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OmicsVolcano_v1_1_UI.r
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# OmicsVolcano V1.1
#
# UPDATED !!!!!!!!!!!!!!!!!!!!
#
# The initial version of OmicsVolcano used shinydashboardPlus() v.0.7.5 function,
# which has been depreciated.
# The software has updated version of shinydashboardPlus() v.2.0.0 now.
#
# rightSidebar() is replaced with dashboardControlbar()
#
# fontawesome package has been added | packageVersion("fontawesome") - '0.2.2'
#
# The software has been tested on R version 4.1.1 (2021-08-10) "Kick Things"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# ====================================================================
# ====================================================================
# ====================================================================
# Title: OmicsVolcano
# Copyright: (C) 2020
# License: GNU General Public
#
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# NON-ACADEMICS:
# CONTACT authors/software developers for any COMMERCIAL USE
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
#
# ====================================================================
# ====================================================================
# ====================================================================
# ====================================================================
# ====================================================================
# ====================================================================
# SOFTWARE DEVELOPERS
# ====================================================================
# ====================================================================
# ====================================================================
# Author: Irina Kuznetsova
# email: irina.kuznetsova@perkins.org.au
# Co-developer: Artur Lugmayr
# email: lartur@acm.org
# Edith Cowan University, WA, AUSTRALIA
# Umea University, Umea, Sweden
# UXMachines Pty Ltd. WA, AUSTRALIA
# ====================================================================
# ====================================================================
# ====================================================================
# LICENSE
# ====================================================================
# ====================================================================
# ====================================================================
# OmicsVolcano is visualization software that enables to explore interactively
# volcano plot for presence of mitochondrial localized genes or proteins.
#
# Copyright (C) 2020 Irina Kuznetsova
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# ====================================================================
# ====================================================================
# ====================================================================
# HELPER FUNCTIONS
# ====================================================================
# ====================================================================
# ====================================================================
modify_stop_propagation = function(x) {
x$children[[1]]$attribs$onclick = "event.stopPropagation()"
x
}
# ====================================================================
# ====================================================================
# ====================================================================
# STATUS BAR IMPLEMENTATION
# ====================================================================
# ====================================================================
# ====================================================================
# ===================================================================================================================================
# ===================================================================================================================================
# 1. STATUS AND ERROR BAR
# ===================================================================================================================================
# ===================================================================================================================================
# TOP ICONS
ui_info_box = box(width = 12,
fluidRow(
width = 12,
# A static infoBox
infoBoxOutput("UI_INFO_GENERAL"),
infoBoxOutput("UI_INFO_PROCESS"),
infoBoxOutput("UI_INFO_EXPLORE")
))
