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ui.R
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ui.R
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library(shiny)
library(shinydashboard)
library(shinyWidgets)
library(shinycssloaders)
library(shinybusy)
library(shinyalert)
library(rvest)
library(dplyr)
library(DT)
library(highcharter)
library(SnowballC)
library(ldatuning)
library(topicmodels)
library(textmineR)
library(chinese.misc)
library(stringr)
library(tidyr)
library(ggplot2)
library(ggrepel)
library(textplot)
library(glasso)
library(qgraph)
library(Matrix)
library(utils)
library(factoextra)
library(shinyBS)
library(quanteda)
library(readxl)
exp.stop <- c()
################################Header##########################################
header <- shinydashboard::dashboardHeader(
title = "LDABiplots",
titleWidth = 400,
tags$li(
class = "dropdown",
actionLink("stop_radiant",
"Stop",
icon = icon("power-off"),
onclick = "setTimeout(function(){window.close();}, 100); ")
)
)
###############################Sidebar##########################################
sidebar <- shinydashboard::dashboardSidebar(
width = 400,
shinydashboard::sidebarMenu(
shinydashboard::menuItem(
"About ",
tabName = "tab0"
),
shinydashboard::menuItem(
"Import or Load Data ",
tabName = "tab1",
icon = icon("file-import")
),
shinydashboard::menuItem(
"Document Term Matrix Visualizations",
tabName = "tab2",
icon = icon("chart-bar")
),
shinydashboard::menuItem(
"Inference (Number of topic)",
tabName = "tab3",
icon = icon("chart-bar")
),
shinydashboard::menuItem("LDA and Biplot",
tabName = "tab4",
icon = icon("desktop"),
shinydashboard::menuSubItem("LDA",
tabName = "tab41"
),
shinydashboard::menuSubItem("Biplot",
tabName = "tab42"
)
)
)
)
###############################Body##########################################
body <- shinydashboard::dashboardBody(
shinybusy::add_busy_spinner(spin = "breeding-rhombus",
height = "200px",
width = "200px",
color = "blue",
position ="top-right"
),
tags$head(
tags$link(
rel = "stylesheet",
type = "text/css",
href = "custom.css"
)
),
shinydashboard::tabItems(
shinydashboard::tabItem(
tabName = "tab0",
shiny::fluidPage(tags$iframe(
src = "LDABIPLOT.html",
width = "100%",
height = "1000px",
frameborder = 0,
scrolling = "auto"
))),
shinydashboard::tabItem (tabName = "tab1",
shinydashboard::box(width = 12,
title = "Import or Load Data and Preprocessing",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
sidebarPanel(
selectInput(
"load",
label = "Please, choose what to do",
choices = c(
" " = "null",
"Import excel file" = "import",
"Load web data" = "load"
#"Use a example" = "demo"
),
selected = "null"
),
conditionalPanel(
condition = "input.load == 'import'",
fileInput("file1",
"Upload the file",
accept = c(".xlsx", ".xls"),
multiple = FALSE),
selectInput(inputId = "worksheet",
label="Worksheet Name",
choices=NULL
),
actionButton(inputId = "getData",
label="Get data"),
conditionalPanel(condition = "input.getData != 0",
helpText(h3("Preprocessing")),
shinyWidgets::awesomeRadio(
inputId = "ngramsxl",
label = "ngrams",
choices = c("Unigrams" = 1L, "Bigrams" = 2L,
"Trigrams" = 3L),
selected = 1L,
status = "primary"
),
shinyWidgets::awesomeCheckbox(
inputId = "removenumberxl",
label = "Remove number",
value = TRUE,
status = "danger"
),
shinyWidgets::pickerInput(
inputId = "Languagexl",
label = "Select language for stopword",
choices = c( "en","es"
),
choicesOpt = list(
subtext = paste(Languages <- c(
"english",
"spanish"))
)
),
textInput("stopwordsxl",
label = "Stop Words",
value = paste(exp.stop, collapse = ", "),
placeholder = "also, such, really..."
