inst/shinyapp/tidymass/ui.R
In tidymass/tidymass: R packages for mass spectrometry data processing and analysis
options(shiny.maxRequestSize = 300 * 1024 ^ 2)
if (!require(tidyverse)) {
install.packages("tidyverse")
library(tidyverse)
}
if (!require(shiny)) {
install.packages("shiny")
library(shiny)
}
if (!require(shinydashboard)) {
install.packages("shinydashboard")
library(shinydashboard)
}
if (!require(shinyjs)) {
install.packages("shinyjs")
library(shinyjs)
}
if (!require(shinyBS)) {
install.packages("shinyBS")
library(shinyBS)
}
if (!require(patchwork)) {
install.packages("patchwork")
library(patchwork)
}
if (!require(shinyWidgets)) {
install.packages("shinyWidgets")
library(shinyWidgets)
}
if (!require(markdown)) {
install.packages("markdown")
library(markdown)
}
if (!require(massdataset)) {
remotes::install_github("tidymass/massdataset")
}
if (!require(tidymass)) {
source("https://www.tidymass.org/tidymass-packages/install_tidymass.txt")
install_tidymass(from = "tidymass.org")
}
if (!require(extrafont)) {
install.packages("extrafont")
library(extrafont)
extrafont::loadfonts()
}
ui <- dashboardPage(
skin = "red",
dashboardHeader(title = "TidyMass"),
###sidebar of the app
dashboardSidebar(
sidebarMenu(
id = "tabs",
menuItem(
"Introduction",
tabName = "introduction",
icon = icon("info-circle")
),
menuItem(
"Totorial",
tabName = "tutorial",
icon = icon("book")
),
menuItem(
"Upload Data",
tabName = "upload_data",
icon = icon("upload")
),
menuItem(
"Enrich Pathways",
tabName = "enrich_pathways",
icon = icon("cogs")
),
menuItem(
"Merge Pathways",
tabName = "merge_pathways",
icon = icon("cogs")
),
menuItem(
"Merge Modules",
tabName = "merge_modules",
icon = icon("cogs")
),
menuItem(
"Translation",
tabName = "translation",
icon = icon("globe")
),
menuItem(
"Data Visualization",
tabName = "data_visualization",
icon = icon("chart-line")
),
menuItem(
"LLM Interpretation",
tabName = "llm_interpretation",
icon = icon("brain")
),
menuItem(
"Results and Report",
tabName = "results",
icon = icon("clipboard-list")
)
)
),
##dashboard body code
dashboardBody(
shinyjs::useShinyjs(),
div(
id = "loading",
hidden = TRUE,
class = "loading-style",
"",
tags$img(src = "loading.gif",
height = "200px")
),
tags$style(
HTML(
"
.content-wrapper {
padding-bottom: 120px;
}
.loading-style {
position: fixed;
top: 50%;
left: 50%;
transform: translate(-50%, -50%);
text-align: center;
z-index: 100;
}
"
)
),
tabItems(
####introduction tab
tabItem(tabName = "introduction",
fluidPage(
titlePanel("Introduction of MAPA"),
fluidRow(
column(12,
includeHTML("files/introduction.html")
)
)
)),
####tutorial tab
tabItem(tabName = "tutorial",
fluidPage(
titlePanel("Tutorials of MAPA"),
fluidRow(
column(12,
includeHTML("files/tutorials.html")
)
)
)),
####upload data tab
tabItem(tabName = "upload_data",
fluidPage(
titlePanel("Upload Data"),
fluidRow(
column(4,
fileInput(
"expression_data",
"Expression data",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".xlsx",
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"application/vnd.ms-excel"
)
),
fileInput(
"sample_info",
"Sample information",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".xlsx",
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"application/vnd.ms-excel"
)
),
fileInput(
"variable_info",
"Variable information",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".xlsx",
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"application/vnd.ms-excel"
)
),
checkboxInput(inputId = "use_example",
label = "Use example",
value = FALSE),
actionButton("create_mass_dataset",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
inputId = "go2enrich_pathways",
label = "Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
inputId = "show_upload_data_code",
label = "Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "Expression data",
shiny::dataTableOutput("expression_data")
),
tabPanel(
title = "Sample information",
shiny::dataTableOutput("sample_info")
),
tabPanel(
title = "Variable information",
shiny::dataTableOutput("variable_info")
),
tabPanel(
title = "R object",
verbatimTextOutput("enriched_pathways_object"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_object",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
)
)
)
)),
####enrich pathways tab
tabItem(tabName = "enrich_pathways",
fluidPage(
titlePanel("Enrich Pathways"),
fluidPage(
fluidRow(
column(4,
checkboxGroupInput(
"pathway_database",
"Database",
choices = c(
"GO" = "go",
"KEGG" = "kegg",
"Reactome" = "reactome"
),
selected = c("go", "kegg", "reactome")
),
selectInput(
"organism",
"Organism",
choices = list(
"Human" = "hsa",
"Rat" = "rno",
"Mouse" = "mmu",
"C. elegans" = "cel",
"Yeast" = "sce",
"Zebrafish" = "dre",
"Fruit fly" = "dme"),
selected = "hsa"
),
numericInput(
"p_value_cutoff",
"P-value cutoff",
value = 0.05,
min = 0,
max = 0.5),
selectInput(
"p_adjust_method",
"P-adjust method",
choices = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"),
selected = "BH"),
sliderInput(
"gene_set_size",
"Gene set size",
min = 5,
max = 2000,
value = c(10, 500)),
actionButton(
"submit_enrich_pathways",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"go2merge_pathways",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_enrich_pathways_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
id = "enriched_pathways_result",
tabPanel(
title = "GO",
shiny::dataTableOutput("enriched_pathways_go"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_go",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "KEGG",
shiny::dataTableOutput("enriched_pathways_kegg"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_kegg",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "Reactome",
shiny::dataTableOutput("enriched_pathways_reactome"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_reactome",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "R object",
verbatimTextOutput("enriched_pathways_object"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_object",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
)
)
)
)
)),
####merge pathways tab
tabItem(tabName = "merge_pathways",
fluidPage(
titlePanel("Merge Pathways"),
fluidPage(
fluidRow(
column(4,
h4("GO"),
fluidRow(
column(6,
numericInput(
"p.adjust.cutoff.go",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5)
),
column(6,
numericInput(
"count.cutoff.go",
"Gene count cutoff",
value = 5,
min = 0,
max = 1000
)
)),
h4("Network"),
fluidRow(
column(6,
selectInput(
"measure.method.go",
"Similarity method",
choices = c("Wang", "Resnik", "Rel", "Jiang",
"Lin", "TCSS", "jaccard"),
selected = "Wang"
)
),
column(6,
numericInput(
"sim.cutoff.go",
"Similarity cutoff",
value = 0.5,
min = 0,
max = 1
)
)),
h4("KEGG"),
fluidRow(
