R/app_ui.R
In spielmanlab/dragon: Deep Time Redox Analysis of the Geobiology Ontology Network
Defines functions
golem_add_external_resources
app_ui
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @import shinydashboard
#' @import shinyWidgets
#' @noRd
app_ui <- function(request) {
tagList(
# Leave this function for adding external resources
golem_add_external_resources(),
# List the first level UI elements here
dashboardPage(skin = "red",
dashboardHeader(title = "dragon: Deep-time Redox Analysis of the Geobiology Ontology Network", titleWidth = "800px",
dropdownMenu(type = "notifications",
icon = shiny::icon("question-circle"),
badgeStatus = NULL,
headerText = "Information:",
notificationItem("You are using THE DEVELOPMENET VERSION OF DRAGON", icon = icon("box-open")),
notificationItem("Source Code", icon = icon("github"), href = "http://github.com/spielmanlab/dragon"),
notificationItem("IMA Database of Mineral Properties", icon = icon("globe"), href = "https://rruff.info/ima/")
)
), ## END dashboardHeader
dashboardSidebar(width = 340,
sidebarMenu(id = "thismusttakeanidapparently", chooseSliderSkin(skin = "Flat"),
## NETWORK DATA SELECTION ---------------------------------------------------------------------------------------------
shinyWidgets::pickerInput("elements_of_interest", tags$span(style="font-weight:400", "Select focal element(s):"),
choices = element_info$element,
options = list(
`actions-box` = TRUE,
size = 6,
`live-search` = TRUE
),
multiple = TRUE
), ## END pickerInput
shinyWidgets::pickerInput("focal_from_mineral","Select focal elements based on mineral composition:",
# TODO: THIS SHOULD USE UPDATED MED DATA WHEN SPECIFIED - has to be a renderUI
# TODO: SHOW FORMULAS ALSO?
choices = sort(unique(med_data_cache$mineral_name)),
choicesOpt = list(
content = sprintf("<span>%s </span>", mineral_names_formulas())
),
#choices = sort(unique(med_data_cache$mineral_name)),
options = list(
`actions-box` = TRUE,
size = 8,
`live-search` = TRUE
),
multiple = TRUE
),
shinyWidgets::sliderTextInput("age_range","Age (Ga) range of minerals:", choices = rev(seq(0, max(med_data_cache$max_age), 0.1)), grid=T, selected=c(max(med_data_cache$max_age),0)),
shinyWidgets::prettyRadioButtons("max_age_type", "Use maximum or minimum age of minerals", inline = TRUE, choices = c("Maximum", "Minimum"), selected="Maximum", status="danger"),
shinyWidgets::prettySwitch("elements_by_redox","Use separate nodes for each element redox",value = FALSE, status="danger"),
conditionalPanel(condition = "input.elements_by_redox == true",{
shinyWidgets::prettySwitch("ignore_na_redox","Ignore elements with unknown redox states",value = FALSE, status="danger")
}),
shinyWidgets::prettySwitch("force_all_elements","Force element intersection in minerals",value = FALSE, status="danger"),
shinyWidgets::prettySwitch("restrict_to_elements","Only consider minerals with focal element(s)",value = FALSE, status="danger"),
shinyWidgets::prettySwitch("build_only","Build network without display",value = FALSE, status="danger"),
fluidRow(
column(12, align="center",
shinyWidgets::actionBttn("go", "Initialize Network", size="md", color = "danger", style = "fill")
)
),
## NETWORK LAYOUT AND CLUSTERING ---------------------------------------------------------------------------------------------
menuItem("Network layout and clustering options",
fluidRow(
column(8,
shinyWidgets::pickerInput("network_layout", tags$span(style="font-weight:400", "Network layout:"),
choices = network_layout_choices, selected = "layout_with_fr"
), style='padding:0px;'
),
column(4,
numericInput("network_layout_seed", tags$span(style="font-weight:400", "Random seed:"), min = 0, max = Inf, value = 1),
style='padding-left:0px'
)
), # fluidRow
fluidRow(
column(12,
conditionalPanel('input.network_layout == "physics"', {
shinyWidgets::pickerInput("physics_solver", tags$span(style="font-weight:400", "Solver for physics layout:"),
choices = physics_choices, selected = "forceAtlas2Based")
}), style='padding:0px'
) # column 12
), # fluidrow
fluidRow(
column(8, shinyWidgets::pickerInput("cluster_algorithm",
tags$span(style="font-weight:400",
"Network community detection (clustering) algorithm:"),
choices = cluster_algorithm_choices, selected = "Louvain"),
style='padding:0px'),
column(4,
numericInput("cluster_seed", tags$span(style="font-weight:400", "Random seed:"), min = 0, max = Inf, value = 1),
style='padding-left:0px'
)
) ## fluidRow
), ## END menuitem
## NETWORK VISUAL STYLE MENUS ---------------------------------------------------------------------------------------------
menuItem(text = "Node Colors",
