel for consensus set
tabPanel(
"Consensus data sunburst plot",
title = "Consensus subtypes",
plotlyOutput("consensus_sunburst_breast")
)
),
# tabBox of tuning sunbursts
tabBox(
title = "Sunburst tuning",
id = "sunburst_tuning_breast",
height = 700,
width = 5,
selected = "Analytical tuning",
# Panel for analytical set
tabPanel(
"Analytical tuning",
title = "Analytical dataset",
shinyjs::useShinyjs(),
# Select variable 1 for analytical set
selectInput(
"sunburst_var1_select_breast",
"Select root variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
Timepoint = "Timepoint_coded",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"Dataset",
"None",
"ER.status",
"Treatment",
"Response"
)
),
selected = "Treatment"
),
# Select variable 2 for analytical set
selectInput(
"sunburst_var2_select_breast",
"Select second variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
Timepoint = "Timepoint_coded",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"Dataset",
"None",
"ER.status",
"Treatment",
"Response"
)
),
selected = "Dataset"
),
# Select variable 3 for analytical set
selectInput(
"sunburst_var3_select_breast",
"Select third variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
Timepoint = "Timepoint_coded",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"Dataset",
"None",
"ER.status",
"Treatment",
"Response"
)
),
selected = "Response"
),
# Select variable 4 for analytical set
selectInput(
"sunburst_var4_select_breast",
"Select fourth variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
Timepoint = "Timepoint_coded",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"Dataset",
"None",
"ER.status",
"Treatment",
"Response"
)
),
selected = "pam50"
),
# add "select all" button for the datasets to choose from
actionButton(
"select_all_sunburst_analytical_breast",
"Select/De-select All",
style = "background-color: #F8ECBB; font-weight: bold; border-radius: 10px;",
icon = icon("check", style = "margin-right: 5px; vertical-align: middle;")
),
# Select the datasets that you want to include in the plot
checkboxGroupInput(
"sunburst_analytical_dataset_checkbox",
"Select studies",
selected = unique(breast_cancer_full_pheno$Dataset),
choices = unique(breast_cancer_full_pheno$Dataset),
inline = TRUE
),
# Select opacity of data points
sliderInput(
"alpha_breast_sunburst_analytical",
"Opacity (alpha)",
min = 0,
max = 1,
value = 0.9
),
# div for action buttons
div(
id = "div_action_buttons_analytical_sunburst_breast",
style = "display: flex; width: 100%; align-content: center; justify-content: center",
# Button to trigger plot generation/update
div(
id = "div_draw_analytical_sunburst_breast",
actionButton(
inputId = "draw_breast_sunburst_analytical",
label = "Draw!",
icon = icon("paintbrush", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'rgb-button')
),
# Button to reset inputs to default
div(
id = "div_default_analytical_sunburst_breast",
actionButton(
inputId = "reset_input_breast_sunburst_analytical",
label = "Default parameters",
icon = icon("repeat", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'default-button'),
style = "padding-top: 0.5%; padding-left: 6.5%;"
),
# Add an info button (pop up with shinyalert())
div(
id = "div_info_analytical_sunburst_breast",
style = "padding-left: 6.5%;",
actionButton(
inputId = "sunburst_analytical_breast_info",
label = "Info",
icon = icon("circle-info", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'info-button')
)
),
bsModal(
"analytical_sunburst_breast_info",
"Information",
"sunburst_analytical_breast_info",
fluidRow(htmlOutput("analytical_sunburst_breast_info_text"))
)
),
# Panel for consensus set
tabPanel(
id = "Consensus tuning",
title = "Consensus subtypes",
shinyjs::useShinyjs(),
# Select variable 1 for consensus set
selectInput(
"sunburst_var1_select_breast_consensus",
"Select root variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
"Timepoint",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"Dataset",
"None",
"ER.status",
"Treatment",
"Response",
"Cluster"
)
),
selected = "Cluster"
),
# Select variable 2 for consensus set
selectInput(
"sunburst_var2_select_breast_consensus",
"Select second variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
"Timepoint",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"Dataset",
"None",
"ER.status",
"Treatment",
"Response",
"Cluster"
)
),
selected = "Dataset"
),
# Select variable 3 for consensus set
selectInput(
"sunburst_var3_select_breast_consensus",
"Select third variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
"Timepoint",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"Dataset",
"None",
"ER.status",
"Treatment",
"Response",
"Cluster"
)
),
selected = "Response"
),
# Select variable 4 for consensus set
selectInput(
"sunburst_var4_select_breast_consensus",
"Select fourth variable",
choices = sort(
c(
"pam50",
"scmod1",
"ClaudinLow",
"Timepoint",
"Mammaprint_risk",
"rorS_risk",
"Location",
"Menopause.status",
"Dataset",
"None",
"ER.status",
"Treatment",
"Response",
"Cluster"
)
),
selected = "Mammaprint_risk"
),
# add "select all" button for the datasets to choose from
actionButton(
"select_all_sunburst_consensus_breast",
"Select/De-select All",
style = "background-color: #F8ECBB; font-weight: bold; border-radius: 10px;",
icon = icon("check", style = "margin-right: 5px; vertical-align: middle;")
),
# Select the datasets that you want to include in the plot
checkboxGroupInput(
"sunburst_consensus_dataset_checkbox",
"Select studies",
selected = unique(breast_cancer_consensus_set$Dataset),
