inst/shiny/ui.R
In jansodoge/awesom_dev_version: Interactive Self-Organizing Maps
shinyUI(fluidPage(
tags$head(HTML("<title>aweSOM</title>")),
#to modify style of help messages (increase font etc. tbd after lunch)
tags$style(
HTML(".shiny-notification {position:fixed; top: 50%; left: 0px; width: 30%;}")
),
rclipboard::rclipboardSetup(),
tabsetPanel(
#### Panel 'Welcome, Import Data'
#########################################################################
tabPanel("Import Data",
includeHTML("js/svg_todataurl.js"),
# data_import -------------------------------------------------------------
fluidRow(
column(4,
h2("aweSOM"),
h4("interactive self-organizing maps"),
wellPanel(
h4("Import Data"),
selectInput('file_type', NULL,
choices = c(
".csv or .txt" = "csv_txt",
"Microsoft Excel .xlsx" = "excel_xlsx",
"Microsoft Excel .xls" = "excel_xls",
"SPSS (.sav, .por)" = "spss",
"SAS Data" = "sas_data",
"Stata (.dta)" = "stata"),
selected = "csv_txt"
),
fileInput('dataFile', 'Choose File'),
# HTML("<b>Import parameters</b>"),
checkboxInput("importParams", "File parameters"),
conditionalPanel(
"input.importParams",
conditionalPanel("input.file_type == 'csv_txt'",
fluidRow(column(4, p('Header:')),
column(8, selectInput('header', NULL,
c("Auto", "Header",
"No Header"),
"Auto"))),
fluidRow(column(4, p('Separator:')),
column(8, selectInput('sep', NULL,
c("Auto", "Comma ','",
"Semicolon ';'",
"Tab","Space"),
"Auto"))),
fluidRow(column(4, p('Quote:')),
column(8, selectInput('quote', NULL,
c("None","Double Quote \"","Single Quote '"),
'Double Quote "'))),
fluidRow(column(4, p('Decimal mark')),
column(8, selectInput('dec', NULL,
c('Period "."', 'Comma ","'),
'Period "."'))),
fluidRow(column(4, p('File Encoding')),
column(8, selectInput('encoding', NULL,
c("unknown", "UTF-8", "whatever else"),
"unknown")))),
conditionalPanel("input.file_type == 'excel_xlsx'",
fluidRow(column(4, p('Column names')),
column(8, selectInput('column_names', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('rows_to_skip', NULL, 0, min= 0))),
fluidRow(column(4, p('Trim whitespaces')),
column(8, selectInput('trim_spaces', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
fluidRow(column(4, checkboxInput("worksheet_specified_bol", "Specify Worksheet", F))),
conditionalPanel("input.worksheet_specified_bol",
textInput("worksheet_specs", NULL, "")
),
fluidRow(column(4, checkboxInput("range_specified_bol", "Specify Range", F))),
conditionalPanel("input.range_specified_bol",
textInput("range_specs", NULL, "")
)),
## Options for xls files
conditionalPanel("input.file_type == 'excel_xls'",
fluidRow(column(4, p('Column names')),
column(8, selectInput('column_names_xls', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('rows_to_skip_xls', NULL, 0, min= 0))),
fluidRow(column(4, p('Trim whitespaces')),
column(8, selectInput('trim_spaces_xls', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
fluidRow(column(4, checkboxInput("worksheet_specified_bol_xls", "Specify Worksheet", F))),
conditionalPanel("input.worksheet_specified_bol_xls",
textInput("worksheet_specs_xls", NULL, "")
),
fluidRow(column(4, checkboxInput("range_specified_bol_xls", "Specify Range", F))),
conditionalPanel("input.range_specified_bol_xls",
textInput("range_specs_xls", NULL, "")
)),
## Options for SPSS files
conditionalPanel("input.file_type == 'spss'",
###specs and params here
## Possible: encoding, user_na, skip, n_max
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('skip_spss', NULL, 0, min= 0)))),
)
),
fluidRow(column(3, HTML("<h4>Help</h4>")),
column(2, actionButton("help_message_intro_to_aweSOM", "", icon = icon("question"), width = NULL)))
),
column(8,
uiOutput("dataImportMessage"),
DT::dataTableOutput("dataView"))
)),
tabPanel("Train",