mod_ui_choose_color_sd_palette("mod_element_colors",
"Color elements based on:",
element_color_by_choices,
"singlecolor",
default_element_color,
default_element_palette),
mod_ui_choose_color_sd_palette("mod_mineral_colors",
"Color minerals based on:",
mineral_color_by_choices,
"singlecolor",
default_mineral_color,
default_mineral_palette),
fluidRow(
column(12,
colourpicker::colourInput("na_color", "Color to use for missing or unknown values:", value = default_na_color),
style = "padding:0px;"
)
),
fluidRow(
column(12,
shinyWidgets::prettySwitch("color_by_cluster", "Color all nodes by community cluster", value = FALSE, status = "danger"),
style = "padding:0px;"
)
),
fluidRow(
column(12,
conditionalPanel(condition = "input.color_by_cluster == true",{
pickerInput("cluster_palette",
label = "Palette:",
choices = qual_palettes_ui$name,
choicesOpt = list(content = qual_palettes_ui$img)
)
}), ## END conditionalPanel
style = "padding:0px;"
) ## end column
) ## end fluidRow
), ## END "Node Colors" menuItem
menuItem(text = "Color individual elements",
fluidRow(
column(6, shinyWidgets::prettySwitch("highlight_element","Color focal element(s)", value = FALSE, status = "danger"), style='padding:0px;'),
column(6, colourpicker::colourInput("highlight_color", "Color:", value = default_highlight_color), style='padding-left:0px;')
),
tags$span("Use the buttons below to add or remove custom groups",
br(),
"of elements to color."),
fluidRow(
column(6, actionButton('insert_custom', 'Add new color group.'), style = "padding:0px;"),
column(6, actionButton('remove_custom', 'Remove color group.'), style = "padding-left:0px;")
),
tags$div(id = 'custom_color_chooser')
), ## END "Color individual elements" menuItem
menuItem(text = "Node Sizes",
fluidRow(
column(6,
shinyWidgets::pickerInput("element_size_by",
"Size elements based on:",
element_size_by_choices,
selected = "singlesize"),
style='padding:0px;'
), ## END column
column(6,
conditionalPanel(condition = "input.element_size_by == 'singlesize'", {
shiny::sliderInput("element_label_size","Element size",value=50,min=10,max=100, step=5) #### !!!!!!! label size - this is how visnetwork does <shrug>!!!!!!!
}), style='padding-left:0px;'
), ## END column
column(6,
conditionalPanel(condition = "input.element_size_by != 'singlesize'", {
shiny::sliderInput("element_size_scale","Scale element size",value=20,min=10,max=100,step=5)
}), style='padding-left:0px;'
) ## END column
), ## END fluidRow
fluidRow(
column(6,
shinyWidgets::pickerInput("mineral_size_by",
"Size minerals based on:",
mineral_size_by_choices,
selected = "singlesize"), style='padding:0px;'
), ## END column
column(6,
conditionalPanel(condition = "input.mineral_size_by == 'singlesize'",{
shiny::sliderInput("mineral_size","Mineral size",value=10,min=0,max=50, step = 5)
}), style='padding-left:0px;'
), ## END column
column(6,
conditionalPanel(condition = "input.mineral_size_by != 'singlesize'", {
shiny::sliderInput("mineral_size_scale","Scale mineral size",value=10,min=1,max=25,step=1)
}), style='padding-left:0px;'
) ## END column
) ## END fluidRow
), ## END "Node Sizes" menuItem
menuItem(text = "Node Shapes",
fluidRow(
column(6, shinyWidgets::pickerInput("element_shape", "Element node shape:", element_shape_choices, selected = default_element_shape), style='padding:0px;'),
column(6, shinyWidgets::pickerInput("mineral_shape", "Mineral node shape:", mineral_shape_choices, selected = default_mineral_shape), style='padding-left:0px;')
) ## END fluidRow
), ## END "Node Shapes" menuItem
menuItem(text = "Node Labels and Font",
fluidRow(
column(12, colourpicker::colourInput("element_label_color", "Element font color (applies only when element shape is not 'text'):", value = default_element_label_color),
style='padding:0px;'),
), ## END fluidRow
fluidRow(
column(6, colourpicker::colourInput("mineral_label_color", "Mineral font color:", value = default_mineral_label_color),
style='padding:0px;'),
column(6, shiny::sliderInput("mineral_label_size","Mineral font size",value=0,min=0,max=50, step = 5),
style='padding-left:0px;')
) ## END fluidRow
), ## END "Node Labels and Font" menuItem
menuItem(text = "Edge Attributes",
mod_ui_choose_color_sd_palette("mod_edge_colors",
"Color edges based on:",
edge_color_by_choices,
"singlecolor",
default_edge_color,
default_edge_palette),
#div(style = "margin-left:15px;margin-right:15px;",
tags$span("Visit the 'Node Colors' menu tab to select the color used",
br(),
"for missing or unknown edge attribute values."),
#),
sliderInput("edge_weight","Edge weight:",value=3,min=1,max=10)
), ## END "Edge Attributes" menuItem
menuItem("Network interaction options",