# ====================================================================
# ====================================================================
# ====================================================================
# UI COMPONENTS AND ELEMENTS
# ====================================================================
# ====================================================================
# ====================================================================
# ===================================================================================================================================
# ===================================================================================================================================
# 1. GENERAL ELEMENTS
# ===================================================================================================================================
# ===================================================================================================================================
ui_menue_body_elements = c("menue_tab_home_body", "menue_tab_file_open_body")
# ===================================================================================================================================
# ===================================================================================================================================
# 2. DOWNLOAD DEMO FILE LINK
# ===================================================================================================================================
# ===================================================================================================================================
ui_download_demo_file =
tags$a(
href = CONST_DEMO_FILE,
target = "_blank",
icon = icon("sliders-h"), # changed in October 2021
#icon("disk"), # commented out October 2021
"Download demo file to local PC...",
download = "demofile.txt")
# ===================================================================================================================================
# ===================================================================================================================================
# 3. FILE UPLOAD
# ===================================================================================================================================
# ===================================================================================================================================
ui_file_input_diag = box (
width = 12,
checkboxInput(
inputId = "UI_INPUT_FILE_REMOVE_DUPLICATES",
label = "Check for Duplicates",
value = TRUE),
radioButtons(
inputId = "UI_INPUT_FILE_SEPARATOR",
"File Separator",
choices = c( Semicolon = ";", Tab = "\t"),
selected= "\t"),
tags$hr(),
ui_download_demo_file,
tags$hr(),
fileInput(
inputId = "UI_INPUT_FILE_NAME",
label = NULL,
buttonLabel = "Open...",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv") ),
DTOutput(outputId = "UI_INPUT_FILE_RESULTS")
)
# ===================================================================================================================================
# ===================================================================================================================================
# 4. THRESHOLD BOX
# ===================================================================================================================================
# ===================================================================================================================================
ui_threshold_configuration = box (id = "ui_threshold_configuration",
color = "orange",
title = "Threshold",
solidHeader = TRUE,
width = 12,
# Vertical threshold
numericInput("VerticalThreshold",
label = "Plot Vertical Threshold",
value = 1,
min = 0.1,
max = 1000,
step = 0.5),
tags$style(
type = "text/css",
".irs-grid-text:nth-child(-2n+18) {color: black; }", #https://stackoverflow.com/questions/50370958/color-tick-mark-tick-mark-labels-in-sliderinput-shiny
".irs-grid-text:nth-child(2n+20) {color: red; font-size:12}",
".irs-grid-pol:nth-of-type(-n+0) {background: black; }",
".irs-grid-pol:nth-of-type(n+0) {background: black}" ),
sliderInput(inputId = "Signif",
label = "Significance",
min = 0,
max = 0.1,
value = c(0.05),
step = 0.01,
round = -3 ))
# ===================================================================================================================================
# ===================================================================================================================================
# 5. EXPLORE ONE MITOCHONDRIAL PROCESS
# ===================================================================================================================================
# ===================================================================================================================================
ui_explore_mitochondrial_process = box (
color = "orange",
title = "Mitochondrial Process",
solidHeader = TRUE,
width = 12,
# Organism of interest
radioButtons(
inputId = "OrganismSource",
label = "Select Organism",
choices = c("Mouse", "Human"),
inline = TRUE),
# A process of interest
selectInput(
inputId = "MtProcess",
label = "Show Mitochondrial Process",