column(6,
numericInput(
"p.adjust.cutoff.kegg",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5)
),
column(6,
numericInput(
"count.cutoff.kegg",
"Gene count cutoff",
value = 5,
min = 0,
max = 1000)
)
),
h4("Network"),
fluidRow(
column(6,
selectInput(
"measure.method.kegg",
"Similarity method",
choices = c("jaccard"),
selected = "jaccard")
),
column(6,
numericInput(
"sim.cutoff.kegg",
"Similarity cutoff",
value = 0.5,
min = 0,
max = 1)
)),
h4("Reactome"),
fluidRow(
column(6,
numericInput(
"p.adjust.cutoff.reactome",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5)
),
column(6,
numericInput(
"count.cutoff.reactome",
"Gene count cutoff",
value = 5,
min = 0,
max = 1000)
)),
h4("Network"),
fluidRow(
column(6,
selectInput(
"measure.method.reactome",
"Similarity method",
choices = c("jaccard"),
selected = "jaccard")
),
column(6,
numericInput(
"sim.cutoff.reactome",
"Similarity cutoff",
value = 0.5,
min = 0,
max = 1)
)),
actionButton(
"submit_merge_pathways",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"go2merge_modules",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_merge_pathways_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel("Table",
tabsetPanel(
tabPanel(
title = "GO",
shiny::dataTableOutput("merged_pathway_go"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_merged_pathway_go",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "KEGG",
shiny::dataTableOutput("merged_pathway_kegg"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_merged_pathway_kegg",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "Reactome",
shiny::dataTableOutput("merged_pathway_reactome"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_merged_pathway_reactome",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
)),
tabPanel(
title = "Data visualization",
tabsetPanel(
tabPanel(
title = "GO",
shiny::plotOutput("enirched_module_go_plot"),
br(),
fluidRow(
column(3,
actionButton("generate_enirched_module_plot_go",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
column(3,
checkboxInput("enirched_module_plot_text_go", "Text", FALSE)
),
column(3,
checkboxInput("enirched_module_plot_text_all_go", "Text all", FALSE)
),
column(3,
numericInput(
"enirched_module_plot_degree_cutoff_go",
"Degree cutoff",
value = 0,
min = 0,
max = 1000)
)
)
),
tabPanel(
title = "KEGG",
shiny::plotOutput("enirched_module_kegg_plot"),
br(),
fluidRow(
column(3,
actionButton("generate_enirched_module_plot_kegg",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
column(3,
checkboxInput("enirched_module_plot_text_kegg", "Text", FALSE)
),
column(3,
checkboxInput("enirched_module_plot_text_all_kegg", "Text all", FALSE)
),
column(3,
numericInput(
"enirched_module_plot_degree_cutoff_kegg",
"Degree cutoff",
value = 0,
min = 0,
max = 1000
)
)
)
),
tabPanel(
title = "Reactome",
shiny::plotOutput("enirched_module_reactome_plot"),
br(),
fluidRow(
column(3,
actionButton("generate_enirched_module_plot_reactome",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
column(3,
checkboxInput("enirched_module_plot_text_reactome", "Text", FALSE)
),
column(3,
checkboxInput("enirched_module_plot_text_all_reactome", "Text all", FALSE)
),
column(3,
numericInput(
"enirched_module_plot_degree_cutoff_reactome",
"Degree cutoff",
value = 0,
min = 0,
max = 1000)
)
)
)
)
),
tabPanel(
title = "R object",
verbatimTextOutput("enriched_modules_object"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_modules_object",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
))
)
)
)),
#### Merge modules tab
tabItem(
tabName = "merge_modules",
fluidPage(titlePanel("Merge Modules"),
fluidPage(
fluidRow(
column(4,
fluidRow(
column(6,
selectInput(
"measure.method.module",
"Similarity method",
choices = c("jaccard"),
selected = "jaccard")
),
column(6,
numericInput(
"sim.cutoff.module",
"Similarity cutoff",
value = 0.5,
min = 0,
max = 1)
)),
actionButton(
"submit_merge_modules",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"go2translation",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_merge_modules_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "Table",
shiny::dataTableOutput("enriched_functional_modules"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_functional_modules",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "Data visualization",
shiny::plotOutput("enirched_functional_module_plot"),
br(),
fluidRow(
column(3,
actionButton("generate_enirched_functional_module",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
column(3,
checkboxInput("enirched_functional_module_plot_text", "Text", FALSE)
),
column(3,
checkboxInput("enirched_functional_module_plot_text_all", "Text all", FALSE)
),
column(3,
numericInput(
"enirched_functional_moduleplot__degree_cutoff",
"Degree cutoff",
value = 0,
min = 0,
max = 1000)
)
)
),
tabPanel(
title = "R object",
verbatimTextOutput("enriched_functional_module_object"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_functional_module_object",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
))
)))
),
#### Translation tab
tabItem(
tabName = "translation",
fluidPage(titlePanel("Translation"),
fluidPage(fluidRow(
column(
4,
fluidRow(column(
5,
selectInput(
"translation_model",
"Model",
choices = c(
"Gemini" = "gemini",
"ChatGPT" = "chatgpt"),
selected = "gemini"
)
),
column(
7,
textInput("translation_model_ai_key",
"AI key",
value = "")
)),
fluidRow(column(
12,
selectInput(
"translation_to",
"Translation to",
choices = c("Chinese" = "chinese",
"Spanish" = "spanish",
"English" = "english",
"French" = "french",
"German" = "german",
"Italian" = "italian",
"Japanese" = "japanese",
"Korean" = "korean",
"Portuguese" = "portuguese",
"Russian" = "russian",
"Spanish" = "spanish"),
selected = "chinese"
)
)),
actionButton(
"submit_translation",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"skip_translation",
"Skip",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"go2data_visualization",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"show_translation_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "R object",
verbatimTextOutput("enriched_functional_module_object2"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_functional_module_object2",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
)
)
)))
),
#### Data visualization tab
tabItem(tabName = "data_visualization",
fluidPage(
titlePanel("Data Visualization"),
tabsetPanel(
tabPanel(
title = "Barplot",
fluidRow(
column(4,
br(),
fluidRow(
column(8,
fileInput(inputId = "upload_enriched_functional_module",
label = tags$span("Upload functional module",
shinyBS::bsButton("upload_functional_module_info",
label = "",
icon = icon("info"),
style = "info",
size = "extra-small")),
accept = ".rda"),
