inst/shinyGUI/ui.R
In mtrussart/CytofRUV: CytofRUV for analysing multiple CyTOF batches
# =================================================================================================
# Options for loaders -> This requires package - shinycssloaders to be added to build package.
# -------------------------------------------------------------------------------------------------
options(spinner.color="#0275D8", spinner.color.background="#ffffff", spinner.size=2)
# =================================================================================================
# Renders Tab Panel
# -------------------------------------------------------------------------------------------------
ui_diagnostic_plots <- fluidPage(
h1("Diagnostic Plots"),
fluidRow(
column(
12,
uiOutput("tab_plots")
)
)
)
# =================================================================================================
# Page 1: Median Intensities
# -------------------------------------------------------------------------------------------------
medIntensities <- fluidPage(
fluidRow(
column(
5,
## Plot 1
h2("Multi-dimensional scaling plot computed using median protein expression"),
## Need to incl library("shinycssloaders") into the package
withSpinner(plotOutput(outputId="plotMDS", height = "600px"), type = 2),
fluidRow(
column(6,
h5(strong("Select the parameter to color by:")),
selectInput("choiceMDS", NULL, choices = list("condition", "batch")),
h5(strong("Press after updating parameter:")),
column(6, uiOutput("MDS_updateReminder")),
column(6, actionButton("mds", "update"))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("mds_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_mds", label = "Download Plot")
)
),
),
column(
7,
## Plot 2
h2("Heatmap of the median protein expression"),
withSpinner(plotOutput(outputId="plotDendogram", width="80%", height = "600px"), type = 2),
h5(strong("Select the file type and Download Plot:")),
fluidRow(
column(2, radioButtons("dendogram_tag", NULL, choices = list("pdf", "png"))),
column(2, downloadButton(outputId = "download_dendogram", label = "Download Plot"))
)
)
)
)
# =================================================================================================
# Page 2: Markers Distribution
# -------------------------------------------------------------------------------------------------
markerDistribution <-fluidPage(
fluidRow(
column(
12,
## Page 2 plot 1
h2("Distribution of protein expression"),
withSpinner(uiOutput("exprsPlot"), type=2)
)
),
fluidRow(
column(5,
selectInput("exprs1", "Select the parameter to color by:", list("Condition" = "condition", "Sample ID" = "sample_id")),
uiOutput("exprs2"),
uiOutput("exprs3"),
h5(strong("Press after updating parameter:")),
column(3,uiOutput("Exprs_update_text")),
column(3,actionButton("exprsPlot", "update"))
),
column(4,
h5(strong("Select the file type and Download Plot:")),
radioButtons("exprsPlot_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_exprsPlot", label = "Download Plot")
)
)
)
# =================================================================================================
# Page 3: Clustering Results
# -------------------------------------------------------------------------------------------------
TNSE_check_box <-fluidPage(
fluidRow(
column(
12,
list(tags$div(align = 'left',
class = 'multicol',
checkboxGroupInput("checkBox_TSNE", NULL,
choices = sampleID_sorted,
selected = sampleID_sorted[1:10],
inline = FALSE,
width = "100%"))),
actionButton("deselectAll_TSNE", "Deselect All Options")
)
)
)
checkBox_TSNE <- shinydashboard::box(
title="Select Up To 10 Sample IDs",
solidHeader=TRUE,
status="warning",
id="box_2",
width=12,
collapsible=TRUE,
TNSE_check_box,
inline = FALSE, choiceNames = NULL,
choiceValues = NULL
)
UMAP_check_box <- fluidPage(
fluidRow(
column(
12,
list(tags$div(align = 'left',
class = 'multicol',
checkboxGroupInput("checkBox_UMAP", NULL,
choices = sampleID_sorted,
selected = sampleID_sorted[1:10],
inline = FALSE,
width = "100%"))),