# IF: mult=F, selectize=F, size - 5 box anables to see 5 options, but to select only one
# IF: mult=T, selectize=T | no size option
multiple =F,
selected ="Show All Mitochondrial Genes",
choices = list( `Processes:` = list(
# choices = list(
"Show All Mitochondrial Genes", "Amino Acid Metabolism",
"Apoptosis", "Bile Acid Synthesis",
"Calcium Signaling & Transport", "Cardiolipin Biosynthesis",
"Fatty Acid Biosynthesis & Elongation",
"Fatty Acid Degradation & Beta-oxidation",
"Fatty Acid Metabolism", "Fe-S Cluster Biosynthesis",
"Folate & Pterin Metabolism", "Fructose Metabolism", "Glycolysis",
"Heme Biosynthesis", "Import & Sorting", "Lipoic Acid Metabolism",
"Metabolism of Lipids & Lipoproteins", "Metabolism of Vitamins & Co-Factors",
"Mitochondrial Carrier", "Mitochondrial Dynamics",
"Mitochondrial Gene Expression", "Mitochondrial Signaling",
"Mitophagy", "Nitrogen Metabolism", "Nucleotide Metabolism",
"Oxidative Phosphorylation", "Pentose Phosphate Pathway",
"Protein Stability & Degradation", "Pyruvate Metabolism",
"Replication & Transcription", "Ribosomal", "ROS Defense", "Transcription (nuclear)",
"Translation", "Transmembrane Transport", "Tricarboxylic Acid Cycle",
"Ubiquinone Biosynthesis", "Unknown MT process", "UPRmt"),
# "Oxidative Phosphorylation (MT)", "Translation (MT)")
`MT DNA encoded:` = list("Oxidative Phosphorylation (MT)", "Translation (MT)"))
)
)
# ===================================================================================================================================
# ===================================================================================================================================
# 6. EXPLORE MULTIPLE MITOCHONDRIAL PROCESSES
# ===================================================================================================================================
# ===================================================================================================================================
ui_explore_multiple_mitochondrial_processes = box(
color = "orange",
title = "Mutliple Mitochondrial Processes",
solidHeader = TRUE,
width = 12,
# ORGANISM OF INTEREST
radioButtons(
inputId = "OrganismSource2",
label = "Select Organism",
choices = c("Mouse", "Human"),
inline = TRUE),
# uiOutput("UI_MMP_PROCESSES")
actionButton(inputId = "UI_MMP_LIST_ACTION",
width = '80px',
label = "Apply"),
# actionButton("selectall", "Select All"),
hr(), # space btw Action button and next info
h4("Select Processes and Colours"),
h6("Hex colour code - #D91414, or colour name - red"),
lapply(1:length(ui_mmp_names), function(x) {
fluidRow( offset = 1,
# CHECK BOXES
column (width = 1,
checkboxInput(
inputId = paste0("UI_MMP_LIST_CHECKBOX_", x),
value = FALSE,
label = NULL)),
# COLOUR PALETTE
column (width = 2,
colourWidget( elementId = paste0("UI_MMP_LIST_COLORPICKER_", x),
value = "#000000",
palette = "square",
showColour = "both",
width = '77px',
height = '20px')),
# PROCESSES
column (width = 9,
h5(ui_mmp_names[x]))
)})
)
# ===================================================================================================================================
# ===================================================================================================================================
# 7. EXPLORE CELLULAR COMPARTMENT LOCALIZATION
# ===================================================================================================================================
# ===================================================================================================================================
ui_explore_cellular_compartment_localiz = box (
color = "orange",
title = "Cellular Compartment Localization (Human)",
solidHeader = TRUE,
width = 12,
# A process of interest
selectInput(
inputId = "CellularLocal",
label = "Cellular Localization",
multiple = F,
selected ="actin",
choices = list("Actin Filaments", "Centrosome", "Cytosol", "Endoplasmic Reticulum", "Golgi Apparatus", "Intermediate Filaments",
"Microtubules", "Mitochondria", "Nucleoli", "Nuclear Membrane", "Plasma Membrane", "Vesicles")
)
)
# ===================================================================================================================================
# ===================================================================================================================================
# 8. EXPLORE CUSTOM GENE LIST
# ===================================================================================================================================
# ===================================================================================================================================
ui_explore_custom_gene_list = box(color = "orange",
title = "Custom Gene List",
solidHeader = TRUE,
width = 12,
radioButtons( inputId = "CustomInputOptions",