bsPopover(
id = "upload_functional_module_info",
title = "",
content = "You can upload the functional module file here for data visualization only.",
placement = "right",
trigger = "hover",
options = list(container = "body")
)
)
),
fluidRow(
column(4,
selectInput(
inputId = "barplot_level",
label = "Level",
choices = c(
"FM" = "functional_module",
"Module" = "module",
"Pathway" = "pathway"),
selected = "functional_module")
),
column(4,
numericInput(
inputId = "barplot_top_n",
label = "Top N",
value = 5,
min = 1,
max = 1000)
),
column(4,
selectInput(
"line_type",
"Line type",
choices = c(
"Straight" = "straight",
"Meteor" = "meteor"))
)
),
fluidRow(
column(4,
numericInput(
"barplot_y_lable_width",
"Y label width",
value = 50,
min = 20,
max = 100)
),
column(4,
numericInput("barplot_p_adjust_cutoff",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5),
),
column(4,
numericInput("barplot_count_cutoff",
"Count cutoff",
value = 5,
min = 1,
max = 1000)
)
),
fluidRow(
column(8,
checkboxGroupInput("barplot_database",
"Database",
choices = c(
"GO" = "go",
"KEGG" = "kegg",
"Reactome" = "reactome"
),
selected = c("go", "kegg", "reactome"),
inline = TRUE)
),
column(4,
checkboxInput("barplot_translation", "Translation", FALSE)
)
),
h4("Database color"),
fluidRow(
column(4,
shinyWidgets::colorPickr(
inputId = "barplot_go_color",
label = "GO",
selected = "#1F77B4FF",
theme = "monolith",
width = "100%")
),
column(4,
shinyWidgets::colorPickr(
inputId = "barplot_kegg_color",
label = "KEGG",
selected = "#FF7F0EFF",
theme = "monolith",
width = "100%")
),
column(4,
shinyWidgets::colorPickr(
inputId = "barplot_reactome_color",
label = "Reactome",
selected = "#2CA02CFF",
theme = "monolith",
width = "100%")
)
),
fluidRow(
column(4,
selectInput("barplot_type", "Type",
choices = c("pdf", "png", "jpeg"))
),
column(4,
numericInput("barplot_width", "Width",
value = 7, min = 4, max = 20)
),
column(4,
numericInput("barplot_height", "Height",
value = 7, min = 4, max = 20)
)
),
fluidRow(
column(12,
actionButton("generate_barplot",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
downloadButton("download_barplot",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
br(),
fluidRow(
column(12,
actionButton(
"go2llm_interpretation_1",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_barplot_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
br(),
shiny::plotOutput("barplot")
)
)
),
tabPanel(
title = "Module Similarity Network",
fluidRow(
column(4,
br(),
fluidRow(
column(6,
selectInput(
"module_similarity_network_database",
"Database",
choices = c("GO" = "go",
"KEGG" = "kegg",
"Reactome" = "reactome"),
selected = "go")
),
column(6,
numericInput(
"module_similarity_network_degree_cutoff",
"Degree cutoff",
value = 0,
min = 0,
max = 1000)
)
),
fluidRow(
column(6,
selectInput(
"module_similarity_network_level",
"Level",
choices = c(
"FM" = "functional_module",
"Module" = "module"),
selected = "functional_module")
)
),
fluidRow(
column(4,
checkboxInput("module_similarity_network_translation", "Translation", FALSE)
),
column(4,
checkboxInput("module_similarity_network_text", "Text", FALSE)
),
column(4,
checkboxInput("module_similarity_network_text_all", "Text all", FALSE)
)
),
fluidRow(
column(4,
selectInput("module_similarity_network_type", "Type",
choices = c("pdf", "png", "jpeg"))
),
column(4,
numericInput("module_similarity_network_width", "Width",
value = 7, min = 4, max = 20)),
column(4,
numericInput("module_similarity_network_height", "Height",
value = 7, min = 4, max = 20))
),
fluidRow(
column(12,
shinyjs::useShinyjs(),
actionButton("generate_module_similarity_network",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
shinyjs::useShinyjs(),
downloadButton("download_module_similarity_network",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
br(),
fluidRow(
column(12,
actionButton(
"go2llm_interpretation_2",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"show_module_similarity_network_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
br(),
shiny::plotOutput("module_similarity_network")
)
)
),
tabPanel(
title = "Module information",
fluidRow(
column(4,
br(),
fluidRow(
column(6,
selectInput(
"module_information_level",
"Level",
choices = c(
"FM" = "functional_module",
"Module" = "module"),
selected = "functional_module")
),
column(6,
selectInput(
"module_information_database",
"Database",
choices = c("GO" = "go",
"KEGG" = "kegg",
"Reactome" = "reactome"),
selected = "go")
)
),
fluidRow(
column(7,
selectInput(
"module_information_module_id",
"Module ID",
choices = NULL)
),
column(5,
checkboxInput("module_information_translation",
"Translation", FALSE)
)
),
fluidRow(
column(4,
selectInput("module_information_type", "Type",
choices = c("pdf", "png", "jpeg"))
),
column(4,
numericInput("module_information_width", "Width",
value = 7, min = 4, max = 30)),
column(4,
numericInput("module_information_height", "Height",
value = 21, min = 4, max = 20))
),
fluidRow(
column(12,
shinyjs::useShinyjs(),
actionButton("generate_module_information",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
downloadButton("download_module_information",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
br(),
fluidRow(
column(12,
shinyjs::useShinyjs(),
actionButton(
"go2llm_interpretation_3",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_module_information_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
br(),
shiny::plotOutput("module_information1"),
shiny::plotOutput("module_information2"),
shiny::plotOutput("module_information3")
)
)
),
tabPanel(
title = "Relationship network",
fluidRow(
column(4,
br(),
fluidRow(
column(5,
checkboxInput("relationship_network_circular_plot",
"Circular layout", FALSE)
),
column(3,
checkboxInput("relationship_network_filter",
"Filter", FALSE)
),
column(4,
checkboxInput("relationship_network_translation",
"Translation", FALSE)
)
),
fluidRow(
column(6,
selectInput(
"relationship_network_level",
"Filter Level",
choices = c(
"FM" = "functional_module",
"Module" = "module"),
selected = "functional_module")
),
column(6,
selectInput(
"relationship_network_module_id",
"Module ID",
choices = NULL,
multiple = TRUE)
)
),
h4("Includes"),
fluidRow(
column(3,
checkboxInput("relationship_network_include_functional_modules",
label = tags$span("FM",
shinyBS::bsButton("functional_module_info",
label = "",
icon = icon("info"),
style = "info",
size = "extra-small")),
TRUE)),
bsPopover(
id = "functional_module_info",
title = "",
content = "FM is functional module",
placement = "right",
trigger = "hover",
options = list(container = "body")
),
column(3,
checkboxInput("relationship_network_include_modules",
"Modules", TRUE)
),
column(3,
checkboxInput("relationship_network_include_pathways",