wellPanel(fluidRow(column(2, h3("Map info:")),
column(10, verbatimTextOutput("Message")))),
fluidRow(column(4, wellPanel(
h3("Train new map:"),
actionButton("trainbutton", HTML("<b>Train SOM</b>"), width= "100%"),
hr(),
fluidRow(column(4, numericInput('kohDimx', "Rows", 4, min= 1)),
column(4, numericInput('kohDimy', "Cols", 4, min= 1)),
column(4, selectInput('kohTopo', "Topology",
c("hexagonal", "rectangular")))),
checkboxInput("trainscale", "Scale training data", T),
fluidRow(column(4, checkboxInput("trainAdvanced", "Advanced options", F)),
column(4, actionButton("help_message_training", "", icon = icon("question"), width = NULL))),
conditionalPanel("input.trainAdvanced",
fluidRow(column(4, p("Initialization")),
column(8, selectInput("kohInit", NULL,
c("PCA Obs"= "pca.sample",
"PCA"= "pca",
"Random Obs"= "random"),
"pca.sample"))),
fluidRow(column(4, p("rlen")),
column(8, numericInput("trainRlen", NULL, 100, 1, 1e6))),
fluidRow(column(4, p("Alpha (start,stop)")),
column(4, numericInput("trainAlpha1", NULL, .05, 1e-6, 1e3)),
column(4, numericInput("trainAlpha2", NULL, .01, 1e-6, 1e3))),
fluidRow(column(4, p("Radius (start,stop)")),
column(4, numericInput("trainRadius1", NULL, .05, 1e-6, 1e3)),
column(4, numericInput("trainRadius2", NULL, .05, 1e-6, 1e3))),
fluidRow(column(4, p("Random seed:")),
column(8, numericInput("trainSeed", NULL, sample(1e5, 1), 1, 1e9)))))),
# wellPanel(
# h3("Import SOM:"),
# fileInput("importmapbutton", "Import (RDS)"))),
column(8,
h3("Training variables:"),
fluidRow(column(4, actionButton("varNum", "Select numeric variables")),
column(4, actionButton("varAll", "Select all variables")),
column(4, actionButton("varNone", "Unselect all variables"))),
p(),
fluidRow(column(2, HTML("<p><b>Weight</b></p>")),
column(8, HTML("<p><b>Variable</b></p>")),
column(2, HTML("<p><b>Type</b></p>"))),
uiOutput("trainVarOptions"),
))),
tabPanel("Plot",
fluidRow(column(4,
## Sélection du graphique et des variables
h4("Plot options:"),
fluidRow(column(6, selectInput("graphWhat", NULL,
choices= c("General Information"= "MapInfo",
"Numeric Variables"= "Numeric",
"Categorical Variables"= "Categorical"),
selected= "MapInfo")),
column(6, selectInput("graphType", NULL,
choices= c("Population map"= "Hitmap",
"Superclass Dendrogram"= "Dendrogram",
"Superclass Scree plot"= "Screeplot",
"Superclass Silhouette"= "Silhouette",
"Neighbour distance"= "UMatrix",
"Smooth distance"= "SmoothDist"
),
selected= "Hitmap"))),
#question about that panel below
conditionalPanel('input.graphType == "Pie" | input.graphType == "CatBarplot" | input.graphType == "Color" | input.graphType == "Names"',
uiOutput("plotVarOne")),
conditionalPanel(paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Radar"'),
uiOutput("plotVarMult")),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist" & input.graphType != "Abstraction"',
uiOutput("plotNames")),
checkboxInput("plotAdvanced", "Advanced options", F),
conditionalPanel("input.plotAdvanced",
## Values to plot: means, medians, prototypes
conditionalPanel(paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Color" | ',
'input.graphType == "Radar"'),
fluidRow(
column(4, p("Values")),
column(7, selectInput("average_format", NULL,
choices = c("Observation means" = "mean",
"Observation medians" = "median",
"Prototypes" = "prototypes"),
selected = "mean")),
column(1, actionButton("help_average_format", "", icon = icon("question"), width = NULL)))),
## Variable scales
conditionalPanel(paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Color" | ',
'input.graphType == "Radar"'),
fluidRow(
column(4, p("Variables scales")),
column(7, selectInput("contrast", NULL,
choices = c("Contrast" = "contrast",
"Observations Range" = "range",
"Same scale" = "same"),
selected = "contrast")),
