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ui.R
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ui.R
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# Define UI and wrap everything in a taglist that first calls useShinyjs()
ui <- tagList(useShinyjs(),
add_busy_spinner(
spin = "fading-circle",
position="bottom-left",
color = "deepskyblue",
margins = c(35,35)
),
# loading message
div(
id = "loading-gray-overlay",
class = "loading-mask",
div(class = "fadein-out busy relative-centered", style = "font-size:xx-large", "Loading app resources...")
),
navbarPage(
title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.0")),
windowTitle = 'FREDA',
id = "top_page",
theme = "yeti.css",
############# Welcome Panel #########################
navbarMenu("Welcome",
tabPanel(title = "Introduction", class = "background_FTICR",
includeMarkdown("./Welcome to FREDA.md"),
h4(tags$b('Citing FREDA')),
tags$p('A publication is forthcoming for FREDA. In the meantime, we ask that you cite FREDA by url', tags$b('(https://msc-viz.emsl.pnnl.gov/FREDA/)'), 'for any figures or analysis included in a publication or report.'),
hr(),
br(),
actionButton('all_tutorials', 'See a playlist of video tutorials',
onclick = "window.open('https://www.youtube.com/watch?v=uU5Q7r_pEGM&list=PLvozcBqO8i7wsMWo5PnOREX0sHSk3mAjE', '_blank')",
class="btn btn-info", icon = icon('facetime-video', lib = 'glyphicon'))
),
tabPanel(title = "Data Requirements", class = "background_FTICR", value = 'data_requirements',
includeMarkdown("./DataRequirements.md"),
downloadButton('downloadData', 'Download')),
tabPanel(title = "Resources/Contact", class = "background_FTICR",
includeMarkdown('resources_and_contact.md')
)
),
################## Groups Panel ###############################################
tabPanel(div("Groups", icon('th-large', lib = 'glyphicon')), value = 'Groups',
fluidRow(style = "display:flex;flex-direction:row;align-items:stretch",
column(4,
wellPanel(style = "height:100%",
tags$h4("Define a Group"),
div(id = "js_group_name", textInput("group_name", "Name of this group:")),
fluidRow(
column(6, uiOutput("group_samples")),
column(6, textInput("group_regex", "Search sample names"))
),
actionButton("add_group", "Add this group"),
br(),
br(),
uiOutput("warnings_groups")
)
),
column(8,
wellPanel(style = "height:100%",
dataTableOutput("group_table"),
actionButton("remove_group", "Remove selected group")
)
)
),
hr(),
actionButton("goto_preprocess_main", "Continue to preprocess tab")
),
################## Preprocess Panel ###############################################
tabPanel(div("Preprocess", icon('cogs')), value = 'Preprocess',
sidebarLayout(
# Sidebar panel
sidebarPanel(
div(class = "adjustdown", uiOutput("which_calcs")),
# Action button: add test columns with results to peakData2
div(
disabled(actionButton('preprocess_click', 'Process Data', icon = icon("cog"), lib = "glyphicon")),
hidden(div('Calculating values, please wait...', id = 'preprocess_waiting',
style = 'font-weight:bold;color:deepskyblue;display:inline', class = 'fadein-out'))
),
br(),
uiOutput("warnings_preprocess")
), # End sidebar panel
mainPanel(
# Set default main panel width
width = 8,
# Include numeric and categorical summaries in a well panel
wellPanel(
tags$div(class = "row",
tags$div(class = "col-sm-5", style = "height:350px;overflow-y:scroll;",
uiOutput("numeric_header"),
dataTableOutput('numeric_summary')
),
tags$div(class = "col-sm-7", style = "height:350px;overflow-y:scroll;",
uiOutput("cat_header"),
uiOutput('categorical_summary')
)
)