shiny::sliderInput("selected_degree", "Node selection highlight degree", min=1, max=5, value = 2, step=1),
shinyWidgets::prettySwitch("hover","Emphasize on hover",value = TRUE, status = "danger"),
shinyWidgets::prettySwitch("hide_edges_on_drag","Hide edges when dragging nodes",value = TRUE, status = "danger"),
shinyWidgets::prettySwitch("drag_view", "Drag network in frame",value = TRUE, status = "danger"),
shinyWidgets::prettySwitch("zoom_view","Scroll in network frame to zoom", value = TRUE, status = "danger"),
shinyWidgets::prettySwitch("nav_buttons","Show navigation buttons", value = FALSE, status = "danger")
)#, ## END "Network interaction options" menuItem
) ## END sidebarMenu
), ## END dashboardSidebar
dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
),
fluidRow(
div(style = "margin-right:1%; margin-left:1%;", ## div0
## MAIN TOP TABBOX ---------------------------------------------------------------------------------------------
tabBox(id = "main-box",width=12,
## VISUALIZE NETWORK PANEL ---------------------------------------------------------------------------------------------
shiny::tabPanel("Visualize Network",
div(style = "height:700px; overflow: hidden;", ## div1
div(style = "font-style:italic;", ## div2
shiny::textOutput("connectivity")
), ## END div2
conditionalPanel('input.build_only == true', {
div(style = "text-align:center; font-weight:bold; color:red; font-size:1.25em;",
br(),br(),br(),br(),
shiny::textOutput("no_network_display")
)
}), ## END `true` conditionalPanel
visNetwork::visNetworkOutput("networkplot", height = "100%") #NOTE: this cannot be in a conditionalPanel; div1 gets ignored
), ## END div1
conditionalPanel('input.build_only == false', {
div(style = "height:75px;padding-left:20px;",
shiny::plotOutput("networklegend", height = "95%", width = "100%")
)
}) ## END 2nd `false` conditionalPanel
), ## END "Visualize Network" tabPanel
## NETWORK INFORMATION PANEL ---------------------------------------------------------------------------------------------
shiny::tabPanel("Explore Network Attributes",
fluidRow(
column(width = 12,
div(style = "float:left;font-weight:bold;",
h3("Network contents:"),
textOutput("modularity"),
textOutput("n_element_nodes"),
textOutput("n_mineral_nodes"),
textOutput("n_edges")
)
), ## END column
br(),
column(width = 12,
h3("Explore Element Attributes:"),
div(style="display:inline-block;vertical-align:top;",
downloadButton("export_element_table", label = "Export table"),
shinyWidgets::radioGroupButtons("export_element_table_fmt",
"",
choices = c("CSV", "Excel"),
checkIcon = list(yes = icon("ok", lib = "glyphicon")),
selected = "CSV")
),
div(style = "font-size:85%;",
DT::dataTableOutput("element_exploration_table"),
shiny::sliderInput("element_table_digits", "Choose the number of digits to show in table:", value = 3, min = 1, max = 16, width = "275px")
),
br(), br(),
h3("Explore Mineral Attributes:"),
div(style="display:inline-block;vertical-align:top;",
downloadButton("export_mineral_table", label = "Export table"),
shinyWidgets::radioGroupButtons("export_mineral_table_fmt",
"",
choices = c("CSV", "Excel"),
checkIcon = list(yes = icon("ok", lib = "glyphicon")),
selected = "CSV")
),
div(style = "font-size:85%;",
DT::dataTableOutput("mineral_exploration_table"),
shiny::sliderInput("mineral_table_digits", "Choose the number of digits to show in table:", value = 3, min = 1, max = 16, width = "275px"),
)
) ## END column
) ## END fluidRow
), ## END "Network Information" tabPanel
## ANALYZE NETWORK PANEL ---------------------------------------------------------------------------------------------
shiny::tabPanel("Analyze Network Minerals",
#helpText("In this tab, you can construct a linear regression model to analyze properties of minerals in the specified network."),
br(),
br(),
br(),
fluidRow(
column(4,
shinyWidgets::pickerInput("response",
tags$b("Select the response (dependent) variable:"),
choices = model_response_choices,
selected=max_age_str
),
shinyWidgets::pickerInput("predictor",
tags$b("Select the predictor (independent) variable:"),
choices = model_predictor_choices,
selected=cov_pauling_str
),
conditionalPanel('input.predictor == "Community cluster"',{
shiny::textOutput("cluster_fyi")
})
), ## END column
column(8,
DT::dataTableOutput("fitted_model"),
br(),br(),
conditionalPanel( condition = 'input.predictor == "Community cluster"', {
DT::dataTableOutput("fitted_tukey")
})
) ## END column
), ## END fluidRow
fluidRow(
column(4,
p(tags$b("Plot styling options:")),
shiny::uiOutput("model_plot_options")
), ## END column
column(8,
div(style="float:center;width:600px;height:400px;",