label = NULL,
choices = c("Insert a list of genes", "Upload a gene file"),
inline = TRUE),
# a-Condition to insert own list of genes
conditionalPanel( condition = "input.CustomInputOptions == 'Insert a list of genes'",
tabPanel( title = "Explore Custom Gene List",
textInput(inputId = "CustomList",
label = "Insert a list of genes separated by space",
value = "ptcd3 sf1 mrp130")
)
),
# b-Condition to upload a file with list of genes
conditionalPanel(
condition = "input.CustomInputOptions == 'Upload a gene file'",
fileInput(inputId = "UserGeneNamesFile",
label = "Upload a gene file")
)
)
# ===================================================================================================================================
# ===================================================================================================================================
# 10. PLOT DOWNLOAD
# ===================================================================================================================================
# ===================================================================================================================================
ui_download_plot = box (selectInput(inputId = "PlotDownload",
label = "Select Plot",
choices = c("Custom Gene List"),
selected = c("Custom Gene List")),
selectInput(
inputId = "Plotfiletype",
label = "Select Plot File Format",
choices = c("svg", "pdf", "jpeg", "png", "tiff"),
selected = "svg"),
downloadButton(outputId = "DownloadPlot",
label = "Download Plot")
)
# ===================================================================================================================================
# --------------------------------------- END --------------------------------------- "PLOT DOWNLOAD"
# ===================================================================================================================================
# ===================================================================================================================================
# ===================================================================================================================================
# 11.TABLE DOWNLOAD
# ===================================================================================================================================
# ===================================================================================================================================
ui_download_table = box ( selectInput(inputId = "TableDownload",
label = "Select Table",
choices = c("Significant", "Mito Processes",
"All Processes in Input Data", "Multiple Processes", "Cellular Localization"),
selected = c("Significant") ),
selectInput(inputId = "Tablefiletype",
label = "Select File Format",
choices = c("csv", "txt"),
selected = "csv"),
downloadButton(outputId = "DownloadTbl",
label = "Download Table")
)
# ===================================================================================================================================
# --------------------------------------- END --------------------------------------- "TABLE DOWNLOAD"
# ===================================================================================================================================
# ====================================================================
# ====================================================================
# ====================================================================
# RIGHT DASHBOARD SIDEBAR
# ====================================================================
# ====================================================================
# ====================================================================
# ===================================================================================================================================
# ===================================================================================================================================
# 1. SETTING OPTIONS FOR THE RIGHT-SIDE DASHBOARD MENUE
# ===================================================================================================================================
# ===================================================================================================================================
function_para_tabs = tagList (tags$style("#UI_RIGHT_SIDEBAR_SELECTMODE { display:none; }"),
tabsetPanel (id = "UI_RIGHT_SIDEBAR_SELECTMODE",
selected = "menue_tab_exp_plot",
ui_threshold_configuration,
tabPanel("menue_tab_exp_plot"),
tabPanel("menue_tab_exp_genelist",
ui_explore_custom_gene_list ),
tabPanel("menue_tab_exp_mitproc",
ui_explore_mitochondrial_process),
tabPanel("menue_tab_exp_cellular_compartment",
ui_explore_cellular_compartment_localiz),
tabPanel("menue_tab_exp_multiple_mitoprocesses",