column(1, actionButton("help_contrast", "", icon = icon("question"), width = NULL)))),
conditionalPanel('input.graphType == "Boxplot"',
checkboxInput("plotOutliers", "Plot outliers", value= T)),
conditionalPanel('input.graphType == "Pie"',
checkboxInput("plotEqualSize", "Equal pie sizes", F)),
conditionalPanel('input.graphType == "Color" | input.graphType == "UMatrix"',
checkboxInput("plotShowSC", "Show superclasses", T)),
## Show axes, re-arrange variables
conditionalPanel(paste0('input.graphType == "Circular" | ',
'input.graphType == "Line" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "CatBarplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Radar"'),
checkboxInput("plotAxes", "Show axes", value= T)),
## Use transparency
conditionalPanel(paste0('input.graphType == "Hitmap" | ',
'input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "CatBarplot" | ',
'input.graphType == "Radar"'),
checkboxInput("plotTransparency", "Use transparency", value= T)),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "Color" & input.graphType != "UMatrix" & input.graphType != "SmoothDist"',
fluidRow(column(4, p("Superclass palette")),
column(8, selectInput("palsc", NULL,
c("viridis", "grey", "rainbow", "heat", "terrain",
"topo", "cm", rownames(RColorBrewer::brewer.pal.info)),
"Set3")))),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "Hitmap"',
fluidRow(column(4, p("Plots palette")),
column(8,selectInput("palplot", NULL,
c("viridis", "grey", "rainbow", "heat", "terrain",
"topo", "cm", rownames(RColorBrewer::brewer.pal.info)),
"viridis"))),
checkboxInput("plotRevPal", "Reverse palette"))
),
fluidRow(column(4, h4("Plot size:")),
column(8, sliderInput("plotSize", NULL, 10, 4000, value= 400))),
hr(),
h4("Superclasses:"),
fluidRow(column(3, numericInput('kohSuperclass', NULL, 2, min= 1)),
column(5, selectInput('sup_clust_method', NULL,
c("hierarchical", "pam"))),
conditionalPanel('input.sup_clust_method == "hierarchical"',
column(4, selectInput("sup_clust_hcmethod", NULL,
c("ward.D2", "ward.D", "single", "complete",
"average", "mcquitty",
"median", "centroid"),
"complete")))),
hr(),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist"',
fluidRow(column(2, h4("Save:")),
column(5, downloadButton('downloadInteractive', "Interactive (html)")),
# column(3, downloadButton('downloadPng', 'png')),
column(5, downloadButton('downloadSvg', 'Static (svg)'))),
hr()),
fluidRow(column(4, h4("Roll the dice:")),
column(8, actionButton('retrainButton', "Train new SOM"))),
uiOutput("plotWarning")),
column(8,
## Display only the chosen graph
conditionalPanel('input.graphType == "Dendrogram"',
plotOutput("plotDendrogram")),
conditionalPanel('input.graphType == "Screeplot"',
plotOutput("plotScreeplot")),
conditionalPanel('input.graphType == "Silhouette"',
plotOutput("plotSilhouette")),
conditionalPanel('input.graphType == "SmoothDist"',
uiOutput("smooth_dist_warning"),
plotOutput("plotSmoothDist")),
# D3-based plots
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist"',
fluidRow(column(9,
HTML('<h4 id="theWidget-info"></h4>'),
HTML('<h4 id="theWidget-message"></h4>'),
aweSOM:::aweSOMoutput("theWidget")),
column(3, conditionalPanel('input.graphType != "Radar" & input.graphType != "Line" & input.graphType != "Heat" & input.graphType != "Hitmap"',
HTML('<svg id="theWidget-legend", width="100%"></svg>')))),
wellPanel(HTML('<p id="theWidget-names">Observation names will appear here.</p>')))
))),
tabPanel("Export data",
fluidRow(
column(4,
h3("Download full map"),
downloadButton("somDownload", "Download SOM (rds file)"),
h3("Download data, SOM cells, and superclasses."),
downloadButton("clustDownload", "Download Clustering (csv file)"),
h4("Selected variables"),
fluidRow(column(4, actionButton("clustSelectNone", "Unselect all")),