shiny::plotOutput("fitted_model_plot", height = "100%", width = "100%")
),
div(style="display:inline-block; float:right;",
shinyWidgets::downloadBttn("download_model_plot", "Download Plot", size = "sm", style = "minimal", color = "danger")
) ## END div
) ## END column
) ## END fluidRow
), ## END "Analyze Network Minerals" tabPanel
## TIMELINE PANEL ---------------------------------------------------------------------------------------------
shiny::tabPanel("Mineral formation timeline",
div(style="float:center;width:100%;height:700px;",
plotOutput("timeline_plot_output", height = "100%", width = "100%")
),
br(),
shinyWidgets::prettySwitch("timeline_view","Display minerals discovered at their oldest known age only. Turn off to display minerals discovered at any age.", value = TRUE, status="danger"),
fluidRow(
## can't use the module here due to sizing
column(4,
div(style="display:inline-block;vertical-align:top;",
shinyWidgets::pickerInput("color_timeline_by",
"Color minerals inside the selected age range based on:",
mineral_timeline_color_by_choices,
selected = "singlecolor", width = "100%")
),
div(style="display:inline-block;vertical-align:top;",
conditionalPanel(condition = "input.color_timeline_by == 'singlecolor'",
{
colourpicker::colourInput("timeline_color", "Color:", value = "#68340e")
}),
conditionalPanel(condition = "input.color_timeline_by != 'singlecolor'",
{
shinyWidgets::pickerInput("timeline_palette",
label = "Mineral color palette:",
choices = sd_palettes_ui$name,
options = list( size = 6),
choicesOpt = list(content = sd_palettes_ui$img),
selected = "YlOrBr", width = "100%")
})
)
),
column(4,
colourpicker::colourInput("outside_range_color", label = "Color for minerals outside the selected age range:", value="#fae9dd")
),
column(4,
br(),
shinyWidgets::downloadBttn("download_timeline", "Download Timeline Plot", size = "md", style = "minimal", color = "danger")
) ## END column 3
) ## END fluidRow
) ## END timeline tabPanel
), ## END TOP tabBox
## RENDER SELECTED NODE TABLE BELOW NETWORK ---------------------------------------------------------
br(),br(),br(),
shiny::uiOutput("show_nodeTable"),
br(),
## NETWORK EXPORT BOX -----------------------------------------------------------------------
box(width = 12, status = "primary", title = "Network Export", collapsible = TRUE,
shinyWidgets::actionBttn("store_position",
"Click to prepare network for export to PDF.",
color = "danger",
style = "fill",
block = TRUE),
br(),br(),
fluidRow(
column(3, br(), shinyWidgets::downloadBttn("export_network_pdf", "Export network as PDF", size = "sm", style = "minimal", color = "danger")),
column(3, shiny::sliderInput("baseline_output_element_size", "Scale network PDF element node size", min = 0.1, max = 5, step = 0.1, value = 1)),
column(3, shiny::sliderInput("baseline_output_element_label_size", "Scale network PDF element label size", min = 0.1, max = 5, step = 0.1, value = 1)),
column(3, shiny::sliderInput("baseline_output_mineral_size", "Scale network PDF mineral node size", min = 0.1, max = 5, step = 0.1, value = 1))
), ## END fluidRow
br(),br(),br(),
fluidRow(
column(3, shinyWidgets::downloadBttn("export_nodes_csv", "Export nodes as CSV", size = "sm", style = "minimal", color = "danger")),
column(3, shinyWidgets::downloadBttn("export_edges_csv", "Export edges as CSV", size = "sm", style = "minimal", color = "danger")),
column(3, shinyWidgets::downloadBttn("export_network_igraph", "Export network as text file", size = "sm", style = "minimal", color = "danger")),
column(3, shinyWidgets::pickerInput("igraph_output_format", label = "Choose network text file format:", choices = igraph_output_format_choices))
), ## END fluidRow
br(),br(),
shinyWidgets::downloadBttn("export_legend_pdf", "Export legend as PDF", size = "sm", style = "minimal", color = "danger")
) ## END box
) ## END div0
) ## END fluidRow
) ## END dashboardBody
) ## END dashboardPage
) ## END tagList
} ## END app_ui
#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @import shiny
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function(){
add_resource_path(
'www', app_sys('app/www')
)
tags$head(
golem::favicon(),
golem::activate_js(),
shinyWidgets::useSweetAlert(), ## May not be necessary per docs except for progress bars, but let's use it.
bundle_resources(
path = app_sys('app/www'),
app_title = 'dragon'
),
tags$style(".palette-style{
display: inline;
vertical-align: middle;
color: black;
font-weight: 600;
padding-left: 7px;}"
)
# Add here other external resources
# for example, you can add shinyalert::useShinyalert()
)
}
spielmanlab/dragon documentation built on Nov. 15, 2023, 3:04 a.m.