),
shinyBS::bsPopover("stopwordsxl",
"Include additional stop words
to remove(words
must be separated by commas)",
placement = "right"),
#options = list(container = "body")
br(),
div(style = "display: inline-block;vertical-align:top; width: 170px;",
shinyWidgets::awesomeCheckbox(
inputId = "checkStemmingxl",
label = "Stemming",
value = FALSE,
status = "danger"
)
),
shinyBS::bsPopover("checkStemmingxl",
"Click if you want to stemming",
options = list(container = "body")
),
conditionalPanel(condition = "input.checkStemmingxl != 0",
div(
style = "display: inline-block;vertical-align:top; width: 200px;",
selectInput("Stemmxl", " Stemming langauge",
choices = c(
"english","spanish")
)
)),
br(),
sliderInput(
inputId = "sparcexl",
h4(
span("Sparcity :"),
span(icon("info-circle"), id = "sparcexl",
style = "color: blue")),
min = 0.0,
max = 0.999,
value = 0.999,
step = 0.005
),
bsPopover("sparce", "Sparcity","remove terms less
than selected threshold",
placement = "bottom", trigger = "click"),
div(
id = "dTmxl",
style = "display:inline-block",
shinyalert::useShinyalert(),
shinyWidgets::actionBttn(
inputId = "dtmexcel.update",
label = "Create DTM",
style = "float",
block = TRUE,
color = "primary"
)
),
bsModalNoClose(
id = "DTMdimxl",
title = "dim DTM",
trigger = "dTmxl",
size = "large",
shinycssloaders::withSpinner(
DT::DTOutput("Table_dimxl"))
)
)),
conditionalPanel(
condition = "input.load == 'load'",
prettyRadioButtons(
inputId = "language",
label = "Choose language:",
choices = c("spanish","english")
),
textInput("search",
label = "Search",
value = paste(exp.stop, collapse = "+"),
placeholder = "also, such,..."
),useShinyalert(),
numericInput(inputId = "numberpag",
"Number of pages",
5,
min = 1,
max = 100,
),
shinyWidgets::actionBttn(
inputId = "runsearch",
label = "Run",
style = "float",
block = TRUE,
color = "primary"
),
br(),
shinyjs::useShinyjs(),
conditionalPanel(condition = "input.runsearch != 0",
selectizeInput(
inputId = "selectnews",
label = "Select/deselect all options",
choices = NULL,
multiple = TRUE
),
br(),
helpText(h3("Preprocessing")),
shinyWidgets::awesomeRadio(
inputId = "ngrams",
label = "ngrams",
choices = c("Unigrams" = 1L, "Bigrams" = 2L,
"Trigrams" = 3L),
selected = 1L,
status = "primary"
),
shinyWidgets::awesomeCheckbox(
inputId = "removenumber",
label = "Remove number",
value = TRUE,
status = "danger"
),
shinyWidgets::pickerInput(
inputId = "Language",
label = "Select language for stopword",
choices = c( "en","es"
),
choicesOpt = list(
subtext = paste(Languages <- c(
"english",
"spanish"))
)
),
textInput("stopwords",
label = "Stop Words",
value = paste(exp.stop, collapse = ", "),
placeholder = "also, such, really..."