actionButton("deselectAll_UMAP", "Deselect All Options")
)
)
)
checkBox_UMAP <- shinydashboard::box(
title="Select Up To 10 Sample IDs",
solidHeader=TRUE,
status="warning",
id="box_3",
width=12,
collapsible=TRUE,
UMAP_check_box,
inline = FALSE, choiceNames = NULL,
choiceValues = NULL
)
clusteringResults <-fluidPage(
fluidRow(
column(
8,
## Plot 1
h2("Heatmap of the median protein expression per cluster"),
withSpinner(plotOutput("cluster_heatmap", height="650px"), type = 2),
h5(strong("Select the file type and Download Plot:")),
fluidRow(
column(3, radioButtons("cluster_Heatmap_tag", NULL, choices = list("pdf", "png"))),
column(3, downloadButton(outputId = "download_cluster_Heatmap", label = "Download Plot"))
)
)
),
fluidRow(
column(
6,
## Plot 2
hr(),
h2(textOutput("TSNE_TEXT1")),
withSpinner(plotOutput("plot_TSNE1", height = "550px"), type = 2),
fluidRow(
column(6,
selectInput("TSNE_Colour_By1", "Select the parameter to color by:", list("Cluster"=cluster_var, "Antigen"="Antigen", "Batch"="batch")),
uiOutput("TSNE_Ant_Choice1"),
h5(strong("Press after updating parameter:")),
column(6,uiOutput("TSNE_update_text")),
column(6, actionButton("update_TSNE1", "update"))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("TSNE_1_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_TSNE_1", label = "Download Plot")
)
)
),
column(
6,
## Plot 3
hr(),
h2(textOutput("Umap_text_1")),
withSpinner(plotOutput("plot_UMAP1", height = "550px"), type = 2),
fluidRow(
column(6,
selectInput("Umap_Colour_By1", "Select the parameter to color by:", list("Cluster"=cluster_var, "Antigen"="Antigen", "Batch"="batch")),
uiOutput("UMAP_Ant_Choice1"),
h5(strong("Press after updating parameter:")),
column(6,uiOutput("UMAP_update_text")),
column(6,div(style="margin-top:0px; margin-bottom:0px;", actionButton("update_UMAP_1", "update")))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("Umap_1_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_Umap_1", label = "Download Plot")
)
)
)
),
fluidRow(
column(
6,
## Plot 4
hr(),
h2(textOutput("TSNE_facet_Text")),
withSpinner(plotOutput("plotTSNE_facet", height = "600px"), type = 2),
fluidRow(
column(6,
selectInput("TSNE_facet_colourBy", "Select the parameter to color by:", list("Cluster"=cluster_var, "Antigen"="Antigen", "Batch"="batch")),
uiOutput("TSNE_Facet_Ant_Choice"),
h5(strong("Press after updating parameter:")),
column(6,uiOutput("TSNE_facet_update_text")),
column(6,div(style="margin-top:0px; margin-bottom:0px;", actionButton("update_TSNE_facet", "update")))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("TSNE_facet_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_TSNE_facet", label = "Download Plot")
)
)
),
column(
6,
## Plot 5
hr(),
h2(textOutput("UMAP_facet_Text")),
withSpinner(plotOutput("plot_UMAP_facet", height = "600px"), type = 2),
fluidRow(
column(6,
selectInput("UMAP_facet_colour_by", "Select the parameter to color by:", list("Cluster"=cluster_var, "Antigen"="Antigen", "Batch"="batch")),
uiOutput("UMAP_Facet_Ant_Choice"),
h5(strong("Press after updating parameter:")),
column(6,uiOutput("UMAP_facet_update_text")),
column(6,div(style="margin-top:0px; margin-bottom:0px;", actionButton("update_UMAP_facet", "update")))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("UMAP_2_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_UMAP_facet", label = "Download Plot")
)
)
)
),
fluidRow(
column(4, checkBox_TSNE),
column(4, offset = 2, checkBox_UMAP)
)
)
# =================================================================================================
# Page 4: Cluster Proportions
# -------------------------------------------------------------------------------------------------
clusterProportions <- fluidPage(
fluidRow(
column(
12,
h2("Cluster proportions across samples"),
withSpinner(plotOutput("Abundance_cluster", height="800px"), type = 2),
h5(strong("Select the file type and Download Plot:")),
fluidRow(
column(2, radioButtons("Abundance_cluster_tag", NULL, choices = list("pdf", "png"))),