column(4, actionButton("clustSelectTrain", "Select train")),
column(4, actionButton("clustSelectAll", "Select all"))),
uiOutput("clustVariables")),
column(8, DT::dataTableOutput("clustTable")))),
tabPanel("R Script",
fluidRow(column(6, h4("Run this script in R to reproduce the results.")),
column(3, uiOutput("copycode")),
column(3, downloadButton("report", "Save html report"))),
verbatimTextOutput("codeTxt")),
tabPanel("About",
fluidRow(column(6,
h1("aweSOM"),
h3("Interactive Self-Organizing Maps"),
wellPanel(HTML('<strong>aweSOM</strong> offers a set of tools to explore and analyze numeric
data with Self-Organizing Maps (also known as <a href="https://en.wikipedia.org/wiki/Self-organizing_map">Kohonen maps</a>
a form of artificial neural network originally created by <a href="https://en.wikipedia.org/wiki/Teuvo_Kohonen">Teuvo Kohonen</a>
) in the 1980s. The package introduces interactive plots, making analysis of the SOM easier.<br>'),
HTML("<br> Use this interface to train and visualize self-organizing maps, using the tabs above in sequence : <br>
<strong>Import Data:</strong> Import the data to analyze<br>
<strong>Train:</strong> Train the SOM on selected variables<br>
<strong>Plot:</strong> Visualize the trained SOM <br>
<strong>Export Data:</strong> Export the trained SOM or clustered data <br>
<strong>R Script:</strong> Generate the R script to reproduce your analysis in R")),
h3("References"),
HTML("Kohonen T. (2001) <em>Self-Organizing Maps</em>, 3rd edition, Springer Press, Berlin.")),
column(6, img(src = "Teuvo-Kohonen.jpg",
alt= "Here a portrait of Teuvo Kohonen.",
width= "100%",
style = "margin:10px; padding: 0px 0px"),
HTML("<p>Teuvo Kohonen, inventor of the SOM, in the early 1980s. \
Image source: wikipedia, <a href='https://creativecommons.org/licenses/by/4.0/deed.en'> CC-BY 4.0 </a></p>")))
)
)
))
jansodoge/awesom_dev_version documentation built on Jan. 26, 2021, 8:53 a.m.
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shinyUI(fluidPage(
tags$head(HTML("<title>aweSOM</title>")),
#to modify style of help messages (increase font etc. tbd after lunch)
tags$style(
HTML(".shiny-notification {position:fixed; top: 50%; left: 0px; width: 30%;}")
),
rclipboard::rclipboardSetup(),
tabsetPanel(
#### Panel 'Welcome, Import Data'
#########################################################################
tabPanel("Import Data",
includeHTML("js/svg_todataurl.js"),
# data_import -------------------------------------------------------------
fluidRow(
column(4,
h2("aweSOM"),
h4("interactive self-organizing maps"),
wellPanel(
h4("Import Data"),
selectInput('file_type', NULL,
choices = c(
".csv or .txt" = "csv_txt",
"Microsoft Excel .xlsx" = "excel_xlsx",
"Microsoft Excel .xls" = "excel_xls",
"SPSS (.sav, .por)" = "spss",
"SAS Data" = "sas_data",
"Stata (.dta)" = "stata"),
selected = "csv_txt"
),
fileInput('dataFile', 'Choose File'),
# HTML("<b>Import parameters</b>"),
checkboxInput("importParams", "File parameters"),
conditionalPanel(
"input.importParams",
conditionalPanel("input.file_type == 'csv_txt'",
fluidRow(column(4, p('Header:')),
column(8, selectInput('header', NULL,
c("Auto", "Header",
"No Header"),
"Auto"))),
fluidRow(column(4, p('Separator:')),
column(8, selectInput('sep', NULL,
c("Auto", "Comma ','",
"Semicolon ';'",
"Tab","Space"),
"Auto"))),
fluidRow(column(4, p('Quote:')),
column(8, selectInput('quote', NULL,
c("None","Double Quote \"","Single Quote '"),
'Double Quote "'))),
fluidRow(column(4, p('Decimal mark')),
column(8, selectInput('dec', NULL,
c('Period "."', 'Comma ","'),
'Period "."'))),
fluidRow(column(4, p('File Encoding')),
column(8, selectInput('encoding', NULL,
c("unknown", "UTF-8", "whatever else"),
"unknown")))),
conditionalPanel("input.file_type == 'excel_xlsx'",