),
shinyBS::bsPopover("stopwords",
"Include additional stop words
to remove(words
must be separated by commas)",
options = list(container = "body")
),
br(),
div(
style = "display: inline-block;vertical-align:top; width: 170px;",
shinyWidgets::awesomeCheckbox(
inputId = "checkStemming",
label = "Stemming",
value = FALSE,
status = "danger"
)
),
shinyBS::bsPopover("checkStemming",
"Click if you want to stemming",
options = list(container = "body")
),
conditionalPanel(
condition = "input.checkStemming != 0",
div(
style = "display: inline-block;vertical-align:top; width: 200px;",
selectInput("Stemm", " Stemming langauge",
choices = c(
"english","spanish")
)
)),
br(),
sliderInput(
inputId = "sparce",
h4(
span("Sparcity :"),
span(icon("info-circle"),
id = "sparce", style = "color: blue")),
min = 0.00,
max = 0.99,
value = 0.95,
step = 0.005
),
bsPopover("sparce", "Sparcity","remove terms less
than selected threshold",
placement = "bottom", trigger = "click"),
br(),
div(
id = "dTm",
style = "display:inline-block",
shinyalert::useShinyalert(),
shinyWidgets::actionBttn(
inputId = "dtm.update",
label = "Create DTM",
style = "float",
block = TRUE,
color = "primary"
)
),
bsModalNoClose(
id = "DTMdim",
title = "dim DTM",
trigger = "dTm",
size = "large",
shinycssloaders::withSpinner(
DT::DTOutput("Table_dim"))
)
))# fincoditionalpanel
),
mainPanel(helpText(h3("Frecuency by Newspapers")),
DT::DTOutput("sum"),
br(),
helpText(h3("news by newspapers")),
DT::DTOutput("text")
))),
shinydashboard::tabItem(
tabName = "tab2",
collapsible = TRUE,
shinydashboard::box(
width = 350,
title = "Visualization",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
## View data action button hidden initially until the dataset is loaded
div(
id = "data_b",
style = "display:inline-block",
shinyWidgets::actionBttn(
inputId = "data",
label = "Data",
icon = icon("table"),
style = "float",
block = TRUE,
color = "primary"
)
),
## View plot action button hidden initially until the dataset is loaded
div(
id = "plot_b",
style = "display:inline-block",
shinyWidgets::actionBttn(
inputId = "plot",
label = "Barplot",
icon = icon("chart-bar"),
style = "float",
block = TRUE,
color = "primary"
)
),
div(
id = "plot_c",
style = "display:inline-block",
shinyWidgets::actionBttn(
inputId = "plot2",
label = "Wordcloud",
icon = icon("chart-bar"),
style = "float",
block = TRUE,
color = "primary"
)
),
div(
id = "plot_d",
style = "display:inline-block",
shinyWidgets::actionBttn(
inputId = "plot3",
label = "Co-ocurrence",
icon = icon("chart-bar"),
style = "float",
block = TRUE,
color = "primary"
)
),
bsModalNoClose(
id = "dataset",
title = "Basic corpus statistics",
trigger = "data",
size = "large",
shinycssloaders::withSpinner(DT::DTOutput("data_b"))
),
## Shiny BS Modal to display the plot inside a modal
## A spinner is also added
bsModalNoClose(
id = "Plot", title = "Barplot", trigger = "plot", size = "large",
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
tags$h5("Customize bar plot")
),
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
shinyWidgets::dropdown(sliderInput(
inputId = "b",
label = "Select number of word",
min = 10,
max = 500,
value = 10
),
textInput("colorbar",
label = "Bar color",
value = "gray"),
shinyBS::bsPopover("colorbar",
"Write the color of your preference.