),
# Drop down list: which histogram should be displayed?
uiOutput('which_hist_out'),
# Plot: histogram
plotlyOutput('preprocess_hist')
) # End main panel on Preprocess tab #
)), # End Preprocess tab #
##################### QUALITY CONTROL PANEL ###########################
tabPanel(div("Quality Control", icon('chart-bar')), value = 'Quality Control',
fluidRow(style = 'display:flex;flex-direction:row;align-items:stretch',
column(4,
wellPanel(style = 'height:100%',
uiOutput('qc_select_groups', style = "width:50%"),
hr(style = 'margin:2px'),
uiOutput('qc_plot_scale', style = "width:50%"),
textInput('qc_boxplot_xlab', "X axis label"),
textInput('qc_boxplot_ylab', 'Y axis label'),
textInput('qc_boxplot_title', 'Title'),
actionButton('update_boxplot_axes', "Update Boxplot Axes"),
br(), br(),
uiOutput('warnings_qc')
)
),
column(8,
wellPanel(style = 'height:100%',
div(id = 'style_qc_boxplots', style = 'border-style:solid;border-width:1px;padding-top:5px',
plotlyOutput("qc_boxplots") %>% withSpinner(color = "orange", type = 8)
)
)
)
),
hr(),
actionButton('goto_filter_fromqc', "Continue to the filter tab")
),
################## Filter Panel ##############################################
tabPanel(div("Filter", icon('filter')), value = 'Filter',
sidebarLayout(
sidebarPanel(
# Set default width for panel
width = 5,
# Checkbox: Mass filter yes/no
bsCollapse(id = 'filter_sidebar',
open = c('samplefilt_collapse', 'massfilt_collapse', 'formfilt_collapse', 'molfilt_collapse'),
multiple = TRUE,
bsCollapsePanel(div('Sample Filter',
div(style = "color:deepskyblue;display:inline-block",
tipify(icon("question-sign", lib = "glyphicon"),
title = "Retain a subset of all samples",
placement = "top", trigger = 'hover')
),
div(style = 'float:right', uiOutput('samplefilter_icon'))
), value = 'samplefilt_collapse',
div(class = "adjustdown",
checkboxInput('samplefilter', tags$b("Apply this filter, keeping only the following samples:", style = "display:inline-block"), value = FALSE)
),
div(id = "js_filter_samples",
uiOutput("filter_samples")
),
textInput('filter_regex', 'Search sample names')
),
bsCollapsePanel(div('Mass Filter',
div(style = "color:deepskyblue;display:inline-block",
tipify(icon("question-sign", lib = "glyphicon"),
title = "Retain peaks within a mass range specified below",
placement = "top", trigger = 'hover')
),
div(style = 'float:right', uiOutput('massfilter_icon'))
), value = 'massfilt_collapse',
div(class = "adjustdown", checkboxInput('massfilter', tags$b("Apply this filter, removing peaks outside the mass range:", style = "display:inline-block"), value = FALSE)
),
# Numeric: Min/max mass filter
splitLayout(
numericInput('min_mass', 'Minimum Mass value',
min = 0, value = 200),
numericInput('max_mass', "Maximum Mass value",
min = 0, value = 900)
)
),
bsCollapsePanel(div('Molecule Filter',
div(style = "color:deepskyblue;display:inline-block",
tipify(icon("question-sign", lib = "glyphicon"),
title = "Retain peaks that are observed in a minimum number of samples, specified below",
placement = "top", trigger = 'hover')
),
div(style = 'float:right', uiOutput('molfilter_icon'))
),
value = 'molfilt_collapse',
# Checkbox: Mass filter yes/no
div(class = "adjustdown", checkboxInput('molfilter', tags$b("Apply this filter, removing peaks with too few observations: ", style = "display:inline-block"), value = FALSE)
),
# Drop-down list: Min/max mass filter
uiOutput('minobs')
),
bsCollapsePanel(div('Formula Presence Filter',
div(style = "color:deepskyblue;display:inline-block",
tipify(icon("question-sign", lib = "glyphicon"),
title = "Retain peaks that have a molecular formula specified or calculated from elemental values",
placement = "top", trigger = 'hover')
),
div(style = 'float:right', uiOutput('formfilter_icon'))
),
value = 'formfilt_collapse',
div(class = "adjustdown", checkboxInput('formfilter', tags$b("Apply this filter, removing peaks without a molecular formula", style = "display:inline-block"), value = FALSE)
)
),
bsCollapsePanel(div('Implement up to 3 custom filters',
div(style = "color:deepskyblue;display:inline-block",