ui_explore_multiple_mitochondrial_processes),
tabPanel("UI_RIGHT_SIDEBAR_NONE",
p(""))
)
)
# ===================================================================================================================================
# --------------------------------------- END -------------------------------- "SETTING OPTIONS FOR THE RIGHT-SIDE DASHBOARD MENUE"
# ===================================================================================================================================
# ===================================================================================================================================
# ===================================================================================================================================
# 2. CONFIGURATION (RIGHT DASHBOARD)
# ===================================================================================================================================
# ===================================================================================================================================
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# START
# Belongs to the initial software version
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#The old rightSidebar() component becomes the dashboardControlbar()
# to ease the transition from shinydashboardPlus to {bs4Dash}, the latter being the Bootstrap 4
# version with a more modern look and feel
#
# ui_right_sidebar = rightSidebar(
# background = "light",
# width = 350,
# fluid = FALSE,
# h1("Settings"),
# function_para_tabs)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Belongs to the initial software version
# END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ui_right_sidebar = dashboardControlbar(
skin = "light",
width = 350,
# fluid = FALSE,
h1("Settings"),
function_para_tabs)
# ===================================================================================================================================
# --------------------------------------- END -------------------------------- "CONFIGURATION"
# ===================================================================================================================================
# ====================================================================
# ====================================================================
# ====================================================================
# LEFT DASHBOARD SIDEBAR
# ====================================================================
# ====================================================================
# ====================================================================
ui_dash_sidebar = dashboardSidebar(
collapsed = FALSE,
disable = FALSE,
sidebarMenu(id = "ui_dashboard_sidebar",
sartExpanded = TRUE,
menuItem("Home Page",
tabName = "menue_tab_home",
icon = icon("home")),
menuItem("File",
icon = icon("database"),
menuSubItem("Open...",
tabName = "menue_tab_file_open",
icon = icon("folder-open")) ),
menuItem("Explore",
icon = icon("eye"),
menuSubItem("Plot",
tabName = "menue_tab_exp_plot",
icon = icon("image")),
menuSubItem("Custom Gene List",
tabName = "menue_tab_exp_genelist",
icon = icon("dna")),
menuSubItem( "Mitochondrial Process",
tabName = "menue_tab_exp_mitproc",
icon = icon("project-diagram") ),
menuSubItem( "Multiple Processes",
tabName = "menue_tab_exp_multiple_mitoprocesses",
icon = icon("balance-scale") ),
menuSubItem( "Cellular Localization",
tabName = "menue_tab_exp_cellular_compartment",
icon = icon("anchor") )),
menuItem( "Export",
icon = icon("save"),
menuSubItem("Plot",
tabName = "menue_tab_download_plot",
icon = icon("file-export")),
menuSubItem("Table",
tabName = "menue_tab_download_table",
icon = icon("file-export")) ),
menuItem("Help", icon = icon("question"), tabName = "menue_tab_help"),
menuItem("About", icon = icon("info"), tabName = "menue_tab_about")
)
)
# ====================================================================
# ====================================================================
# ====================================================================
# BODY ELEMENTS
# ====================================================================
# ====================================================================
# ====================================================================
# ===================================================================================================================================
# ===================================================================================================================================
# I. MENUE ITEMS FOR BODY TAB
# ===================================================================================================================================
# ===================================================================================================================================
# 1. HOMEPAGE
menue_tab_home_body = tabItem("menue_tab_home",