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Defines functions golem_add_external_resources app_ui
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @import shinydashboard
#' @import shinyWidgets
#' @noRd
app_ui <- function(request) {
tagList(
# Leave this function for adding external resources
golem_add_external_resources(),
# List the first level UI elements here
dashboardPage(skin = "red",
dashboardHeader(title = "dragon: Deep-time Redox Analysis of the Geobiology Ontology Network", titleWidth = "800px",
dropdownMenu(type = "notifications",
icon = shiny::icon("question-circle"),
badgeStatus = NULL,
headerText = "Information:",
notificationItem("You are using THE DEVELOPMENET VERSION OF DRAGON", icon = icon("box-open")),
notificationItem("Source Code", icon = icon("github"), href = "http://github.com/spielmanlab/dragon"),
notificationItem("IMA Database of Mineral Properties", icon = icon("globe"), href = "https://rruff.info/ima/")
)
), ## END dashboardHeader
dashboardSidebar(width = 340,
sidebarMenu(id = "thismusttakeanidapparently", chooseSliderSkin(skin = "Flat"),
## NETWORK DATA SELECTION ---------------------------------------------------------------------------------------------
shinyWidgets::pickerInput("elements_of_interest", tags$span(style="font-weight:400", "Select focal element(s):"),
choices = element_info$element,
options = list(
`actions-box` = TRUE,
size = 6,
`live-search` = TRUE
),
multiple = TRUE
), ## END pickerInput
shinyWidgets::pickerInput("focal_from_mineral","Select focal elements based on mineral composition:",
# TODO: THIS SHOULD USE UPDATED MED DATA WHEN SPECIFIED - has to be a renderUI
# TODO: SHOW FORMULAS ALSO?
choices = sort(unique(med_data_cache$mineral_name)),
choicesOpt = list(
content = sprintf("<span>%s </span>", mineral_names_formulas())
),
#choices = sort(unique(med_data_cache$mineral_name)),
options = list(
`actions-box` = TRUE,
size = 8,
`live-search` = TRUE
),
multiple = TRUE
),
shinyWidgets::sliderTextInput("age_range","Age (Ga) range of minerals:", choices = rev(seq(0, max(med_data_cache$max_age), 0.1)), grid=T, selected=c(max(med_data_cache$max_age),0)),
shinyWidgets::prettyRadioButtons("max_age_type", "Use maximum or minimum age of minerals", inline = TRUE, choices = c("Maximum", "Minimum"), selected="Maximum", status="danger"),
shinyWidgets::prettySwitch("elements_by_redox","Use separate nodes for each element redox",value = FALSE, status="danger"),
conditionalPanel(condition = "input.elements_by_redox == true",{
shinyWidgets::prettySwitch("ignore_na_redox","Ignore elements with unknown redox states",value = FALSE, status="danger")
}),
shinyWidgets::prettySwitch("force_all_elements","Force element intersection in minerals",value = FALSE, status="danger"),
shinyWidgets::prettySwitch("restrict_to_elements","Only consider minerals with focal element(s)",value = FALSE, status="danger"),
shinyWidgets::prettySwitch("build_only","Build network without display",value = FALSE, status="danger"),
fluidRow(
column(12, align="center",
shinyWidgets::actionBttn("go", "Initialize Network", size="md", color = "danger", style = "fill")
)
),
## NETWORK LAYOUT AND CLUSTERING ---------------------------------------------------------------------------------------------
menuItem("Network layout and clustering options",
fluidRow(
column(8,
shinyWidgets::pickerInput("network_layout", tags$span(style="font-weight:400", "Network layout:"),
choices = network_layout_choices, selected = "layout_with_fr"
), style='padding:0px;'
),
column(4,
numericInput("network_layout_seed", tags$span(style="font-weight:400", "Random seed:"), min = 0, max = Inf, value = 1),
style='padding-left:0px'
)
), # fluidRow
fluidRow(
column(12,
conditionalPanel('input.network_layout == "physics"', {
shinyWidgets::pickerInput("physics_solver", tags$span(style="font-weight:400", "Solver for physics layout:"),
choices = physics_choices, selected = "forceAtlas2Based")
}), style='padding:0px'
) # column 12
), # fluidrow
fluidRow(
column(8, shinyWidgets::pickerInput("cluster_algorithm",
tags$span(style="font-weight:400",
"Network community detection (clustering) algorithm:"),
choices = cluster_algorithm_choices, selected = "Louvain"),
style='padding:0px'),
column(4,
numericInput("cluster_seed", tags$span(style="font-weight:400", "Random seed:"), min = 0, max = Inf, value = 1),
style='padding-left:0px'
)
) ## fluidRow
), ## END menuitem
## NETWORK VISUAL STYLE MENUS ---------------------------------------------------------------------------------------------
menuItem(text = "Node Colors",
mod_ui_choose_color_sd_palette("mod_element_colors",