(for Example, red or #5faeb3 )",
options = list(container = "body")),
style = "unite",
#icon = icon("gear"),
status = "danger",
width = "500px",
animate = shinyWidgets::animateOptions(
enter = shinyWidgets::animations$fading_entrances$fadeInLeftBig,
exit = shinyWidgets::animations$fading_exits$fadeOutRightBig
)
)
),
shinycssloaders::withSpinner(highcharter::highchartOutput("plot_gg"))
),
bsModalNoClose(
id = "Plot2",
title = "Wordcloud",
trigger = "plot2",
size = "large",
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
tags$h5("Select number of term")
),
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
shinyWidgets::dropdown(sliderInput(
inputId = "c",
label = "Select number of word",
min = 10,
max = 500,
value = 10
),
style = "unite",
#icon = icon("gear"),
status = "danger",
width = "500px",
animate = shinyWidgets::animateOptions(
enter = animations$fading_entrances$fadeInLeftBig,
exit = animations$fading_exits$fadeOutRightBig
)
)
),
shinycssloaders::withSpinner(highcharter::highchartOutput("plot_gf"))
),
bsModalNoClose(
id = "Plot3",
title = "Co-ocurrence",
trigger = "plot3",
size = "large",
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
tags$h5("Select number of term and download plot")
),
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
shinyWidgets::dropdown(sliderInput(
inputId = "d",
label = "Select number of word",
min = 2,
max = 1000,
value = 25
),
radioButtons("downplotco",
"Select the Option",
choices = list("png","pdf")),
downloadButton("downplotco",
label = "Download the plot"),
style = "unite",
#icon = icon("gear"),
status = "danger",
width = "500px",
animate = shinyWidgets::animateOptions(
enter = animations$fading_entrances$fadeInLeftBig,
exit = animations$fading_exits$fadeOutRightBig
)
)
),
shinycssloaders::withSpinner(plotOutput("plotcoc"))
)
)
),
shinydashboard::tabItem(
tabName = "tab3",
shinydashboard::box(
width = 12,
title = " Inference (Number of topic)",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
sidebarPanel(helpText(
h3("Candidate number of topics k")),
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
numericInput(
inputId = "num1",
label = "from",
value = 2,
min = 2
)
),
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
numericInput(
inputId = "num2",
label = "to",
value = 2,
min = 2
)
),
div(
style = "display: inline-block;vertical-align:top; width: 110px;",
numericInput(
inputId = "num3",
label = "by",
value = 1,
min = 1
)
),
textInput(
inputId = "OtherKCoherence",
label = "Others K",
value = paste(exp.stop, collapse = ", "),
placeholder = "Enter values separated by a comma...50, 100, 150,..."
),
textOutput("OthKcoh"),
br(),
helpText(h3("Parameters control Gibbs sampling")),
div(
style = "display: inline-block;vertical-align:top; width: 110px;",
numericInput(
inputId = "num4",
h4(
span("Iteration :"),
span(icon("info-circle"), id = "iterationnt",
style = "color: blue")),
value = 10,
min = 10
),
shinyBS::bsPopover(
id = "iterationnt","Iterations",
"Specifies number of iterations for Gibbs Sampling",
options = list(container = "body")
)
),
div(
style = "display: inline-block;vertical-align:top; width: 150px;",
numericInput(
inputId = "num5",
h4(
span("Burn-in :"),
span(icon("info-circle"), id = "burninnt",
style = "color: blue")),
value = 5,
min = 5
),
shinyBS::bsPopover(
id = "burninnt","Burn-in",
"Specifies how many iterations are discarded.",
options = list(container = "body")
)
),
br(),
helpText(h3("Hyper-parameter")),
withMathJax(),
div(
style = "display: inline-block;vertical-align:top; width: 110px;",
numericInput(