column(2, downloadButton(outputId = "download_Abundance_cluster", label = "Download Plot"))
)
)
)
)
# =================================================================================================
# Define Design of Tab Panel
# -------------------------------------------------------------------------------------------------
tab_plots <- shinydashboard::tabBox(
side = "left",
# selected = "Median Intensities",
width = 12,
tabPanel(h4("Median Protein Expression"), medIntensities),
tabPanel(h4("Protein Expression Distributions"), markerDistribution),
tabPanel(h4("Clustering Results"), clusteringResults),
tabPanel(h4("Cluster Proportions"), clusterProportions)
)
header <- dashboardHeader(
title = a(href="https://www.wehi.edu.au/",
div(class=".box",
style="display:flex;justify-content:left",
img(src="https://www.wehi.edu.au/sites/default/files/wehi-logo-2020.png",
style="padding-top:5px;padding-left:5px;",
height="70px")
)
),
tags$li(class = "dropdown",
# Set height of dashboardHeader
tags$style(".main-header {max-height: 65px;}"),
tags$style(".main-header .logo {height: 75px;width:auto;}"),
tags$style(".main-header .navbar {margin-left: 215px;}"),
# CheckBox inputs
tags$style(
HTML(".box {
margin-top: 10px;
}
.checkbox-inline {
margin-left: 10px;
margin-right: 10px;
}
.multicol {
height: 150px;
overflow-y: auto;
}")),
# Blue Update Text for Plots.
tags$style(
"#MDS_updateReminder{color: blue; font-size: 13px;}
#Exprs_update_text{color: blue; font-size: 13px;}
#TSNE_update_text{color: blue; font-size: 13px;}
#UMAP_update_text{color: blue; font-size: 13px;}
#TSNE_facet_update_text{color: blue; font-size: 13px;}
#UMAP_facet_update_text{color: blue; font-size: 13px;}"
))
)
sidebar <- dashboardSidebar(disable = TRUE)
body <- dashboardBody(
tags$head(tags$script(HTML(freezeButtonsScript))),
fluidRow(
ui_diagnostic_plots
)
)
ui <- dashboardPage(header, sidebar, body, skin="black")
mtrussart/CytofRUV documentation built on Aug. 3, 2022, 2:28 a.m.
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# =================================================================================================
# Options for loaders -> This requires package - shinycssloaders to be added to build package.
# -------------------------------------------------------------------------------------------------
options(spinner.color="#0275D8", spinner.color.background="#ffffff", spinner.size=2)
# =================================================================================================
# Renders Tab Panel
# -------------------------------------------------------------------------------------------------
ui_diagnostic_plots <- fluidPage(
h1("Diagnostic Plots"),
fluidRow(
column(
12,
uiOutput("tab_plots")
)
)
)
# =================================================================================================
# Page 1: Median Intensities
# -------------------------------------------------------------------------------------------------
medIntensities <- fluidPage(
fluidRow(
column(
5,
## Plot 1
h2("Multi-dimensional scaling plot computed using median protein expression"),
## Need to incl library("shinycssloaders") into the package
withSpinner(plotOutput(outputId="plotMDS", height = "600px"), type = 2),
fluidRow(
column(6,
h5(strong("Select the parameter to color by:")),
selectInput("choiceMDS", NULL, choices = list("condition", "batch")),
h5(strong("Press after updating parameter:")),
column(6, uiOutput("MDS_updateReminder")),
column(6, actionButton("mds", "update"))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("mds_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_mds", label = "Download Plot")
)
),
),
column(
7,
## Plot 2
h2("Heatmap of the median protein expression"),
withSpinner(plotOutput(outputId="plotDendogram", width="80%", height = "600px"), type = 2),
h5(strong("Select the file type and Download Plot:")),
fluidRow(
column(2, radioButtons("dendogram_tag", NULL, choices = list("pdf", "png"))),