h1("Home Page"),
# Textual info at HOME page
mainPanel(tags$div( h3("OmicsVolcano"),
p("OmicsVolcano is a visualization software tool that enables to explore interactively volcano plot for presence of mitochondrial localized genes or proteins"),
img(src = './images/OmicsVolcano_example.svg',
height = '300px',
width = '600px',
align = "middle"),
br(),
br(),
p("Copyright (C) 2020") )) )
# ===================================================================================================================================
# --------------------------------------- END --------------------------------------- "MENUE ITEMS FOR BODY TAB"
# ===================================================================================================================================
# ===================================================================================================================================
# ===================================================================================================================================
# II. EXPLORE PLOT VALUES
# ===================================================================================================================================
# ===================================================================================================================================
# 1. PLOT enables to explore and visualize all values
# LOCATION: "PLOT" tab (left-hand side menue tab)
menue_tab_exp_plot_body = tabItem("menue_tab_exp_plot",
h1("Explore Plot Values"),
helpText("Explore your data for any genes/proteins of interest"),
# Loading message
div(id = "loading-content1",
h4("Loading Data...")),
plotlyOutput(outputId = "volcanoPlotNuclear"),
br(),
br(),
tabBox(
width = 12,
# Table INPUT, SIGNIF
tabPanel(title = "Input Data",
DTOutput(outputId = "InputOriginalData1")),
tabPanel(title = "Signif",
DTOutput(outputId = "SignifData1")) ))
# 2. PLOT enables to visualize custom gene list which may be related to specific process
# LOCATION: "CUSTOM GENE LIST" (left-hand side menue tab)
menue_tab_exp_genelist_body = tabItem("menue_tab_exp_genelist",
h1("Explore Custom Gene List"),
# Plot3 and Table # ui_explore_custom_gene_list
helpText("Type in a list of gene names of interest in 'Explore Custom Gene List' tab, separated by space or upload own file with one gene per row Genes that are present in your data will be visualized on Volcano Plot"),
# Loading message
div(id = "loading-content2",
h4("Loading Data...")),
plotlyOutput(outputId = "CustomisedPlot"),
br(),
br(),
tabBox(width = 12,
tabPanel(
title = "Selected Gene(s) Info",
DTOutput(outputId = "CustomisedTable2") )) )
# 3. EXPLORE ONE MITO PROCESS
# LOCATION: "MITOCHONDRIAL PROCESS" (left-hand side menue tab)
menue_tab_exp_mitproc_body = tabItem( "menue_tab_exp_mitproc",
h1("Explore Mitochondrial Process"),
title = "Explore Mitochondrial Processes",
#Plot2
helpText("Explore your data for mitochondrial processes"),
# Loading message
div(id = "loading-content3",
h4("Loading Data...")),
plotlyOutput(outputId = "VolcanoPlotOutExploreMito"),
br(),
br(),
tabBox (
width = 12,
# Table INPUT, SIGNIF, PROCESSES
tabPanel(title = "All Processes",
DTOutput(outputId = "InputOriginalData3")),
tabPanel(title = "Signif",
DTOutput(outputId = "SignifData3")),
tabPanel(title = "MITO Processes",
DTOutput(outputId = "ProcessesData3")),
tabPanel(title="Selected Process",
DTOutput(outputId = "ProcessesDataSubset3"))))
# 4. EXPLORE MITO MULTIPLE PROCESSES
# LOCATION: "MULTIPLE PROCESSES" (left-hand side menu tab)
menue_tab_exp_multiple_mitoprocesses_body = tabItem( "menue_tab_exp_multiple_mitoprocesses",
h1("Explore Multiple Mitochondrial Processes"),
title = "Explore Multiple Mitochondrial Processes",
#Plot2
helpText("Explore multiple mitochondrial processes"),
# Loading message
div(id = "loading-content4",
h4("Select Processes and colours from the right-hand pannel, press Apply to visualize plot")),
column(12,
plotlyOutput(outputId = "VolcanoPlotOutMultipleProcessesMito")),
br(),
br(),
tabBox (
width = 12,
# Table INPUT, SIGNIF, PROCESSES
tabPanel(title = "All Processes",
DTOutput(outputId = "InputOriginalDataMult4")),
tabPanel(title="Selected Multiple Processes",
DTOutput(outputId = "ProcessesDataSubsetMult4"))))
# 5. EXPLORE CELL CELLULAR COMPARTMENT
# LOCATION: "MULTIPLE PROCESSES" (left-hand side menu tab)
menue_tab_exp_cellular_compartment_body = tabItem( "menue_tab_exp_cellular_compartment",
h1("Explore Cellular Compartment Localizations"),
title = "Explore Cellular Compartment Localization",
#Plot
helpText("Explore cellular compartment localization (Human)"),
# # Loading message
div(id = "loading-content5",
h4("Loading Data...")),