"Color elements based on:",
element_color_by_choices,
"singlecolor",
default_element_color,
default_element_palette),
mod_ui_choose_color_sd_palette("mod_mineral_colors",
"Color minerals based on:",
mineral_color_by_choices,
"singlecolor",
default_mineral_color,
default_mineral_palette),
fluidRow(
column(12,
colourpicker::colourInput("na_color", "Color to use for missing or unknown values:", value = default_na_color),
style = "padding:0px;"
)
),
fluidRow(
column(12,
shinyWidgets::prettySwitch("color_by_cluster", "Color all nodes by community cluster", value = FALSE, status = "danger"),
style = "padding:0px;"
)
),
fluidRow(
column(12,
conditionalPanel(condition = "input.color_by_cluster == true",{
pickerInput("cluster_palette",
label = "Palette:",
choices = qual_palettes_ui$name,
choicesOpt = list(content = qual_palettes_ui$img)
)
}), ## END conditionalPanel
style = "padding:0px;"
) ## end column
) ## end fluidRow
), ## END "Node Colors" menuItem
menuItem(text = "Color individual elements",
fluidRow(
column(6, shinyWidgets::prettySwitch("highlight_element","Color focal element(s)", value = FALSE, status = "danger"), style='padding:0px;'),
column(6, colourpicker::colourInput("highlight_color", "Color:", value = default_highlight_color), style='padding-left:0px;')
),
tags$span("Use the buttons below to add or remove custom groups",
br(),
"of elements to color."),
fluidRow(
column(6, actionButton('insert_custom', 'Add new color group.'), style = "padding:0px;"),
column(6, actionButton('remove_custom', 'Remove color group.'), style = "padding-left:0px;")
),
tags$div(id = 'custom_color_chooser')
), ## END "Color individual elements" menuItem
menuItem(text = "Node Sizes",
fluidRow(
column(6,
shinyWidgets::pickerInput("element_size_by",
"Size elements based on:",
element_size_by_choices,
selected = "singlesize"),
style='padding:0px;'
), ## END column
column(6,
conditionalPanel(condition = "input.element_size_by == 'singlesize'", {
shiny::sliderInput("element_label_size","Element size",value=50,min=10,max=100, step=5) #### !!!!!!! label size - this is how visnetwork does <shrug>!!!!!!!
}), style='padding-left:0px;'
), ## END column
column(6,
conditionalPanel(condition = "input.element_size_by != 'singlesize'", {
shiny::sliderInput("element_size_scale","Scale element size",value=20,min=10,max=100,step=5)
}), style='padding-left:0px;'
) ## END column
), ## END fluidRow
fluidRow(
column(6,
shinyWidgets::pickerInput("mineral_size_by",
"Size minerals based on:",
mineral_size_by_choices,
selected = "singlesize"), style='padding:0px;'
), ## END column
column(6,
conditionalPanel(condition = "input.mineral_size_by == 'singlesize'",{
shiny::sliderInput("mineral_size","Mineral size",value=10,min=0,max=50, step = 5)
}), style='padding-left:0px;'
), ## END column
column(6,
conditionalPanel(condition = "input.mineral_size_by != 'singlesize'", {
shiny::sliderInput("mineral_size_scale","Scale mineral size",value=10,min=1,max=25,step=1)
}), style='padding-left:0px;'
) ## END column
) ## END fluidRow
), ## END "Node Sizes" menuItem
menuItem(text = "Node Shapes",
fluidRow(
column(6, shinyWidgets::pickerInput("element_shape", "Element node shape:", element_shape_choices, selected = default_element_shape), style='padding:0px;'),
column(6, shinyWidgets::pickerInput("mineral_shape", "Mineral node shape:", mineral_shape_choices, selected = default_mineral_shape), style='padding-left:0px;')
) ## END fluidRow
), ## END "Node Shapes" menuItem
menuItem(text = "Node Labels and Font",
fluidRow(
column(12, colourpicker::colourInput("element_label_color", "Element font color (applies only when element shape is not 'text'):", value = default_element_label_color),
style='padding:0px;'),
), ## END fluidRow
fluidRow(
column(6, colourpicker::colourInput("mineral_label_color", "Mineral font color:", value = default_mineral_label_color),
style='padding:0px;'),
column(6, shiny::sliderInput("mineral_label_size","Mineral font size",value=0,min=0,max=50, step = 5),
style='padding-left:0px;')
) ## END fluidRow
), ## END "Node Labels and Font" menuItem
menuItem(text = "Edge Attributes",
mod_ui_choose_color_sd_palette("mod_edge_colors",
"Color edges based on:",
edge_color_by_choices,
"singlecolor",
default_edge_color,
default_edge_palette),
#div(style = "margin-left:15px;margin-right:15px;",
tags$span("Visit the 'Node Colors' menu tab to select the color used",
br(),
"for missing or unknown edge attribute values."),
#),
sliderInput("edge_weight","Edge weight:",value=3,min=1,max=10)
), ## END "Edge Attributes" menuItem
menuItem("Network interaction options",