fluidRow(column(4, p('Column names')),
column(8, selectInput('column_names', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('rows_to_skip', NULL, 0, min= 0))),
fluidRow(column(4, p('Trim whitespaces')),
column(8, selectInput('trim_spaces', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
fluidRow(column(4, checkboxInput("worksheet_specified_bol", "Specify Worksheet", F))),
conditionalPanel("input.worksheet_specified_bol",
textInput("worksheet_specs", NULL, "")
),
fluidRow(column(4, checkboxInput("range_specified_bol", "Specify Range", F))),
conditionalPanel("input.range_specified_bol",
textInput("range_specs", NULL, "")
)),
## Options for xls files
conditionalPanel("input.file_type == 'excel_xls'",
fluidRow(column(4, p('Column names')),
column(8, selectInput('column_names_xls', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('rows_to_skip_xls', NULL, 0, min= 0))),
fluidRow(column(4, p('Trim whitespaces')),
column(8, selectInput('trim_spaces_xls', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
fluidRow(column(4, checkboxInput("worksheet_specified_bol_xls", "Specify Worksheet", F))),
conditionalPanel("input.worksheet_specified_bol_xls",
textInput("worksheet_specs_xls", NULL, "")
),
fluidRow(column(4, checkboxInput("range_specified_bol_xls", "Specify Range", F))),
conditionalPanel("input.range_specified_bol_xls",
textInput("range_specs_xls", NULL, "")
)),
## Options for SPSS files
conditionalPanel("input.file_type == 'spss'",
###specs and params here
## Possible: encoding, user_na, skip, n_max
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('skip_spss', NULL, 0, min= 0)))),
)
),
fluidRow(column(3, HTML("<h4>Help</h4>")),
column(2, actionButton("help_message_intro_to_aweSOM", "", icon = icon("question"), width = NULL)))
),
column(8,
uiOutput("dataImportMessage"),
DT::dataTableOutput("dataView"))
)),
tabPanel("Train",
wellPanel(fluidRow(column(2, h3("Map info:")),
column(10, verbatimTextOutput("Message")))),
fluidRow(column(4, wellPanel(
h3("Train new map:"),
actionButton("trainbutton", HTML("<b>Train SOM</b>"), width= "100%"),
hr(),
fluidRow(column(4, numericInput('kohDimx', "Rows", 4, min= 1)),
column(4, numericInput('kohDimy', "Cols", 4, min= 1)),
column(4, selectInput('kohTopo', "Topology",
c("hexagonal", "rectangular")))),
checkboxInput("trainscale", "Scale training data", T),
fluidRow(column(4, checkboxInput("trainAdvanced", "Advanced options", F)),
column(4, actionButton("help_message_training", "", icon = icon("question"), width = NULL))),
conditionalPanel("input.trainAdvanced",
fluidRow(column(4, p("Initialization")),
column(8, selectInput("kohInit", NULL,
c("PCA Obs"= "pca.sample",
"PCA"= "pca",
"Random Obs"= "random"),
"pca.sample"))),
fluidRow(column(4, p("rlen")),
column(8, numericInput("trainRlen", NULL, 100, 1, 1e6))),
fluidRow(column(4, p("Alpha (start,stop)")),
column(4, numericInput("trainAlpha1", NULL, .05, 1e-6, 1e3)),
column(4, numericInput("trainAlpha2", NULL, .01, 1e-6, 1e3))),
fluidRow(column(4, p("Radius (start,stop)")),
column(4, numericInput("trainRadius1", NULL, .05, 1e-6, 1e3)),
column(4, numericInput("trainRadius2", NULL, .05, 1e-6, 1e3))),
fluidRow(column(4, p("Random seed:")),
column(8, numericInput("trainSeed", NULL, sample(1e5, 1), 1, 1e9)))))),
# wellPanel(
# h3("Import SOM:"),
# fileInput("importmapbutton", "Import (RDS)"))),
column(8,
h3("Training variables:"),
fluidRow(column(4, actionButton("varNum", "Select numeric variables")),
column(4, actionButton("varAll", "Select all variables")),
column(4, actionButton("varNone", "Unselect all variables"))),
p(),
fluidRow(column(2, HTML("<p><b>Weight</b></p>")),
column(8, HTML("<p><b>Variable</b></p>")),
column(2, HTML("<p><b>Type</b></p>"))),
uiOutput("trainVarOptions"),
))),
tabPanel("Plot",
fluidRow(column(4,