plotlyOutput(outputId = "CellularCompartmentLocalPlot"),
br(),
br(),
tabBox (
width = 12,
# Table INPUT, SIGNIF, PROCESSES
tabPanel(title = "All Processes",
DTOutput(outputId = "InputOriginalDataMult5")),
tabPanel(title="Selected Cellular Compartment(s)",
DTOutput(outputId = "ProcessesDataSubsetMult5"))))
# ===================================================================================================================================
# --------------------------------------- END --------------------------------------- "EXPLORE PLOT VALUES"
# ===================================================================================================================================
# ===================================================================================================================================
# ===================================================================================================================================
# III. SOFTWARE NAVIGATION BUTTONS
# ===================================================================================================================================
# ===================================================================================================================================
# OPEN FILE
menue_tab_file_open_body = tabItem("menue_tab_file_open",
h1("Open File"),
ui_file_input_diag)
# DOWNLOAD PLOT
menue_tab_download_plot_body = tabItem("menue_tab_download_plot",
ui_download_plot)
# DOWNLOAD TABLE
menue_tab_download_table_body = tabItem ("menue_tab_download_table",
ui_download_table)
# ABOUT
menue_tab_help_body = tabItem ("menue_tab_about",
h1("About"),
includeHTML("www/AboutPage2.html"))
# HELP
menue_tab_about_body = tabItem ("menue_tab_help",
h1("Help"),
includeHTML("www/HelpPage2.html"))
# ===================================================================================================================================
# --------------------------------------- END --------------------------------------- "SOFTWARE NAVIGATION BUTTONS"
# ===================================================================================================================================
# ====================================================================
# ====================================================================
# ====================================================================
# MAIN USER INTERFACE CONTAINER
# ====================================================================
# ====================================================================
# ====================================================================
# https://rinterface.github.io/shinydashboardPlus/news/index.html
# Remove all sidebar related parameters of dashboardPagePlus(). They now belong to
# dashboardSidebarPlus() to Align with {shinydashboard}
ui = dashboardPage(header= dashboardHeader(
disable = FALSE,
title = "OmicsVolcano"),
sidebar =ui_dash_sidebar,
body=dashboardBody (useShinyjs(),
fluidRow (width = 12,
ui_info_box),
fluidRow (
column(width = 8,
fluidRow (
width = 12,
tabItems (
menue_tab_file_open_body,
menue_tab_home_body,
menue_tab_exp_plot_body,
menue_tab_exp_genelist_body,
menue_tab_exp_mitproc_body,
menue_tab_exp_multiple_mitoprocesses_body,
menue_tab_exp_cellular_compartment_body,
menue_tab_download_plot_body,
menue_tab_download_table_body,
menue_tab_help_body,
menue_tab_about_body )
)),
column (width = 4,
function_para_tabs))),
skin = "yellow")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Belongs to the initial software version
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# ui = dashboardPagePlus(skin = "yellow",
#
# dashboardHeaderPlus(
# dropdownMenuOutput("UI_NOTIFICATIONS"),
# enable_rightsidebar = FALSE,
# rightSidebarIcon = "gears",
# title = "OmicsVolcano"),
#
# ui_dash_sidebar,
# # alternative right sidebar
#
# dashboardBody (useShinyjs(),
# fluidRow (width = 12,
# ui_info_box),
# fluidRow (
# column(width = 8,
# fluidRow (
# width = 12,
# tabItems (
# menue_tab_file_open_body,
# menue_tab_home_body,
# menue_tab_exp_plot_body,
# menue_tab_exp_genelist_body,
# menue_tab_exp_mitproc_body,
# menue_tab_exp_multiple_mitoprocesses_body,
# menue_tab_exp_cellular_compartment_body,
# menue_tab_download_plot_body,
# menue_tab_download_table_body,
# menue_tab_help_body,
# menue_tab_about_body # menue_tab_exit_body
# )
# )),
# column (width = 4,
# function_para_tabs) )) )
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# ====================================================================
# ====================================================================
# ====================================================================
# PACKAGES VERSION
# ====================================================================
# ====================================================================
# ====================================================================
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# START