"Pathways", TRUE)
),
column(3,
checkboxInput("relationship_network_include_molecules",
"Molecules", TRUE)
)
),
h4("Colors"),
fluidRow(
column(3,
shinyWidgets::colorPickr(
inputId = "relationship_network_functional_module_color",
label = "FM",
selected = "#F05C3BFF",
theme = "monolith",
width = "100%"
)
),
column(3,
shinyWidgets::colorPickr(
inputId = "relationship_network_module_color",
label = "Module",
selected = "#46732EFF",
theme = "monolith",
width = "100%"
)
),
column(3,
shinyWidgets::colorPickr(
inputId = "relationship_network_pathway_color",
label = "Pathway",
selected = "#197EC0FF",
theme = "monolith",
width = "100%"
)
),
column(3,
shinyWidgets::colorPickr(
inputId = "relationship_network_molecule_color",
label = "Molecule",
selected = "#3B4992FF",
theme = "monolith",
width = "100%"
)
)
),
h4("Text"),
fluidRow(
column(3,
checkboxInput("relationship_network_functional_module_text",
"FM", TRUE)
),
column(3,
checkboxInput("relationship_network_module_text",
"Module", TRUE)
),
column(3,
checkboxInput("relationship_network_pathway_text",
"Pathway", TRUE)
),
column(3,
checkboxInput("relationship_network_molecule_text",
"Molecules", FALSE)
)
),
h4("Text size"),
fluidRow(
column(3,
numericInput("relationship_network_functional_module_text_size",
"FM",
value = 3, min = 0.3, max = 10)
),
column(3,
numericInput("relationship_network_module_text_size",
"Module",
value = 3, min = 0.3, max = 10)
),
column(3,
numericInput("relationship_network_pathway_text_size",
"Pathway",
value = 3, min = 0.3, max = 10)
),
column(3,
numericInput("relationship_network_molecule_text_size",
"Molecule",
value = 3, min = 0.3, max = 10)
)
),
h4("Arrange posision"),
fluidRow(
column(3,
checkboxInput("relationship_network_functional_module_arrange_position",
"FM", TRUE)
),
column(3,
checkboxInput("relationship_network_module_arrange_position",
"Module", TRUE)
),
column(3,
checkboxInput("relationship_network_pathway_arrange_position",
"Pathway", TRUE)
),
column(3,
checkboxInput("relationship_network_molecule_arrange_position",
"Molecules", FALSE)
)
),
h4("Posision limits"),
fluidRow(
column(6,
sliderInput(
"relationship_network_functional_module_position_limits",
"Functional module",
min = 0, max = 1,
value = c(0, 1))
),
column(6,
sliderInput(
"relationship_network_module_position_limits",
"Module",
min = 0, max = 1,
value = c(0, 1))
)
),
fluidRow(
column(6,
sliderInput(
"relationship_network_pathway_position_limits",
"Pathway",
min = 0, max = 1,
value = c(0, 1))
),
column(6,
sliderInput(
"relationship_network_molecule_position_limits",
"Molecule",
min = 0, max = 1,
value = c(0, 1))
)
),
fluidRow(
column(4,
selectInput("relationship_network_type",
"Type",
choices = c("pdf", "png", "jpeg")
)
),
column(4,
numericInput("relationship_network_width",
"Width",
value = 21, min = 4, max = 30)
),
column(4,
numericInput("relationship_network_height",
"Height",
value = 7, min = 4, max = 20)
)
),
fluidRow(
column(12,
actionButton("generate_relationship_network",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
shinyjs::useShinyjs(),
downloadButton("download_relationship_network",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
br(),
fluidRow(
column(12,
actionButton(
"go2llm_interpretation_4",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_relationship_network_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
)
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
br(),
shiny::plotOutput("relationship_network")
)
)
)
)
)),
#### LLM Interpretation tab
tabItem(
tabName = "llm_interpretation",
fluidPage(titlePanel("LLM Interpretation"),
fluidPage(fluidRow(
column(
4,
fluidRow(column(
5,
selectInput(
"llm_model",
"LLM model",
choices = c("ChatGPT" = "chatgpt"),
selected = "chatgpt"
)
),
column(
7,
textInput("openai_key",
"OpenAI key",
value = "")
)),
fluidRow(column(
12,
textInput(
"llm_interpretation_disease",
"Disease or phenotype",
value = "pregnancy",
width = "100%"
)
)),
fluidRow(
column(4,
numericInput("llm_interpretation_top_n",
"Top N",
value = 5,
min = 1,
max = 1000)
),
column(4,
numericInput("llm_interpretation_p_adjust_cutoff",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5),
),
column(4,
numericInput("llm_interpretation_count_cutoff",
"Count cutoff",
value = 5,
min = 1,
max = 1000)
)
),
actionButton(
"submit_llm_interpretation",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"go2results",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"show_llm_interpretation_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "LLM interpretation results",
uiOutput("llm_interpretation_result"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_llm_interpretation_result",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "Functional module table 1",
shiny::dataTableOutput("llm_enriched_functional_modules1")
),
tabPanel(
title = "Functional module table 2",
shiny::dataTableOutput("llm_enriched_functional_modules2")
)
)
)
)))
),
#### result tab
tabItem(
tabName = "results",
fluidPage(titlePanel("Results and Report"),
fluidPage(
column(4,
br(),
fluidRow(
actionButton(
inputId = "generate_report",
label = "Generate report",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
shinyjs::useShinyjs(),
downloadButton("download_report",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
inputId = "show_report_code",
label = "Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "Report",
uiOutput("mapa_report")
))
)
)
)
)
),
tags$footer(
div(
style = "background-color: #ecf0f4; display: flex; align-items: center; justify-content: left; padding: 10px; height: 80px; position: fixed; bottom: 0; width: 100%; z-index: 100; border-top: 1px solid #ccc;",
tags$img(
src = "shen_lab_logo.png",
height = "50px",
style = "margin-right: 15px;"
),
div(
HTML("The Shen Lab at Nanyang Technological University Singapore"),
HTML("<br>"),
tags$a(
href = "http://www.shen-lab.org",
target = "_blank",
tags$i(class = "fa fa-house", style = "color: #e04c3c;"),
" Shen Lab",
style = "text-align: left; margin-left: 10px;"
),
tags$a(
href = "https://www.shen-lab.org/#contact",
target = "_blank",
tags$i(class = "fa fa-envelope", style = "color: #e04c3c;"),
" Email",
style = "text-align: left; margin-left: 10px;"
),
tags$a(
href = "https://github.com/jaspershen/mapa",
target = "_blank",
tags$i(class = "fa fa-github", style = "color: #e04c3c;"),
" GitHub",
style = "text-align: left; margin-left: 10px;"
),
style = "text-align: left;"
),
tags$img(
src = "tidymass_logo.png",
height = "50px",
style = "margin-left: 15px;"
)
)
)
)
)
tidymass/tidymass documentation built on Jan. 30, 2024, 2:57 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
options(shiny.maxRequestSize = 300 * 1024 ^ 2)
if (!require(tidyverse)) {