tipify(icon("question-sign", lib = "glyphicon"),
title = "Filter based on up to 3 variables in the post-processed molecular identification file",
placement = "top", trigger = 'hover')
),
div(style = 'float:right', uiOutput('customfilter_icon'))
),
value = 'customfilt_collapse',
div(class = "adjustdown", checkboxInput('customfilterz', tags$b("Show dropdowns and apply all specified filters", style = "display:inline-block"), value = FALSE)
),
conditionalPanel(id = "custom_cond_panel", condition = "input.customfilterz == true",
uiOutput("filter1UI"),
uiOutput("customfilter1UI"),
uiOutput("filter2UI"),
uiOutput("customfilter2UI"),
uiOutput("filter3UI"),
uiOutput("customfilter3UI")
)
)
), # end collapse panel
hr(),
disabled(
fluidRow(
column(
width = 6, actionButton('filter_click', "Filter Data", icon = icon("cog", lib = "glyphicon"))
),
column(
width = 6, actionButton('reset_filters', "Reset Filters", icon = icon("trash", lib = "glyphicon"))
)
)
),
br(),
br(),
div(id = "warnings_filter", style = "overflow-y:auto;max-height:150px", uiOutput("warnings_filter_UI"))
), # End sidebar panel on Filter tab
mainPanel(
# Set default width for panel
width = 7,
# waiting messages for large data during filtering and plot calculation
hidden(div('Applying your filters, please wait...', id = 'calc_filter', class = 'fadein-out',
style = 'color:deepskyblue;font-weight:bold;margin-bottom:5px')),
hidden(div('Drawing your plot, please wait...', id = 'draw_large_filter_plot', class = 'fadein-out',
style = 'color:deepskyblue;font-weight:bold;margin-bottom:5px')),
# Summary panel: display summary of filters
wellPanel(
tableOutput('summary_filter')
),
# Plot: Show number of peaks before/after filters applied
plotOutput('barplot_filter')
) # End main panel on Filter tab
)), # End Filter tab
################## Visualize Panel ###############################################
navbarMenu(div('Visualize', icon('eye-open', lib = 'glyphicon'), style = 'display:inline-block'),
# Main plot creation sub-panel
tabPanel(div("Create Plots"), value = 'Visualize',
fluidRow(
# Sidebar Panel
div(id = 'viz_sidebar_column', column(4,
# Begin collapsible section
bsCollapse(id = 'viz_sidebar', open = c('peakplots', 'axlabs'), multiple = TRUE,
# Plot Parameters
bsCollapsePanel(div('Construct a plot', div(style = 'float:right', uiOutput('chooseplots_icon'))), value = 'peakplots',
# Select Plot Type
inlineCSS("#chooseplots .btn{font-size:10.5pt;} #chooseplots .btn-group-container-sw{display:block;}"),
uiOutput('plot_type', style = "margin-top:-10px"),
# Select samples/groups
uiOutput('plotUI'),
uiOutput('pcoa_dist'),
uiOutput('viztab_select_groups'),
# Single dropdown for 1 sample/group or....
hidden(div(id = "js_toggle_single", uiOutput("plotUI_single"))),
# ...two dropdowns and extra options for group comparison
hidden(div(id = "js_toggle_groups",
tagList(div(id = "js_whichGroups1", uiOutput("plotUI_comparison_1")),
div(id = "js_whichGroups2", uiOutput("plotUI_comparison_2"))
)
)
),
hidden(div(id = 'js_summary_fxn', uiOutput("summary_fxn_out", class = "adjustdown")
)
)
),
# Axes Options
bsCollapsePanel(div('Axes labels', div(style = 'float:right', uiOutput('axlabs_icon'))), value = 'axlabs',
splitLayout(
uiOutput("title_out"),
tags$div(id = "js_legend_title_input", uiOutput("legend_title_out"))
),
splitLayout(
uiOutput("x_axis_out"),
uiOutput("y_axis_out")
)
),
bsCollapsePanel(div('Coloring/Appearance', div(style = 'float:right', uiOutput('dynamic_opts_icon'))), value = 'reactive_plot_opts',
# plot options
wellPanel(
# color and van-krevelen bounds dropdowns
fluidRow(
column(width = 6, class = "grey_out", id = "js_vk_colors",
disabled(selectInput("vk_colors", "Color by:", choices = NULL, selected = NULL))
),
column(width = 6, class = "grey_out", id = "js_vkbounds",
disabled(selectInput('vkbounds', 'Van Krevelen boundary set:',
choices = c('BS1' = 'bs1', 'BS2' = 'bs2', 'None' = 0),
selected = 0))
)
),
# x and y axis variable dropdowns for custom scatter plot
fluidRow(
column(width = 6, class = "grey_out", id = "js_scatter_x",