inputId = "num6",
h4(
span("\\( \\alpha \\)"),
span(icon("info-circle"), id = "hyperalpha",
style = "color: blue")),
value = 0.1,
min = 0.01,
max = 1,
step = 0.01
),
shinyBS::bsPopover(
id = "hyperalpha","alpha",
"α=(0.1,50/K);(0.1,0.1);(1/K,1/K)",
options = list(container = "body")
)
),
br(),
shinyBS::bsPopover("num6",
"Assuming symmetric Dirichlet
distributions (for simplicity),
a low alpha value places more weight
on having each document composed
of only a few dominant topics",
options = list(container = "body")
),
br(),
shinyalert::useShinyalert(),
div(
id = "Run1",
style = "display:inline-block",
shinyWidgets::actionBttn(
inputId = "Run.model1",
label = "Run",
style = "float",
block = TRUE,
color = "primary"
)
)),
mainPanel(verbatimTextOutput("timeCoherence"),
highcharter::highchartOutput("plot_gi")))
),
shinydashboard::tabItem(
tabName = "tab41",
shinydashboard::box(
width = 12,
title = "LDA model",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
sidebarPanel(
helpText(h3("k parameter (topic) ")),
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
numericInput("num25",
label = "",
value = 2,
min = 2
)
),
br(),
numericInput("num26",
h4(
span("Iteration :"),
span(icon("info-circle"), id = "iterationmodel",
style = "color: blue")),
value = 10,
min = 10
),
shinyBS::bsPopover("iterationmodel","Iteration",
"Specifies number of iterations for Gibbs Sampling.",
options = list(container = "body")
),
numericInput("num27",
h4(span("Burn-in :"),
span(icon("info-circle"), id = "burninmodel",
style = "color: blue")),
value = 5,
min = 5
),
shinyBS::bsPopover("burninmodel","Burn-in",
"Specifies how many iterations are discarded.",
options = list(container = "body")
),
br(), helpText(h3("Hyper-parameter")),
withMathJax(),
numericInput("num28",
h4(span("\\( \\alpha \\)"),
span(icon("info-circle"),
id = "hyper", style = "color: blue")),
value = 0.1,
min = 0.01,
max = 1,
step = 0.01
),
shinyBS::bsPopover(
id = "hyper","alpha ",
"α=(0.1,50/K);(0.1,0.1);(1/K,1/K)",
options = list(container = "body")
),
br(),
div(
id = "Run5",
style = "display:inline-block",
actionBttn("Run.model5",
"Run LDA Model",
style = "float",
block = TRUE,
color = "primary"
)
)
),
mainPanel(
tabsetPanel(
tabPanel("Tabular result",
helpText(h3("Summary Model LDA")),
br(),
sliderInput(
inputId = "Topterm",
label = "Select number of term",
min = 1,
max = 50,
value = 10,
step = 1
),
sliderInput(
inputId = "Labels",
label = "Select number of label",
min = 1,
max = 5,
value = 1,
step = 1
),
sliderInput(
inputId = "assignments",
label = "Select assignments",
min = 0,
max = 1,
value = 0.05,
step = 0.01
),
verticalLayout(
DT::DTOutput("summLDA"),
helpText(h3("Theta Matrix")),
DT::DTOutput("theta"),
br(),
helpText(h3("Phi Matrix")),
DT::DTOutput("phi")
)),
tabPanel("Worcloud by topic",
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
shinyWidgets::dropdown(
numericInput("num29",
label = "topic #",
value = 1,
min = 1),
div(
style = "display: inline-block;vertical-align:top; width: 120px;",
sliderInput(
inputId = "cloud",
label = "Select number of word",
min = 5,
max = 100,
value = 10)),
style = "unite",
#icon = icon("gear"),
status = "danger",
width = "500px",
tooltip = tooltipOptions(
title = "Click to see inputs!"),
animate = animateOptions(
enter = animations$fading_entrances$fadeInLeftBig,
exit = animations$fading_exits$fadeOutRightBig
)
)
),
highcharter::highchartOutput("plot_worcloud"),
),
tabPanel("Heatmap",
highcharter::highchartOutput("plot_heatmap")),
tabPanel("Cluster",#plotOutput("num_cluster"),
br(),
pickerInput(