shiny::sliderInput("selected_degree", "Node selection highlight degree", min=1, max=5, value = 2, step=1),
shinyWidgets::prettySwitch("hover","Emphasize on hover",value = TRUE, status = "danger"),
shinyWidgets::prettySwitch("hide_edges_on_drag","Hide edges when dragging nodes",value = TRUE, status = "danger"),
shinyWidgets::prettySwitch("drag_view", "Drag network in frame",value = TRUE, status = "danger"),
shinyWidgets::prettySwitch("zoom_view","Scroll in network frame to zoom", value = TRUE, status = "danger"),
shinyWidgets::prettySwitch("nav_buttons","Show navigation buttons", value = FALSE, status = "danger")
)#, ## END "Network interaction options" menuItem
) ## END sidebarMenu
), ## END dashboardSidebar
dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
),
fluidRow(
div(style = "margin-right:1%; margin-left:1%;", ## div0
## MAIN TOP TABBOX ---------------------------------------------------------------------------------------------
tabBox(id = "main-box",width=12,
## VISUALIZE NETWORK PANEL ---------------------------------------------------------------------------------------------
shiny::tabPanel("Visualize Network",
div(style = "height:700px; overflow: hidden;", ## div1
div(style = "font-style:italic;", ## div2
shiny::textOutput("connectivity")
), ## END div2
conditionalPanel('input.build_only == true', {
div(style = "text-align:center; font-weight:bold; color:red; font-size:1.25em;",
br(),br(),br(),br(),
shiny::textOutput("no_network_display")
)
}), ## END `true` conditionalPanel
visNetwork::visNetworkOutput("networkplot", height = "100%") #NOTE: this cannot be in a conditionalPanel; div1 gets ignored
), ## END div1
conditionalPanel('input.build_only == false', {
div(style = "height:75px;padding-left:20px;",
shiny::plotOutput("networklegend", height = "95%", width = "100%")
)
}) ## END 2nd `false` conditionalPanel
), ## END "Visualize Network" tabPanel
## NETWORK INFORMATION PANEL ---------------------------------------------------------------------------------------------
shiny::tabPanel("Explore Network Attributes",
fluidRow(
column(width = 12,
div(style = "float:left;font-weight:bold;",
h3("Network contents:"),
textOutput("modularity"),
textOutput("n_element_nodes"),
textOutput("n_mineral_nodes"),
textOutput("n_edges")
)
), ## END column
br(),
column(width = 12,
h3("Explore Element Attributes:"),
div(style="display:inline-block;vertical-align:top;",
downloadButton("export_element_table", label = "Export table"),
shinyWidgets::radioGroupButtons("export_element_table_fmt",
"",
choices = c("CSV", "Excel"),
checkIcon = list(yes = icon("ok", lib = "glyphicon")),
selected = "CSV")
),
div(style = "font-size:85%;",
DT::dataTableOutput("element_exploration_table"),
shiny::sliderInput("element_table_digits", "Choose the number of digits to show in table:", value = 3, min = 1, max = 16, width = "275px")
),
br(), br(),
h3("Explore Mineral Attributes:"),
div(style="display:inline-block;vertical-align:top;",
downloadButton("export_mineral_table", label = "Export table"),
shinyWidgets::radioGroupButtons("export_mineral_table_fmt",
"",
choices = c("CSV", "Excel"),
checkIcon = list(yes = icon("ok", lib = "glyphicon")),
selected = "CSV")
),
div(style = "font-size:85%;",
DT::dataTableOutput("mineral_exploration_table"),
shiny::sliderInput("mineral_table_digits", "Choose the number of digits to show in table:", value = 3, min = 1, max = 16, width = "275px"),
)
) ## END column
) ## END fluidRow
), ## END "Network Information" tabPanel
## ANALYZE NETWORK PANEL ---------------------------------------------------------------------------------------------
shiny::tabPanel("Analyze Network Minerals",
#helpText("In this tab, you can construct a linear regression model to analyze properties of minerals in the specified network."),
br(),
br(),
br(),
fluidRow(
column(4,
shinyWidgets::pickerInput("response",
tags$b("Select the response (dependent) variable:"),
choices = model_response_choices,
selected=max_age_str
),
shinyWidgets::pickerInput("predictor",
tags$b("Select the predictor (independent) variable:"),
choices = model_predictor_choices,
selected=cov_pauling_str
),
conditionalPanel('input.predictor == "Community cluster"',{
shiny::textOutput("cluster_fyi")
})
), ## END column
column(8,
DT::dataTableOutput("fitted_model"),
br(),br(),
conditionalPanel( condition = 'input.predictor == "Community cluster"', {
DT::dataTableOutput("fitted_tukey")
})
) ## END column
), ## END fluidRow
fluidRow(
column(4,
p(tags$b("Plot styling options:")),
shiny::uiOutput("model_plot_options")
), ## END column
column(8,
div(style="float:center;width:600px;height:400px;",