disabled(selectInput("scatter_x", "Horizontal axis variable:", choices = NULL, selected = NULL))
),
column(width = 6, class = "grey_out", id = "js_scatter_y",
disabled(selectInput("scatter_y", "Vertical axis variable:", choices = NULL, selected = NULL))
)
),
# color pallete options and button to flip colorscale direction
fluidRow(
column(6,
tags$div(id = "js_colorpal", uiOutput("colorpal_out"), style = "display:inline-block"),
actionButton("flip_colors", "Invert color scale")
)
)
)
)
)
)), # End sidebar conditionals on Visualize tab #
# Plot panel and generate plot buttons
column(8,
inlineCSS("#FxnPlot {width:inherit;}"),
wellPanel(style = "margin-top:-10px",
div(class = 'plot_border', style = "width:65%",
plotlyOutput('FxnPlot', width = 'auto', height = '600px') %>%
withSpinner(color = "orange", type = 8)
),
# Separate buttons to generate plot or simply update labels without recalculating data
disabled(
div(style = 'display:inline-block;margin-top:10px',
bsButton("plot_submit", label = "Generate Plot", icon = icon("plus"), lib = "glyphicon"),
bsButton("update_axes", label = "Update Labels", icon = icon("refresh"), lib = "glyphicon"),
hidden(bsButton('make_goto_linked', label = 'Compare in Linked Plots', icon = icon('link')))
)
),
br(),
br(),
div(id = "warnings_visualize", style = "overflow-y:auto;max-height:150px", uiOutput("warnings_visualize"))
),
) # End main panel on Visualize tab #
) # end fluidrow
),
# Linked plots sub-panel
tabPanel('Linked Plots', value = 'Linked Plots',
bsCollapse(id = 'linked_plots_collapse', open = c('lp_select_plots'), multiple = TRUE,
bsCollapsePanel(title = 'Choose Two Plots to Compare', value = 'lp_select_plots',
tags$i(info_text[['VALID_LINKED_PLOTS']]),
tags$hr(),
DTOutput('lp_plot_table'),
bsButton('lp_compare_plots', 'Compare These Plots')),
# bsCollapsePanel(title = 'Create A Linked Plot', value = 'lp_create_plot',
# DTOutput('lp_plot_table'),
# bsButton('lp_create_plot', 'Create and Compare With Selected Plot')),
bsCollapsePanel(title = 'View and Interact', value = 'lp_mainpanel',
splitLayout(cellArgs = list(class = 'plot_border'),
withSpinner(plotlyOutput('lp_left', height = '600px'), color = 'orange', type = 8),
withSpinner(plotlyOutput('lp_right', height = '600px'), color = 'orange', type = 8)
)
)
)
)
), # End Visualize tab #
################## Database Mapping Panel ####################
tabPanel(div('Database Mapping', icon('th-list', lib = 'glyphicon')), value = 'Database Mapping',
fluidRow(style = "display:flex;flex-direction:row;align-items:stretch",
column(4,
bsCollapse(id = 'db_mapping_sidebar', open = c('mappings'), multiple = TRUE,
bsCollapsePanel('Choose which mappings to calculate', value = 'mappings',
radioGroupButtons('database_select', label = "Choose a Database", choices = c('Kegg', 'MetaCyc')),
numericInput('max_records_database', 'Exclude formulae that map to more than this many records:', value = 5),
checkboxGroupButtons('which_mappings', label = "Include which variables in mapping:",
choices = c('Reactions' = 'comp2react', 'Modules' = 'react2mod', 'Pathways' = 'mod2path')),
hr(),
tags$p('Make unique rows for which variable?'),
div(
div(style = 'display:inline-block',
uiOutput('which_unique')
),
bsButton('create_mapping', 'Perform Mapping', style = 'info')
),
uiOutput('warnings_database')
)
)
), # column 4
column(8,
bsCollapse(id = 'database_tables_parent_collapse', open = 'database_tables', multiple = TRUE,
bsCollapsePanel('Table Preview', value = 'database_tables',
span(id = "toggle_table",
div(style = 'display:inline-block;margin-top:10px;margin-right:10px;font-weight:bold', "Display results:"),
div(style = 'display:inline-block', radioGroupButtons('which_table', choices = c('Kegg' = 1, 'MetaCyc' = 2))),
div(style = 'display:inline-block', bsButton('save_db_table', 'Save current table', style = 'info')),
div(style = 'display:inline-block', bsButton('view_db_tables', uiOutput('n_saved_db_tables'), style = 'info'))
),
uiOutput('conditional_database_table')
),
bsCollapsePanel('Summary Counts', value = 'database_plots',