install.packages("tidyverse")
library(tidyverse)
}
if (!require(shiny)) {
install.packages("shiny")
library(shiny)
}
if (!require(shinydashboard)) {
install.packages("shinydashboard")
library(shinydashboard)
}
if (!require(shinyjs)) {
install.packages("shinyjs")
library(shinyjs)
}
if (!require(shinyBS)) {
install.packages("shinyBS")
library(shinyBS)
}
if (!require(patchwork)) {
install.packages("patchwork")
library(patchwork)
}
if (!require(shinyWidgets)) {
install.packages("shinyWidgets")
library(shinyWidgets)
}
if (!require(markdown)) {
install.packages("markdown")
library(markdown)
}
if (!require(massdataset)) {
remotes::install_github("tidymass/massdataset")
}
if (!require(tidymass)) {
source("https://www.tidymass.org/tidymass-packages/install_tidymass.txt")
install_tidymass(from = "tidymass.org")
}
if (!require(extrafont)) {
install.packages("extrafont")
library(extrafont)
extrafont::loadfonts()
}
ui <- dashboardPage(
skin = "red",
dashboardHeader(title = "TidyMass"),
###sidebar of the app
dashboardSidebar(
sidebarMenu(
id = "tabs",
menuItem(
"Introduction",
tabName = "introduction",
icon = icon("info-circle")
),
menuItem(
"Totorial",
tabName = "tutorial",
icon = icon("book")
),
menuItem(
"Upload Data",
tabName = "upload_data",
icon = icon("upload")
),
menuItem(
"Enrich Pathways",
tabName = "enrich_pathways",
icon = icon("cogs")
),
menuItem(
"Merge Pathways",
tabName = "merge_pathways",
icon = icon("cogs")
),
menuItem(
"Merge Modules",
tabName = "merge_modules",
icon = icon("cogs")
),
menuItem(
"Translation",
tabName = "translation",
icon = icon("globe")
),
menuItem(
"Data Visualization",
tabName = "data_visualization",
icon = icon("chart-line")
),
menuItem(
"LLM Interpretation",
tabName = "llm_interpretation",
icon = icon("brain")
),
menuItem(
"Results and Report",
tabName = "results",
icon = icon("clipboard-list")
)
)
),
##dashboard body code
dashboardBody(
shinyjs::useShinyjs(),
div(
id = "loading",
hidden = TRUE,
class = "loading-style",
"",
tags$img(src = "loading.gif",
height = "200px")
),
tags$style(
HTML(
"
.content-wrapper {
padding-bottom: 120px;
}
.loading-style {
position: fixed;
top: 50%;
left: 50%;
transform: translate(-50%, -50%);
text-align: center;
z-index: 100;
}
"
)
),
tabItems(
####introduction tab
tabItem(tabName = "introduction",
fluidPage(
titlePanel("Introduction of MAPA"),
fluidRow(
column(12,
includeHTML("files/introduction.html")
)
)
)),
####tutorial tab
tabItem(tabName = "tutorial",
fluidPage(
titlePanel("Tutorials of MAPA"),
fluidRow(
column(12,
includeHTML("files/tutorials.html")
)
)
)),
####upload data tab
tabItem(tabName = "upload_data",
fluidPage(
titlePanel("Upload Data"),
fluidRow(
column(4,
fileInput(
"expression_data",
"Expression data",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".xlsx",
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"application/vnd.ms-excel"
)
),
fileInput(
"sample_info",
"Sample information",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".xlsx",
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"application/vnd.ms-excel"
)
),
fileInput(
"variable_info",
"Variable information",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".xlsx",
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"application/vnd.ms-excel"
)
),
checkboxInput(inputId = "use_example",
label = "Use example",
value = FALSE),
actionButton("create_mass_dataset",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
inputId = "go2enrich_pathways",
label = "Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
inputId = "show_upload_data_code",
label = "Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "Expression data",
shiny::dataTableOutput("expression_data")
),
tabPanel(
title = "Sample information",
shiny::dataTableOutput("sample_info")
),
tabPanel(
title = "Variable information",
shiny::dataTableOutput("variable_info")
),
tabPanel(
title = "R object",
verbatimTextOutput("enriched_pathways_object"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_object",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
)
)
)
)),
####enrich pathways tab
tabItem(tabName = "enrich_pathways",
fluidPage(
titlePanel("Enrich Pathways"),
fluidPage(
fluidRow(
column(4,
checkboxGroupInput(
"pathway_database",
"Database",
choices = c(
"GO" = "go",
"KEGG" = "kegg",
"Reactome" = "reactome"
),
selected = c("go", "kegg", "reactome")
),
selectInput(
"organism",
"Organism",
choices = list(
"Human" = "hsa",
"Rat" = "rno",
"Mouse" = "mmu",
"C. elegans" = "cel",
"Yeast" = "sce",
"Zebrafish" = "dre",
"Fruit fly" = "dme"),
selected = "hsa"
),
numericInput(
"p_value_cutoff",
"P-value cutoff",
value = 0.05,
min = 0,
max = 0.5),
selectInput(
"p_adjust_method",
"P-adjust method",
choices = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"),
selected = "BH"),
sliderInput(
"gene_set_size",
"Gene set size",
min = 5,
max = 2000,
value = c(10, 500)),
actionButton(
"submit_enrich_pathways",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"go2merge_pathways",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_enrich_pathways_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
id = "enriched_pathways_result",
tabPanel(
title = "GO",
shiny::dataTableOutput("enriched_pathways_go"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_go",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "KEGG",
shiny::dataTableOutput("enriched_pathways_kegg"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_kegg",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "Reactome",
shiny::dataTableOutput("enriched_pathways_reactome"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_reactome",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "R object",
verbatimTextOutput("enriched_pathways_object"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_pathways_object",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
)
)
)
)
)),
####merge pathways tab
tabItem(tabName = "merge_pathways",
fluidPage(
titlePanel("Merge Pathways"),
fluidPage(
fluidRow(
column(4,
h4("GO"),
fluidRow(
column(6,
numericInput(
"p.adjust.cutoff.go",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5)
),
column(6,
numericInput(
"count.cutoff.go",
"Gene count cutoff",
value = 5,
min = 0,
max = 1000
)
)),
h4("Network"),
fluidRow(
column(6,
selectInput(
"measure.method.go",
"Similarity method",
choices = c("Wang", "Resnik", "Rel", "Jiang",
"Lin", "TCSS", "jaccard"),
selected = "Wang"
)
),
column(6,
numericInput(
"sim.cutoff.go",
"Similarity cutoff",
value = 0.5,
min = 0,
max = 1
)
)),
h4("KEGG"),
fluidRow(
column(6,
numericInput(
"p.adjust.cutoff.kegg",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5)
),
column(6,
numericInput(
"count.cutoff.kegg",
"Gene count cutoff",