column(2, downloadButton(outputId = "download_dendogram", label = "Download Plot"))
)
)
)
)
# =================================================================================================
# Page 2: Markers Distribution
# -------------------------------------------------------------------------------------------------
markerDistribution <-fluidPage(
fluidRow(
column(
12,
## Page 2 plot 1
h2("Distribution of protein expression"),
withSpinner(uiOutput("exprsPlot"), type=2)
)
),
fluidRow(
column(5,
selectInput("exprs1", "Select the parameter to color by:", list("Condition" = "condition", "Sample ID" = "sample_id")),
uiOutput("exprs2"),
uiOutput("exprs3"),
h5(strong("Press after updating parameter:")),
column(3,uiOutput("Exprs_update_text")),
column(3,actionButton("exprsPlot", "update"))
),
column(4,
h5(strong("Select the file type and Download Plot:")),
radioButtons("exprsPlot_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_exprsPlot", label = "Download Plot")
)
)
)
# =================================================================================================
# Page 3: Clustering Results
# -------------------------------------------------------------------------------------------------
TNSE_check_box <-fluidPage(
fluidRow(
column(
12,
list(tags$div(align = 'left',
class = 'multicol',
checkboxGroupInput("checkBox_TSNE", NULL,
choices = sampleID_sorted,
selected = sampleID_sorted[1:10],
inline = FALSE,
width = "100%"))),
actionButton("deselectAll_TSNE", "Deselect All Options")
)
)
)
checkBox_TSNE <- shinydashboard::box(
title="Select Up To 10 Sample IDs",
solidHeader=TRUE,
status="warning",
id="box_2",
width=12,
collapsible=TRUE,
TNSE_check_box,
inline = FALSE, choiceNames = NULL,
choiceValues = NULL
)
UMAP_check_box <- fluidPage(
fluidRow(
column(
12,
list(tags$div(align = 'left',
class = 'multicol',
checkboxGroupInput("checkBox_UMAP", NULL,
choices = sampleID_sorted,
selected = sampleID_sorted[1:10],
inline = FALSE,
width = "100%"))),
actionButton("deselectAll_UMAP", "Deselect All Options")
)
)
)
checkBox_UMAP <- shinydashboard::box(
title="Select Up To 10 Sample IDs",
solidHeader=TRUE,
status="warning",
id="box_3",
width=12,
collapsible=TRUE,
UMAP_check_box,
inline = FALSE, choiceNames = NULL,
choiceValues = NULL
)
clusteringResults <-fluidPage(
fluidRow(
column(
8,
## Plot 1
h2("Heatmap of the median protein expression per cluster"),
withSpinner(plotOutput("cluster_heatmap", height="650px"), type = 2),
h5(strong("Select the file type and Download Plot:")),
fluidRow(
column(3, radioButtons("cluster_Heatmap_tag", NULL, choices = list("pdf", "png"))),
column(3, downloadButton(outputId = "download_cluster_Heatmap", label = "Download Plot"))
)
)
),
fluidRow(
column(
6,
## Plot 2
hr(),
h2(textOutput("TSNE_TEXT1")),
withSpinner(plotOutput("plot_TSNE1", height = "550px"), type = 2),
fluidRow(
column(6,
selectInput("TSNE_Colour_By1", "Select the parameter to color by:", list("Cluster"=cluster_var, "Antigen"="Antigen", "Batch"="batch")),
uiOutput("TSNE_Ant_Choice1"),
h5(strong("Press after updating parameter:")),
column(6,uiOutput("TSNE_update_text")),
column(6, actionButton("update_TSNE1", "update"))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("TSNE_1_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_TSNE_1", label = "Download Plot")
)
)
),
column(
6,
## Plot 3
hr(),
h2(textOutput("Umap_text_1")),
withSpinner(plotOutput("plot_UMAP1", height = "550px"), type = 2),
fluidRow(
column(6,
selectInput("Umap_Colour_By1", "Select the parameter to color by:", list("Cluster"=cluster_var, "Antigen"="Antigen", "Batch"="batch")),
uiOutput("UMAP_Ant_Choice1"),
h5(strong("Press after updating parameter:")),
column(6,uiOutput("UMAP_update_text")),
column(6,div(style="margin-top:0px; margin-bottom:0px;", actionButton("update_UMAP_1", "update")))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("Umap_1_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_Umap_1", label = "Download Plot")
)
)
)
),
fluidRow(
column(
6,
## Plot 4
hr(),