DTOutput('mapping_summary'),
uiOutput('conditional_database_barplot')
# splitLayout(plotlyOutput('kegg_barplot'),
# plotlyOutput('mc_barplot'))
)
) # parent collapse
) # column 8
) # fluidrow
), # tabpanel
################## Download Panel ##############################################
tabPanel(div('Download', icon('download')), value = 'Download',
fluidRow(style = "display:flex;flex-direction:row;align-items:stretch",
column(width = 6,
wellPanel(style = "height:100%",
tags$h4(icon("table", "fa-2x"), tags$b("Processed Data")),
checkboxGroupInput("download_selection", label = "Check Download Selection",
choices = c('Data File as one .csv and Molecular Identification File as another .csv' = "separate",
'Merged Data File and Molecular Identification File as a single .csv' = "merged",
'Data summaries for grouped plots' = "group_data"),
width = "80%")
)
),
column(width = 5,
wellPanel(style = "height:100%",
tags$h4(icon("align-left", "fa-2x"), tags$b("Summary Report and Database Mapping Tables")),
checkboxInput("report_selection", label = "Download a summary of preprocessing and filtering", value = TRUE),
checkboxInput("download_mappings", label = "Download Database Mapping Tables", value = FALSE)
)
)
),
fluidRow(style = "margin-top:10px",
column(width = 11,
wellPanel(
div(style = 'display:flex',
column(width = 5,
tags$h4(icon("image", "fa-2x"), tags$b("Figures")),
tags$h5(tags$b("Select figures by row. When clicked, the download selection will highlight.")),
DTOutput("download_plot_table")
),
column(width = 7,
div(style = 'height:100%', class = 'plot_border', uiOutput('download_plot'))
)
),
hr(),
br(),
div(style = 'display:flex',
div(style = 'float:left;width:50%;margin-left:10px',
bsButton('mark_plot_download', 'Select/de-select for download', icon = icon('minus')),
bsButton('remove_plot_download', 'Remove selected plot', icon = icon('remove'))
),
div(style = 'float:right;width:50%', class = 'spaced_flexbox',
inlineCSS('[id=download_dimensions] > .shiny-input-container {width:49%;display:inline-block;}'),
div(id = 'download_dimensions',
numericInput('download_img_width', 'Download width', value = 1600, min = 100, max = 2000, step = 1),
numericInput('download_img_height', 'Download height', value = 900, min = 100, max = 2000, step = 1)
),
radioButtons(inputId = "image_format", label = "Select an image format",
choices = c("png", "pdf", "jpeg"), selected = "png", inline = TRUE)
)
),
uiOutput('warnings_download')
)
)
),
div(style = 'width:75%',
actionButton('makezipfile', label = tags$b('Bundle up all selected items'), icon = icon("briefcase"), lib = "glyphicon", style = 'width:45%'),
disabled(downloadButton('download_processed_data', tags$b('Download bundle'), style = 'width:45%;float:right'))
),
tags$br()
),
################## Glossary Panel ##############################################
tabPanel(div('Glossary', icon('question-sign', lib = 'glyphicon')), value = 'Glossary',
withMathJax(includeMarkdown("./README/Glossary.md"))
)
),
hidden(div(id = "corems_to_peakdata_toggle", style = "position:fixed;left:15px;bottom:15px", uiOutput("corems_to_peakdata_UI"))),
div(id = "js_helpbutton", style = "position:absolute;top:3px;right:16px;z-index:1000;width:11%",
div(style = 'float:right;width:25%',
tipify(
hidden(bsButton("helpbutton", icon("question-sign", lib = "glyphicon", style = "color:white"), style = "info")),
ttip_text[['page_help']]
)
),
div(style = 'float:right;width:50%%;margin-left:1px;margin-right:1px',
tipify(
hidden(bsButton("viewplots", uiOutput('viewplots_label', style = 'float:left;margin-right:10px'), style = "info", icon = icon("folder-open", lib = "glyphicon"))),
ttip_text[['plot_review']]
)
),
div(style = 'float:right;width:25%',
tipify(
hidden(bsButton("saveplot", icon("save", lib = "glyphicon"), style = "info")),
ttip_text[['plot_save']]
)
),
hidden(bsButton('datareqs_video', 'Data requirements tutorial',
onclick = "window.open('https://youtu.be/uU5Q7r_pEGM', '_blank')",
style = 'info', icon = icon('facetime-video', lib = 'glyphicon'))),
),
uiOutput("enter_debugger")
)