value = 5,
min = 0,
max = 1000)
)
),
h4("Network"),
fluidRow(
column(6,
selectInput(
"measure.method.kegg",
"Similarity method",
choices = c("jaccard"),
selected = "jaccard")
),
column(6,
numericInput(
"sim.cutoff.kegg",
"Similarity cutoff",
value = 0.5,
min = 0,
max = 1)
)),
h4("Reactome"),
fluidRow(
column(6,
numericInput(
"p.adjust.cutoff.reactome",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5)
),
column(6,
numericInput(
"count.cutoff.reactome",
"Gene count cutoff",
value = 5,
min = 0,
max = 1000)
)),
h4("Network"),
fluidRow(
column(6,
selectInput(
"measure.method.reactome",
"Similarity method",
choices = c("jaccard"),
selected = "jaccard")
),
column(6,
numericInput(
"sim.cutoff.reactome",
"Similarity cutoff",
value = 0.5,
min = 0,
max = 1)
)),
actionButton(
"submit_merge_pathways",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"go2merge_modules",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_merge_pathways_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel("Table",
tabsetPanel(
tabPanel(
title = "GO",
shiny::dataTableOutput("merged_pathway_go"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_merged_pathway_go",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "KEGG",
shiny::dataTableOutput("merged_pathway_kegg"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_merged_pathway_kegg",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "Reactome",
shiny::dataTableOutput("merged_pathway_reactome"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_merged_pathway_reactome",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
)),
tabPanel(
title = "Data visualization",
tabsetPanel(
tabPanel(
title = "GO",
shiny::plotOutput("enirched_module_go_plot"),
br(),
fluidRow(
column(3,
actionButton("generate_enirched_module_plot_go",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
column(3,
checkboxInput("enirched_module_plot_text_go", "Text", FALSE)
),
column(3,
checkboxInput("enirched_module_plot_text_all_go", "Text all", FALSE)
),
column(3,
numericInput(
"enirched_module_plot_degree_cutoff_go",
"Degree cutoff",
value = 0,
min = 0,
max = 1000)
)
)
),
tabPanel(
title = "KEGG",
shiny::plotOutput("enirched_module_kegg_plot"),
br(),
fluidRow(
column(3,
actionButton("generate_enirched_module_plot_kegg",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
column(3,
checkboxInput("enirched_module_plot_text_kegg", "Text", FALSE)
),
column(3,
checkboxInput("enirched_module_plot_text_all_kegg", "Text all", FALSE)
),
column(3,
numericInput(
"enirched_module_plot_degree_cutoff_kegg",
"Degree cutoff",
value = 0,
min = 0,
max = 1000
)
)
)
),
tabPanel(
title = "Reactome",
shiny::plotOutput("enirched_module_reactome_plot"),
br(),
fluidRow(
column(3,
actionButton("generate_enirched_module_plot_reactome",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
column(3,
checkboxInput("enirched_module_plot_text_reactome", "Text", FALSE)
),
column(3,
checkboxInput("enirched_module_plot_text_all_reactome", "Text all", FALSE)
),
column(3,
numericInput(
"enirched_module_plot_degree_cutoff_reactome",
"Degree cutoff",
value = 0,
min = 0,
max = 1000)
)
)
)
)
),
tabPanel(
title = "R object",
verbatimTextOutput("enriched_modules_object"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_modules_object",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
))
)
)
)),
#### Merge modules tab
tabItem(
tabName = "merge_modules",
fluidPage(titlePanel("Merge Modules"),
fluidPage(
fluidRow(
column(4,
fluidRow(
column(6,
selectInput(
"measure.method.module",
"Similarity method",
choices = c("jaccard"),
selected = "jaccard")
),
column(6,
numericInput(
"sim.cutoff.module",
"Similarity cutoff",
value = 0.5,
min = 0,
max = 1)
)),
actionButton(
"submit_merge_modules",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"go2translation",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_merge_modules_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "Table",
shiny::dataTableOutput("enriched_functional_modules"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_functional_modules",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "Data visualization",
shiny::plotOutput("enirched_functional_module_plot"),
br(),
fluidRow(
column(3,
actionButton("generate_enirched_functional_module",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
column(3,
checkboxInput("enirched_functional_module_plot_text", "Text", FALSE)
),
column(3,
checkboxInput("enirched_functional_module_plot_text_all", "Text all", FALSE)
),
column(3,
numericInput(
"enirched_functional_moduleplot__degree_cutoff",
"Degree cutoff",
value = 0,
min = 0,
max = 1000)
)
)
),
tabPanel(
title = "R object",
verbatimTextOutput("enriched_functional_module_object"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_functional_module_object",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
))
)))
),
#### Translation tab
tabItem(
tabName = "translation",
fluidPage(titlePanel("Translation"),
fluidPage(fluidRow(
column(
4,
fluidRow(column(
5,
selectInput(
"translation_model",
"Model",
choices = c(
"Gemini" = "gemini",
"ChatGPT" = "chatgpt"),
selected = "gemini"
)
),
column(
7,
textInput("translation_model_ai_key",
"AI key",
value = "")
)),
fluidRow(column(
12,
selectInput(
"translation_to",
"Translation to",
choices = c("Chinese" = "chinese",
"Spanish" = "spanish",
"English" = "english",
"French" = "french",
"German" = "german",
"Italian" = "italian",
"Japanese" = "japanese",
"Korean" = "korean",
"Portuguese" = "portuguese",
"Russian" = "russian",
"Spanish" = "spanish"),
selected = "chinese"
)
)),
actionButton(
"submit_translation",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"skip_translation",
"Skip",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"go2data_visualization",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"show_translation_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "R object",
verbatimTextOutput("enriched_functional_module_object2"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_enriched_functional_module_object2",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
)
)
)))
),
#### Data visualization tab
tabItem(tabName = "data_visualization",
fluidPage(
titlePanel("Data Visualization"),
tabsetPanel(
tabPanel(
title = "Barplot",
fluidRow(
column(4,
br(),
fluidRow(
column(8,
fileInput(inputId = "upload_enriched_functional_module",
label = tags$span("Upload functional module",
shinyBS::bsButton("upload_functional_module_info",
label = "",
icon = icon("info"),
style = "info",
size = "extra-small")),
accept = ".rda"),
bsPopover(
id = "upload_functional_module_info",
title = "",
content = "You can upload the functional module file here for data visualization only.",