## Sélection du graphique et des variables
h4("Plot options:"),
fluidRow(column(6, selectInput("graphWhat", NULL,
choices= c("General Information"= "MapInfo",
"Numeric Variables"= "Numeric",
"Categorical Variables"= "Categorical"),
selected= "MapInfo")),
column(6, selectInput("graphType", NULL,
choices= c("Population map"= "Hitmap",
"Superclass Dendrogram"= "Dendrogram",
"Superclass Scree plot"= "Screeplot",
"Superclass Silhouette"= "Silhouette",
"Neighbour distance"= "UMatrix",
"Smooth distance"= "SmoothDist"
),
selected= "Hitmap"))),
#question about that panel below
conditionalPanel('input.graphType == "Pie" | input.graphType == "CatBarplot" | input.graphType == "Color" | input.graphType == "Names"',
uiOutput("plotVarOne")),
conditionalPanel(paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Radar"'),
uiOutput("plotVarMult")),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist" & input.graphType != "Abstraction"',
uiOutput("plotNames")),
checkboxInput("plotAdvanced", "Advanced options", F),
conditionalPanel("input.plotAdvanced",
## Values to plot: means, medians, prototypes
conditionalPanel(paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Color" | ',
'input.graphType == "Radar"'),
fluidRow(
column(4, p("Values")),
column(7, selectInput("average_format", NULL,
choices = c("Observation means" = "mean",
"Observation medians" = "median",
"Prototypes" = "prototypes"),
selected = "mean")),
column(1, actionButton("help_average_format", "", icon = icon("question"), width = NULL)))),
## Variable scales
conditionalPanel(paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Color" | ',
'input.graphType == "Radar"'),
fluidRow(
column(4, p("Variables scales")),
column(7, selectInput("contrast", NULL,
choices = c("Contrast" = "contrast",
"Observations Range" = "range",
"Same scale" = "same"),
selected = "contrast")),
column(1, actionButton("help_contrast", "", icon = icon("question"), width = NULL)))),
conditionalPanel('input.graphType == "Boxplot"',
checkboxInput("plotOutliers", "Plot outliers", value= T)),
conditionalPanel('input.graphType == "Pie"',
checkboxInput("plotEqualSize", "Equal pie sizes", F)),
conditionalPanel('input.graphType == "Color" | input.graphType == "UMatrix"',
checkboxInput("plotShowSC", "Show superclasses", T)),
## Show axes, re-arrange variables
conditionalPanel(paste0('input.graphType == "Circular" | ',
'input.graphType == "Line" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "CatBarplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Radar"'),
checkboxInput("plotAxes", "Show axes", value= T)),
## Use transparency
conditionalPanel(paste0('input.graphType == "Hitmap" | ',
'input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "CatBarplot" | ',
'input.graphType == "Radar"'),
checkboxInput("plotTransparency", "Use transparency", value= T)),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "Color" & input.graphType != "UMatrix" & input.graphType != "SmoothDist"',
fluidRow(column(4, p("Superclass palette")),
column(8, selectInput("palsc", NULL,
c("viridis", "grey", "rainbow", "heat", "terrain",
"topo", "cm", rownames(RColorBrewer::brewer.pal.info)),
"Set3")))),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "Hitmap"',
fluidRow(column(4, p("Plots palette")),
column(8,selectInput("palplot", NULL,
c("viridis", "grey", "rainbow", "heat", "terrain",
"topo", "cm", rownames(RColorBrewer::brewer.pal.info)),
"viridis"))),
checkboxInput("plotRevPal", "Reverse palette"))
),
fluidRow(column(4, h4("Plot size:")),
column(8, sliderInput("plotSize", NULL, 10, 4000, value= 400))),
hr(),
h4("Superclasses:"),
fluidRow(column(3, numericInput('kohSuperclass', NULL, 2, min= 1)),
column(5, selectInput('sup_clust_method', NULL,
c("hierarchical", "pam"))),