inputId = "methodaglo",
label = "Agglomeration method",
choices = c("complete", "single", "ward.D",
"ward.D2", "average", "mcquitty","median",
"centroid")
), helpText(h4("Cophenetic correlation ")),
verbatimTextOutput("cophenetic"),
br(),
sliderInput(
inputId = "numberclu",
label = "Select k (number cluster)",
min = 2,
max = 50,
value = 5),
br(),
pickerInput(
inputId = "type",
label = "type of plot",
choices = c("rectangle",
"circular", "phylogenic")
),
sliderInput(
inputId = "numM",
label = "Select (number term)",
min = 2,
max = 20,
value = 3),
br(),
plotOutput("plot_cluster"),
br(),
br(),
radioButtons("butdowncluster",
"Select the Option",
choices = list("png","pdf")),
downloadButton("downcluster",
label = "Download the plot")
)
))#fin mainpanel
)
),
tabItem(tabName = "tab42",shinydashboard::box(
width = 12,
title = " Biplot",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
sidebarPanel(
radioGroupButtons(
inputId = "selectypebiplot",
label = "Biplot",
choices = c("HJ_Biplot",
"JK_Biplot", "GH_Biplot"),
individual = TRUE,
checkIcon = list(
yes = tags$i(class = "fa fa-circle",
style = "color: steelblue"),
no = tags$i(class = "fa fa-circle-o",
style = "color: steelblue"))
),
awesomeRadio(
inputId = "biptransf",
label = "Transform.Data",
choices = c("scale", "center","center_scale","none" ),
selected = "scale",
inline = TRUE,
checkbox = TRUE
),
shinyWidgets::actionBttn(
inputId = "runbiplot",
label = "Run",
style = "float",
block = TRUE,
color = "primary"),
conditionalPanel(
condition = "input.runbiplot != 0" ,
helpText(h3("Options to Customize the biplot")),
shinyWidgets::awesomeRadio(
inputId = "biphide",
label = "Hide",
choices = c("none", "ind", "var"),
selected = "none",
inline = TRUE,
checkbox = TRUE
),
selectInput("themebi", " Theme",
choices = names(themesb)
),
numericInput(
inputId = "axisx",
label = "Axis-X",
value = 1,
min = 1
),
numericInput("axisy",
label = "Axis-Y",
value = 2,
min = 1),
textInput("colorind",
label = "Color ind",
value = "#d92d5e"),
textInput("colorvar",
label = "Color var",
value = "black"),
div(
style = "display: inline-block;vertical-align:top; width: 70px;",
switchInput(
inputId = "indlabel",
label = "Label ind",
onLabel = "Yes",
offLabel = "No",
size = "mini")),
div(
style = "display: inline-block;vertical-align:top; width: 70px;",
switchInput(
inputId = "varlabel",
label = "Label var",
onLabel = "Yes",
offLabel = "No",
size = "mini")),
div(
style = "display: inline-block;vertical-align:top; width: 70px;",
switchInput(
inputId = "angle",
label = "Angle label var",
onLabel = "Yes",
offLabel = "No",
size = "mini")),
sliderInput(
inputId = "pch",
label = " Point shape" ,
min = 0 ,
max =20 ,
value = 19),
sliderInput(inputId = "sizeind",
label = "Size ind" ,
min = 0.01 ,
max = 20 ,
step = 0.1,
value = 5),
sliderInput(inputId = "labelsize",
label = "Label size ind" ,
min = 0.1 ,
max = 20,
step = 0.1,
value = 5),
sliderInput(inputId = "sizeaxis",
label = "Size axis title " ,
min = 0.1 ,
max = 30,
step = 0.1,
value = 16),
sliderInput(inputId = "axistest",
label = "Size axis text " ,
min = 0.1 ,
max = 30,
step = 0.1,
value = 16),
sliderInput(
inputId= "varsize",
label = "Var size",
min = 0.01,
max = 20,
value = 0.5,
step = 0.1),
sliderInput(inputId = "varlabelsize",
label = "Label size var" ,
min = 0.01 ,
max = 20 ,
value = 5,
step = 0.01))
),
mainPanel(
tabsetPanel(
tabPanel("Tabular result",
helpText(h3("Eigenvalues")),
DT::DTOutput("eigen"),
br(),
helpText(h3("Variance explained")),
DT::DTOutput("variance"),
br(),
helpText(h3("Loading")),
DT::DTOutput("loading"),
br(),