h2(textOutput("TSNE_facet_Text")),
withSpinner(plotOutput("plotTSNE_facet", height = "600px"), type = 2),
fluidRow(
column(6,
selectInput("TSNE_facet_colourBy", "Select the parameter to color by:", list("Cluster"=cluster_var, "Antigen"="Antigen", "Batch"="batch")),
uiOutput("TSNE_Facet_Ant_Choice"),
h5(strong("Press after updating parameter:")),
column(6,uiOutput("TSNE_facet_update_text")),
column(6,div(style="margin-top:0px; margin-bottom:0px;", actionButton("update_TSNE_facet", "update")))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("TSNE_facet_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_TSNE_facet", label = "Download Plot")
)
)
),
column(
6,
## Plot 5
hr(),
h2(textOutput("UMAP_facet_Text")),
withSpinner(plotOutput("plot_UMAP_facet", height = "600px"), type = 2),
fluidRow(
column(6,
selectInput("UMAP_facet_colour_by", "Select the parameter to color by:", list("Cluster"=cluster_var, "Antigen"="Antigen", "Batch"="batch")),
uiOutput("UMAP_Facet_Ant_Choice"),
h5(strong("Press after updating parameter:")),
column(6,uiOutput("UMAP_facet_update_text")),
column(6,div(style="margin-top:0px; margin-bottom:0px;", actionButton("update_UMAP_facet", "update")))
),
column(6,
h5(strong("Select the file type and Download Plot:")),
radioButtons("UMAP_2_tag", NULL, choices = list("pdf", "png")),
downloadButton(outputId = "download_UMAP_facet", label = "Download Plot")
)
)
)
),
fluidRow(
column(4, checkBox_TSNE),
column(4, offset = 2, checkBox_UMAP)
)
)
# =================================================================================================
# Page 4: Cluster Proportions
# -------------------------------------------------------------------------------------------------
clusterProportions <- fluidPage(
fluidRow(
column(
12,
h2("Cluster proportions across samples"),
withSpinner(plotOutput("Abundance_cluster", height="800px"), type = 2),
h5(strong("Select the file type and Download Plot:")),
fluidRow(
column(2, radioButtons("Abundance_cluster_tag", NULL, choices = list("pdf", "png"))),
column(2, downloadButton(outputId = "download_Abundance_cluster", label = "Download Plot"))
)
)
)
)
# =================================================================================================
# Define Design of Tab Panel
# -------------------------------------------------------------------------------------------------
tab_plots <- shinydashboard::tabBox(
side = "left",
# selected = "Median Intensities",
width = 12,
tabPanel(h4("Median Protein Expression"), medIntensities),
tabPanel(h4("Protein Expression Distributions"), markerDistribution),
tabPanel(h4("Clustering Results"), clusteringResults),
tabPanel(h4("Cluster Proportions"), clusterProportions)
)
header <- dashboardHeader(
title = a(href="https://www.wehi.edu.au/",
div(class=".box",
style="display:flex;justify-content:left",
img(src="https://www.wehi.edu.au/sites/default/files/wehi-logo-2020.png",
style="padding-top:5px;padding-left:5px;",
height="70px")
)
),
tags$li(class = "dropdown",
# Set height of dashboardHeader
tags$style(".main-header {max-height: 65px;}"),
tags$style(".main-header .logo {height: 75px;width:auto;}"),
tags$style(".main-header .navbar {margin-left: 215px;}"),
# CheckBox inputs
tags$style(
HTML(".box {
margin-top: 10px;
}
.checkbox-inline {
margin-left: 10px;
margin-right: 10px;
}
.multicol {
height: 150px;
overflow-y: auto;
}")),
# Blue Update Text for Plots.
tags$style(
"#MDS_updateReminder{color: blue; font-size: 13px;}
#Exprs_update_text{color: blue; font-size: 13px;}
#TSNE_update_text{color: blue; font-size: 13px;}
#UMAP_update_text{color: blue; font-size: 13px;}
#TSNE_facet_update_text{color: blue; font-size: 13px;}
#UMAP_facet_update_text{color: blue; font-size: 13px;}"
))
)
sidebar <- dashboardSidebar(disable = TRUE)
body <- dashboardBody(
tags$head(tags$script(HTML(freezeButtonsScript))),
fluidRow(
ui_diagnostic_plots
)
)
ui <- dashboardPage(header, sidebar, body, skin="black")
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