placement = "right",
trigger = "hover",
options = list(container = "body")
)
)
),
fluidRow(
column(4,
selectInput(
inputId = "barplot_level",
label = "Level",
choices = c(
"FM" = "functional_module",
"Module" = "module",
"Pathway" = "pathway"),
selected = "functional_module")
),
column(4,
numericInput(
inputId = "barplot_top_n",
label = "Top N",
value = 5,
min = 1,
max = 1000)
),
column(4,
selectInput(
"line_type",
"Line type",
choices = c(
"Straight" = "straight",
"Meteor" = "meteor"))
)
),
fluidRow(
column(4,
numericInput(
"barplot_y_lable_width",
"Y label width",
value = 50,
min = 20,
max = 100)
),
column(4,
numericInput("barplot_p_adjust_cutoff",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5),
),
column(4,
numericInput("barplot_count_cutoff",
"Count cutoff",
value = 5,
min = 1,
max = 1000)
)
),
fluidRow(
column(8,
checkboxGroupInput("barplot_database",
"Database",
choices = c(
"GO" = "go",
"KEGG" = "kegg",
"Reactome" = "reactome"
),
selected = c("go", "kegg", "reactome"),
inline = TRUE)
),
column(4,
checkboxInput("barplot_translation", "Translation", FALSE)
)
),
h4("Database color"),
fluidRow(
column(4,
shinyWidgets::colorPickr(
inputId = "barplot_go_color",
label = "GO",
selected = "#1F77B4FF",
theme = "monolith",
width = "100%")
),
column(4,
shinyWidgets::colorPickr(
inputId = "barplot_kegg_color",
label = "KEGG",
selected = "#FF7F0EFF",
theme = "monolith",
width = "100%")
),
column(4,
shinyWidgets::colorPickr(
inputId = "barplot_reactome_color",
label = "Reactome",
selected = "#2CA02CFF",
theme = "monolith",
width = "100%")
)
),
fluidRow(
column(4,
selectInput("barplot_type", "Type",
choices = c("pdf", "png", "jpeg"))
),
column(4,
numericInput("barplot_width", "Width",
value = 7, min = 4, max = 20)
),
column(4,
numericInput("barplot_height", "Height",
value = 7, min = 4, max = 20)
)
),
fluidRow(
column(12,
actionButton("generate_barplot",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
downloadButton("download_barplot",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
br(),
fluidRow(
column(12,
actionButton(
"go2llm_interpretation_1",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_barplot_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
br(),
shiny::plotOutput("barplot")
)
)
),
tabPanel(
title = "Module Similarity Network",
fluidRow(
column(4,
br(),
fluidRow(
column(6,
selectInput(
"module_similarity_network_database",
"Database",
choices = c("GO" = "go",
"KEGG" = "kegg",
"Reactome" = "reactome"),
selected = "go")
),
column(6,
numericInput(
"module_similarity_network_degree_cutoff",
"Degree cutoff",
value = 0,
min = 0,
max = 1000)
)
),
fluidRow(
column(6,
selectInput(
"module_similarity_network_level",
"Level",
choices = c(
"FM" = "functional_module",
"Module" = "module"),
selected = "functional_module")
)
),
fluidRow(
column(4,
checkboxInput("module_similarity_network_translation", "Translation", FALSE)
),
column(4,
checkboxInput("module_similarity_network_text", "Text", FALSE)
),
column(4,
checkboxInput("module_similarity_network_text_all", "Text all", FALSE)
)
),
fluidRow(
column(4,
selectInput("module_similarity_network_type", "Type",
choices = c("pdf", "png", "jpeg"))
),
column(4,
numericInput("module_similarity_network_width", "Width",
value = 7, min = 4, max = 20)),
column(4,
numericInput("module_similarity_network_height", "Height",
value = 7, min = 4, max = 20))
),
fluidRow(
column(12,
shinyjs::useShinyjs(),
actionButton("generate_module_similarity_network",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
shinyjs::useShinyjs(),
downloadButton("download_module_similarity_network",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
br(),
fluidRow(
column(12,
actionButton(
"go2llm_interpretation_2",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"show_module_similarity_network_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
br(),
shiny::plotOutput("module_similarity_network")
)
)
),
tabPanel(
title = "Module information",
fluidRow(
column(4,
br(),
fluidRow(
column(6,
selectInput(
"module_information_level",
"Level",
choices = c(
"FM" = "functional_module",
"Module" = "module"),
selected = "functional_module")
),
column(6,
selectInput(
"module_information_database",
"Database",
choices = c("GO" = "go",
"KEGG" = "kegg",
"Reactome" = "reactome"),
selected = "go")
)
),
fluidRow(
column(7,
selectInput(
"module_information_module_id",
"Module ID",
choices = NULL)
),
column(5,
checkboxInput("module_information_translation",
"Translation", FALSE)
)
),
fluidRow(
column(4,
selectInput("module_information_type", "Type",
choices = c("pdf", "png", "jpeg"))
),
column(4,
numericInput("module_information_width", "Width",
value = 7, min = 4, max = 30)),
column(4,
numericInput("module_information_height", "Height",
value = 21, min = 4, max = 20))
),
fluidRow(
column(12,
shinyjs::useShinyjs(),
actionButton("generate_module_information",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
downloadButton("download_module_information",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
br(),
fluidRow(
column(12,
shinyjs::useShinyjs(),
actionButton(
"go2llm_interpretation_3",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_module_information_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
br(),
shiny::plotOutput("module_information1"),
shiny::plotOutput("module_information2"),
shiny::plotOutput("module_information3")
)
)
),
tabPanel(
title = "Relationship network",
fluidRow(
column(4,
br(),
fluidRow(
column(5,
checkboxInput("relationship_network_circular_plot",
"Circular layout", FALSE)
),
column(3,
checkboxInput("relationship_network_filter",
"Filter", FALSE)
),
column(4,
checkboxInput("relationship_network_translation",
"Translation", FALSE)
)
),
fluidRow(
column(6,
selectInput(
"relationship_network_level",
"Filter Level",
choices = c(
"FM" = "functional_module",
"Module" = "module"),
selected = "functional_module")
),
column(6,
selectInput(
"relationship_network_module_id",
"Module ID",
choices = NULL,
multiple = TRUE)
)
),
h4("Includes"),
fluidRow(
column(3,
checkboxInput("relationship_network_include_functional_modules",
label = tags$span("FM",
shinyBS::bsButton("functional_module_info",
label = "",
icon = icon("info"),
style = "info",
size = "extra-small")),
TRUE)),
bsPopover(
id = "functional_module_info",
title = "",
content = "FM is functional module",
placement = "right",
trigger = "hover",
options = list(container = "body")
),
column(3,
checkboxInput("relationship_network_include_modules",
"Modules", TRUE)
),
column(3,
checkboxInput("relationship_network_include_pathways",
"Pathways", TRUE)
),
column(3,
checkboxInput("relationship_network_include_molecules",
"Molecules", TRUE)
)
),
h4("Colors"),
fluidRow(
column(3,