shiny::plotOutput("fitted_model_plot", height = "100%", width = "100%")
),
div(style="display:inline-block; float:right;",
shinyWidgets::downloadBttn("download_model_plot", "Download Plot", size = "sm", style = "minimal", color = "danger")
) ## END div
) ## END column
) ## END fluidRow
), ## END "Analyze Network Minerals" tabPanel
## TIMELINE PANEL ---------------------------------------------------------------------------------------------
shiny::tabPanel("Mineral formation timeline",
div(style="float:center;width:100%;height:700px;",
plotOutput("timeline_plot_output", height = "100%", width = "100%")
),
br(),
shinyWidgets::prettySwitch("timeline_view","Display minerals discovered at their oldest known age only. Turn off to display minerals discovered at any age.", value = TRUE, status="danger"),
fluidRow(
## can't use the module here due to sizing
column(4,
div(style="display:inline-block;vertical-align:top;",
shinyWidgets::pickerInput("color_timeline_by",
"Color minerals inside the selected age range based on:",
mineral_timeline_color_by_choices,
selected = "singlecolor", width = "100%")
),
div(style="display:inline-block;vertical-align:top;",
conditionalPanel(condition = "input.color_timeline_by == 'singlecolor'",
{
colourpicker::colourInput("timeline_color", "Color:", value = "#68340e")
}),
conditionalPanel(condition = "input.color_timeline_by != 'singlecolor'",
{
shinyWidgets::pickerInput("timeline_palette",
label = "Mineral color palette:",
choices = sd_palettes_ui$name,
options = list( size = 6),
choicesOpt = list(content = sd_palettes_ui$img),
selected = "YlOrBr", width = "100%")
})
)
),
column(4,
colourpicker::colourInput("outside_range_color", label = "Color for minerals outside the selected age range:", value="#fae9dd")
),
column(4,
br(),
shinyWidgets::downloadBttn("download_timeline", "Download Timeline Plot", size = "md", style = "minimal", color = "danger")
) ## END column 3
) ## END fluidRow
) ## END timeline tabPanel
), ## END TOP tabBox
## RENDER SELECTED NODE TABLE BELOW NETWORK ---------------------------------------------------------
br(),br(),br(),
shiny::uiOutput("show_nodeTable"),
br(),
## NETWORK EXPORT BOX -----------------------------------------------------------------------
box(width = 12, status = "primary", title = "Network Export", collapsible = TRUE,
shinyWidgets::actionBttn("store_position",
"Click to prepare network for export to PDF.",
color = "danger",
style = "fill",
block = TRUE),
br(),br(),
fluidRow(
column(3, br(), shinyWidgets::downloadBttn("export_network_pdf", "Export network as PDF", size = "sm", style = "minimal", color = "danger")),
column(3, shiny::sliderInput("baseline_output_element_size", "Scale network PDF element node size", min = 0.1, max = 5, step = 0.1, value = 1)),
column(3, shiny::sliderInput("baseline_output_element_label_size", "Scale network PDF element label size", min = 0.1, max = 5, step = 0.1, value = 1)),
column(3, shiny::sliderInput("baseline_output_mineral_size", "Scale network PDF mineral node size", min = 0.1, max = 5, step = 0.1, value = 1))
), ## END fluidRow
br(),br(),br(),
fluidRow(
column(3, shinyWidgets::downloadBttn("export_nodes_csv", "Export nodes as CSV", size = "sm", style = "minimal", color = "danger")),
column(3, shinyWidgets::downloadBttn("export_edges_csv", "Export edges as CSV", size = "sm", style = "minimal", color = "danger")),
column(3, shinyWidgets::downloadBttn("export_network_igraph", "Export network as text file", size = "sm", style = "minimal", color = "danger")),
column(3, shinyWidgets::pickerInput("igraph_output_format", label = "Choose network text file format:", choices = igraph_output_format_choices))
), ## END fluidRow
br(),br(),
shinyWidgets::downloadBttn("export_legend_pdf", "Export legend as PDF", size = "sm", style = "minimal", color = "danger")
) ## END box
) ## END div0
) ## END fluidRow
) ## END dashboardBody
) ## END dashboardPage
) ## END tagList
} ## END app_ui
#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @import shiny
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function(){
add_resource_path(
'www', app_sys('app/www')
)
tags$head(
golem::favicon(),
golem::activate_js(),
shinyWidgets::useSweetAlert(), ## May not be necessary per docs except for progress bars, but let's use it.
bundle_resources(
path = app_sys('app/www'),
app_title = 'dragon'
),
tags$style(".palette-style{
display: inline;
vertical-align: middle;
color: black;
font-weight: 600;
padding-left: 7px;}"
)
# Add here other external resources
# for example, you can add shinyalert::useShinyalert()
)
}
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