# October 2021
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# > sessionInfo()
# R version 4.1.1 (2021-08-10)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 19043)
#
# Matrix products: default
#
# locale:
# [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252
# [4] LC_NUMERIC=C LC_TIME=English_Australia.1252
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] fontawesome_0.2.2 gridExtra_2.3 colourpicker_1.1.1 shinyjs_2.0.0
# [5] shinythemes_1.2.0 shinydashboardPlus_2.0.3 config_0.3.1 crosstalk_1.1.1
# [9] stringr_1.4.0 svglite_2.0.0 DT_0.19 plotly_4.10.0
# [13] ggplot2_3.3.5 shinyWidgets_0.6.2 shinydashboard_0.7.2 dplyr_1.0.7
# [17] shiny_1.7.1
#
# loaded via a namespace (and not attached):
# [1] Rcpp_1.0.7 tidyr_1.1.4 assertthat_0.2.1 digest_0.6.28 utf8_1.2.2 mime_0.12
# [7] R6_2.5.1 evaluate_0.14 httr_1.4.2 pillar_1.6.4 rlang_0.4.11 lazyeval_0.2.2
# [13] data.table_1.14.2 miniUI_0.1.1.1 jquerylib_0.1.4 rmarkdown_2.11 labeling_0.4.2 htmlwidgets_1.5.4
# [19] munsell_0.5.0 compiler_4.1.1 httpuv_1.6.3 xfun_0.26 pkgconfig_2.0.3 systemfonts_1.0.3
# [25] htmltools_0.5.2 tidyselect_1.1.1 tibble_3.1.5 fansi_0.5.0 viridisLite_0.4.0 crayon_1.4.1
# [31] withr_2.4.2 later_1.3.0 grid_4.1.1 jsonlite_1.7.2 xtable_1.8-4 gtable_0.3.0
# [37] lifecycle_1.0.1 DBI_1.1.1 magrittr_2.0.1 scales_1.1.1 stringi_1.7.5 cachem_1.0.6
# [43] promises_1.2.0.1 bslib_0.3.1 ellipsis_0.3.2 generics_0.1.0 vctrs_0.3.8 tools_4.1.1
# [49] glue_1.4.2 purrr_0.3.4 fastmap_1.1.0 yaml_2.2.1 colorspace_2.0-2 knitr_1.36
# [55] sass_0.4.0
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# October 2021
# END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# > sessionInfo()
# R version 3.6.1 (2019-07-05)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 17134)
#
# Matrix products: default
#
# Random number generation:
# RNG: Mersenne-Twister
# Normal: Inversion
# Sample: Rounding
#
# locale:
# [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
# [5] LC_TIME=English_Australia.1252
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] colourpicker_1.1.0 shinyjs_2.0.0 shinyalert_1.1 shinythemes_1.1.2 shinydashboardPlus_0.7.5 config_0.3
# [7] crosstalk_1.0.0 stringr_1.4.0 svglite_1.2.3 DT_0.12 plotly_4.9.1 ggplot2_3.2.1
# [13] shinyWidgets_0.5.0 shinydashboard_0.7.1 dplyr_0.8.3 shiny_1.4.0
#
# loaded via a namespace (and not attached):
# [1] tidyselect_0.2.5 purrr_0.3.3 colorspace_1.4-1 vctrs_0.2.2 miniUI_0.1.1.1 htmltools_0.4.0 viridisLite_0.3.0
# [8] yaml_2.2.1 rlang_0.4.2 later_1.0.0 pillar_1.4.3 glue_1.3.1 withr_2.1.2 gdtools_0.2.1
# [15] lifecycle_0.1.0 munsell_0.5.0 gtable_0.3.0 htmlwidgets_1.5.1 fastmap_1.0.1 httpuv_1.5.2 Rcpp_1.0.3
# [22] xtable_1.8-4 promises_1.1.0 scales_1.1.0 EnhancedVolcano_1.4.0 jsonlite_1.6.1 mime_0.9 systemfonts_0.1.1
# [29] digest_0.6.23 stringi_1.4.4 ggrepel_0.8.1 grid_3.6.1 tools_3.6.1 magrittr_1.5 lazyeval_0.2.2
# [36] tibble_2.1.3 crayon_1.3.4 tidyr_1.0.2 pkgconfig_2.0.3 data.table_1.12.8 assertthat_0.2.1 httr_1.4.1
# [43] rstudioapi_0.11 R6_2.4.1 compiler_3.6.1
# ====================================================================
# V. Versions updated R and RStudio 2021
# ====================================================================
# R version 4.0.3 (2020-10-10)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 18363)
#
# Matrix products: default
#
# locale:
# [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252
# [4] LC_NUMERIC=C LC_TIME=English_Australia.1252
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] gridExtra_2.3 colourpicker_1.1.0 shinyjs_2.0.0 shinythemes_1.2.0 shinydashboardPlus_0.7.5
# [6] config_0.3.1 crosstalk_1.1.1 stringr_1.4.0 svglite_1.2.3.2 DT_0.17
# [11] plotly_4.9.3 ggplot2_3.3.3 shinyWidgets_0.5.6 shinydashboard_0.7.1 dplyr_1.0.3
# [16] shiny_1.6.0
#
# loaded via a namespace (and not attached):
# [1] Rcpp_1.0.6 tidyr_1.1.2 assertthat_0.2.1 digest_0.6.27 mime_0.9 R6_2.5.0 evaluate_0.14
# [8] httr_1.4.2 pillar_1.4.7 gdtools_0.2.3 rlang_0.4.10 lazyeval_0.2.2 data.table_1.13.6 miniUI_0.1.1.1
# [15] jquerylib_0.1.3 rmarkdown_2.6 labeling_0.4.2 htmlwidgets_1.5.3 munsell_0.5.0 tinytex_0.29 compiler_4.0.3
# [22] httpuv_1.5.5 xfun_0.20 pkgconfig_2.0.3 systemfonts_0.3.2 htmltools_0.5.1.1 tidyselect_1.1.0 tibble_3.0.5
# [29] viridisLite_0.3.0 crayon_1.4.0 withr_2.4.1 later_1.1.0.1 grid_4.0.3 jsonlite_1.7.2 xtable_1.8-4
# [36] gtable_0.3.0 lifecycle_0.2.0 DBI_1.1.1 magrittr_2.0.1 scales_1.1.1 cachem_1.0.1 stringi_1.5.3
# [43] promises_1.1.1 bslib_0.2.4 ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.6 tools_4.0.3 glue_1.4.2
# [50] purrr_0.3.4 fastmap_1.1.0 yaml_2.2.1 colorspace_2.0-0 knitr_1.31 sass_0.3.1