choices = unique(breast_cancer_consensus_set$Dataset),
inline = TRUE
),
# Select opacity of data points
sliderInput(
"alpha_breast_sunburst_consensus",
"Opacity (alpha)",
min = 0,
max = 1,
value = 0.9
),
# div for action buttons
div(
id = "div_action_buttons_consensus_sunburst_breast",
style = "display: flex; width: 100%; align-content: center; justify-content: center",
# Button to trigger plot generation/update
div(
id = "div_draw_consensus_sunburst_breast",
actionButton(
inputId = "draw_breast_sunburst_consensus",
label = "Draw!",
icon = icon("paintbrush", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'rgb-button')
),
# Button to reset inputs to default
div(
id = "div_default_consensus_sunburst_breast",
actionButton(
inputId = "reset_input_breast_sunburst_consensus",
label = "Default parameters",
icon = icon("repeat", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'default-button'),
style = "padding-top: 0.5%; padding-left: 6.5%;"
),
# Add an info button (pop up with shinyalert())
div(
id = "div_info_consensus_sunburst_breast",
style = "padding-left: 6.5%;",
actionButton(
inputId = "sunburst_consensus_breast_info",
label = "Info",
icon = icon("circle-info", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = 'info-button')
)
),
bsModal(
"consensus_sunburst_breast_info",
"Information",
"sunburst_consensus_breast_info",
fluidRow(htmlOutput("consensus_sunburst_breast_info_text"))
)
)
)
)
),
# Breast Cancer - volcano #####
tabItem(
tabName = "breast_cancer_subItem_volcano",
h2("Neoadjuvant Treatment (NAT) in Breast Cancer"),
tags$head(
tags$link(rel = "stylesheet",
type = "text/css",
href = "volcano_waiter_adjustment.css")
),
fluidRow(
# Volcano plot
div(
id = "div_volcano_plot_box",
box(
id = "Volcano_plot_breast",
title = "Volcano plot",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = 8,
height = 820,
useWaiter(),
plotlyOutput("breast_volcano")
)
),
# Interactive switches and tools for plotting the volcano
box(
id = "Volcano_tuning_breast",
title = "Volcano tuning",
status = "warning",
solidHeader = TRUE,
collapsible = TRUE,
width = 4,
height = 820,
shinyjs::useShinyjs(),
# Select p-value for y-axis (corrected/uncorrected)
selectInput(
"pval_selector_breast",
"p-value to plot",
choices = c("P.Value", "adj.P.Val"),
selected = "adj.P.Val"
),
# Select x-coordinate for vertical logFC lines
numericInput(
"logFC_breast",
"DET: Diff. Exp. Threshold - vertical lines",
value = 0.25,
min = 0,
max = Inf
),
# Select y-coordinate for p-value threshold
numericInput(
"pval_breast",
"PVT (adj.P.Val threshold) - horizontal line",
value = 0.05,
min = 0,
max = Inf
),
# Select colors for scatter points
colourpicker::colourInput(
"scatter_color_breast_NS",
"Color for p>PVT (n.s. results)",
value = "#BEBEBE"
),
colourpicker::colourInput(
"scatter_color_breast_p_only",
"Color for DE<|DET| & p<PVT",
value = "#FFC0CB"
),
colourpicker::colourInput(
"scatter_color_breast_downr",
"Color for DE<-|DET| & p<PVT",
value = "royalblue"
),
colourpicker::colourInput(
"scatter_color_breast_upr",
"Color for DE>|DET| & p<PVT",
value = "red4"
),
# Select opacity of data points
sliderInput(
"alpha_breast_volcano",
"Opacity (alpha)",
min = 0,
max = 1,
value = 0.7
),
# Write down a representative title for the plot
textInput(
"breast_volcano_title",
"Set a title for your plot",
value = c("Volcano plot: NAT responders vs. non-responders")
),
div(
id = "div_action_buttons_consensus_sunburst_breast",
style = "display: flex; width: 100%; align-content: center; justify-content: center",
# Button to trigger plot generation/update
div(
id = "div_draw_breast_volcano",
actionButton(
inputId = "draw_breast_volcano",
label = "Draw!",
icon = icon("paintbrush", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = "rgb-button")
),
# Button to reset inputs to default
div(
id = "div_default_breast_volcano",
actionButton(
inputId = "reset_input_breast_volcano",
label = "Default parameters",
icon = icon("repeat", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = "default-button"),
style = "padding-left: 5%;"
),
# Add an info button (pop up with shinyalert())
div(
id = "div_breast_volcano_info_button",
style = "padding-left: 5%; padding-top: -5%;",
actionButton(
inputId = "volcano_breast_info",
label = "Info",
icon = icon("circle-info", style = "margin-right: 5px; vertical-align: middle;")
) %>%
tagAppendAttributes(class = "info-button")
)
),
bsModal(
"preset_volcano_breast_info",
"Information",
"volcano_breast_info",
fluidRow(htmlOutput("volcano_breast_info_text"))
)
),
# Hovering info in tuning parameters
bsTooltip(
"pval_selector_breast",
"Select p-value for plotting on y-axis (-log10(p-value))",
placement = "bottom",
trigger = "hover",
options = NULL
),
bsTooltip(
"logFC_breast",
"x-coordinate for symmetrical vertical lines (illustrative purposes)",
placement = "bottom",
trigger = "hover",
options = NULL
),
bsTooltip(
"pval_breast",
"y-coordinate for horizontal p-value threshold (default:0.05)",
placement = "bottom",
trigger = "hover",
options = NULL
)
)
),
# Breast Cancer - Machine Learning (Response prediction models) #####
tabItem(
tabName = "breast_cancer_subItem_ml",
h2("Machine Learning"),
fluidRow(
# Interactive model and data selection panel
box(
id = "ML_control_breast",
title = "Select model and data",
status = "primary",
solidHeader = TRUE,
width = 12,
height = 270,
shinyjs::useShinyjs(),
splitLayout(
cellWidths = c("200px", "250px", "350px", "200px"),
style = "border:1px;padding:10px;white-space:normal;",
# Select ML model category