shinyWidgets::colorPickr(
inputId = "relationship_network_functional_module_color",
label = "FM",
selected = "#F05C3BFF",
theme = "monolith",
width = "100%"
)
),
column(3,
shinyWidgets::colorPickr(
inputId = "relationship_network_module_color",
label = "Module",
selected = "#46732EFF",
theme = "monolith",
width = "100%"
)
),
column(3,
shinyWidgets::colorPickr(
inputId = "relationship_network_pathway_color",
label = "Pathway",
selected = "#197EC0FF",
theme = "monolith",
width = "100%"
)
),
column(3,
shinyWidgets::colorPickr(
inputId = "relationship_network_molecule_color",
label = "Molecule",
selected = "#3B4992FF",
theme = "monolith",
width = "100%"
)
)
),
h4("Text"),
fluidRow(
column(3,
checkboxInput("relationship_network_functional_module_text",
"FM", TRUE)
),
column(3,
checkboxInput("relationship_network_module_text",
"Module", TRUE)
),
column(3,
checkboxInput("relationship_network_pathway_text",
"Pathway", TRUE)
),
column(3,
checkboxInput("relationship_network_molecule_text",
"Molecules", FALSE)
)
),
h4("Text size"),
fluidRow(
column(3,
numericInput("relationship_network_functional_module_text_size",
"FM",
value = 3, min = 0.3, max = 10)
),
column(3,
numericInput("relationship_network_module_text_size",
"Module",
value = 3, min = 0.3, max = 10)
),
column(3,
numericInput("relationship_network_pathway_text_size",
"Pathway",
value = 3, min = 0.3, max = 10)
),
column(3,
numericInput("relationship_network_molecule_text_size",
"Molecule",
value = 3, min = 0.3, max = 10)
)
),
h4("Arrange posision"),
fluidRow(
column(3,
checkboxInput("relationship_network_functional_module_arrange_position",
"FM", TRUE)
),
column(3,
checkboxInput("relationship_network_module_arrange_position",
"Module", TRUE)
),
column(3,
checkboxInput("relationship_network_pathway_arrange_position",
"Pathway", TRUE)
),
column(3,
checkboxInput("relationship_network_molecule_arrange_position",
"Molecules", FALSE)
)
),
h4("Posision limits"),
fluidRow(
column(6,
sliderInput(
"relationship_network_functional_module_position_limits",
"Functional module",
min = 0, max = 1,
value = c(0, 1))
),
column(6,
sliderInput(
"relationship_network_module_position_limits",
"Module",
min = 0, max = 1,
value = c(0, 1))
)
),
fluidRow(
column(6,
sliderInput(
"relationship_network_pathway_position_limits",
"Pathway",
min = 0, max = 1,
value = c(0, 1))
),
column(6,
sliderInput(
"relationship_network_molecule_position_limits",
"Molecule",
min = 0, max = 1,
value = c(0, 1))
)
),
fluidRow(
column(4,
selectInput("relationship_network_type",
"Type",
choices = c("pdf", "png", "jpeg")
)
),
column(4,
numericInput("relationship_network_width",
"Width",
value = 21, min = 4, max = 30)
),
column(4,
numericInput("relationship_network_height",
"Height",
value = 7, min = 4, max = 20)
)
),
fluidRow(
column(12,
actionButton("generate_relationship_network",
"Generate plot",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
shinyjs::useShinyjs(),
downloadButton("download_relationship_network",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
)
),
br(),
fluidRow(
column(12,
actionButton(
"go2llm_interpretation_4",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
"show_relationship_network_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
)
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
br(),
shiny::plotOutput("relationship_network")
)
)
)
)
)),
#### LLM Interpretation tab
tabItem(
tabName = "llm_interpretation",
fluidPage(titlePanel("LLM Interpretation"),
fluidPage(fluidRow(
column(
4,
fluidRow(column(
5,
selectInput(
"llm_model",
"LLM model",
choices = c("ChatGPT" = "chatgpt"),
selected = "chatgpt"
)
),
column(
7,
textInput("openai_key",
"OpenAI key",
value = "")
)),
fluidRow(column(
12,
textInput(
"llm_interpretation_disease",
"Disease or phenotype",
value = "pregnancy",
width = "100%"
)
)),
fluidRow(
column(4,
numericInput("llm_interpretation_top_n",
"Top N",
value = 5,
min = 1,
max = 1000)
),
column(4,
numericInput("llm_interpretation_p_adjust_cutoff",
"P-adjust cutoff",
value = 0.05,
min = 0,
max = 0.5),
),
column(4,
numericInput("llm_interpretation_count_cutoff",
"Count cutoff",
value = 5,
min = 1,
max = 1000)
)
),
actionButton(
"submit_llm_interpretation",
"Submit",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"go2results",
"Next",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
actionButton(
"show_llm_interpretation_code",
"Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "LLM interpretation results",
uiOutput("llm_interpretation_result"),
br(),
shinyjs::useShinyjs(),
downloadButton("download_llm_interpretation_result",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;")
),
tabPanel(
title = "Functional module table 1",
shiny::dataTableOutput("llm_enriched_functional_modules1")
),
tabPanel(
title = "Functional module table 2",
shiny::dataTableOutput("llm_enriched_functional_modules2")
)
)
)
)))
),
#### result tab
tabItem(
tabName = "results",
fluidPage(titlePanel("Results and Report"),
fluidPage(
column(4,
br(),
fluidRow(
actionButton(
inputId = "generate_report",
label = "Generate report",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
),
shinyjs::useShinyjs(),
downloadButton("download_report",
"Download",
class = "btn-primary",
style = "background-color: #d83428; color: white;"),
actionButton(
inputId = "show_report_code",
label = "Code",
class = "btn-primary",
style = "background-color: #d83428; color: white;"
)
),
style = "border-right: 1px solid #ddd; padding-right: 20px;"
),
column(8,
tabsetPanel(
tabPanel(
title = "Report",
uiOutput("mapa_report")
))
)
)
)
)
),
tags$footer(
div(
style = "background-color: #ecf0f4; display: flex; align-items: center; justify-content: left; padding: 10px; height: 80px; position: fixed; bottom: 0; width: 100%; z-index: 100; border-top: 1px solid #ccc;",
tags$img(
src = "shen_lab_logo.png",
height = "50px",
style = "margin-right: 15px;"
),
div(
HTML("The Shen Lab at Nanyang Technological University Singapore"),
HTML("<br>"),
tags$a(
href = "http://www.shen-lab.org",
target = "_blank",
tags$i(class = "fa fa-house", style = "color: #e04c3c;"),
" Shen Lab",
style = "text-align: left; margin-left: 10px;"
),
tags$a(
href = "https://www.shen-lab.org/#contact",
target = "_blank",
tags$i(class = "fa fa-envelope", style = "color: #e04c3c;"),
" Email",
style = "text-align: left; margin-left: 10px;"
),
tags$a(
href = "https://github.com/jaspershen/mapa",
target = "_blank",
tags$i(class = "fa fa-github", style = "color: #e04c3c;"),
" GitHub",
style = "text-align: left; margin-left: 10px;"
),
style = "text-align: left;"
),
tags$img(
src = "tidymass_logo.png",
height = "50px",
style = "margin-left: 15px;"
)
)
)
)
)
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