conditionalPanel('input.sup_clust_method == "hierarchical"',
column(4, selectInput("sup_clust_hcmethod", NULL,
c("ward.D2", "ward.D", "single", "complete",
"average", "mcquitty",
"median", "centroid"),
"complete")))),
hr(),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist"',
fluidRow(column(2, h4("Save:")),
column(5, downloadButton('downloadInteractive', "Interactive (html)")),
# column(3, downloadButton('downloadPng', 'png')),
column(5, downloadButton('downloadSvg', 'Static (svg)'))),
hr()),
fluidRow(column(4, h4("Roll the dice:")),
column(8, actionButton('retrainButton', "Train new SOM"))),
uiOutput("plotWarning")),
column(8,
## Display only the chosen graph
conditionalPanel('input.graphType == "Dendrogram"',
plotOutput("plotDendrogram")),
conditionalPanel('input.graphType == "Screeplot"',
plotOutput("plotScreeplot")),
conditionalPanel('input.graphType == "Silhouette"',
plotOutput("plotSilhouette")),
conditionalPanel('input.graphType == "SmoothDist"',
uiOutput("smooth_dist_warning"),
plotOutput("plotSmoothDist")),
# D3-based plots
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist"',
fluidRow(column(9,
HTML('<h4 id="theWidget-info"></h4>'),
HTML('<h4 id="theWidget-message"></h4>'),
aweSOM:::aweSOMoutput("theWidget")),
column(3, conditionalPanel('input.graphType != "Radar" & input.graphType != "Line" & input.graphType != "Heat" & input.graphType != "Hitmap"',
HTML('<svg id="theWidget-legend", width="100%"></svg>')))),
wellPanel(HTML('<p id="theWidget-names">Observation names will appear here.</p>')))
))),
tabPanel("Export data",
fluidRow(
column(4,
h3("Download full map"),
downloadButton("somDownload", "Download SOM (rds file)"),
h3("Download data, SOM cells, and superclasses."),
downloadButton("clustDownload", "Download Clustering (csv file)"),
h4("Selected variables"),
fluidRow(column(4, actionButton("clustSelectNone", "Unselect all")),
column(4, actionButton("clustSelectTrain", "Select train")),
column(4, actionButton("clustSelectAll", "Select all"))),
uiOutput("clustVariables")),
column(8, DT::dataTableOutput("clustTable")))),
tabPanel("R Script",
fluidRow(column(6, h4("Run this script in R to reproduce the results.")),
column(3, uiOutput("copycode")),
column(3, downloadButton("report", "Save html report"))),
verbatimTextOutput("codeTxt")),
tabPanel("About",
fluidRow(column(6,
h1("aweSOM"),
h3("Interactive Self-Organizing Maps"),
wellPanel(HTML('<strong>aweSOM</strong> offers a set of tools to explore and analyze numeric
data with Self-Organizing Maps (also known as <a href="https://en.wikipedia.org/wiki/Self-organizing_map">Kohonen maps</a>
a form of artificial neural network originally created by <a href="https://en.wikipedia.org/wiki/Teuvo_Kohonen">Teuvo Kohonen</a>
) in the 1980s. The package introduces interactive plots, making analysis of the SOM easier.<br>'),
HTML("<br> Use this interface to train and visualize self-organizing maps, using the tabs above in sequence : <br>
<strong>Import Data:</strong> Import the data to analyze<br>
<strong>Train:</strong> Train the SOM on selected variables<br>
<strong>Plot:</strong> Visualize the trained SOM <br>
<strong>Export Data:</strong> Export the trained SOM or clustered data <br>
<strong>R Script:</strong> Generate the R script to reproduce your analysis in R")),
h3("References"),
HTML("Kohonen T. (2001) <em>Self-Organizing Maps</em>, 3rd edition, Springer Press, Berlin.")),
column(6, img(src = "Teuvo-Kohonen.jpg",
alt= "Here a portrait of Teuvo Kohonen.",
width= "100%",
style = "margin:10px; padding: 0px 0px"),
HTML("<p>Teuvo Kohonen, inventor of the SOM, in the early 1980s. \
Image source: wikipedia, <a href='https://creativecommons.org/licenses/by/4.0/deed.en'> CC-BY 4.0 </a></p>")))
)
)
))
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