Nothing
inst/shiny/ui.R
In aweSOM: Interactive Self-Organizing Maps
shinyUI(
navbarPage(
"aweSOM",
## Theme with bslib (requires shiny 1.6)
theme = bslib::bs_theme(bootswatch = "united",
primary = "#ff9733ff", secondary = "#ffc46dff",
"navbar-dark-color"= "#111"),
############################################################################
#### Panel 'Welcome, Import Data'
############################################################################
tabPanel(
"Import Data",
rclipboard::rclipboardSetup(),
includeHTML("js/svg_todataurl.js"),
fluidRow(
column(
4,
HTML('<table><tr>
<td width= "50%" height= "139" align="center" valign="middle">
<img src="logo.png" alt="<aweSOM>" width="120"/></td>
<td width="50%" height="139" align="left" valign="middle">
<h3>interactive self-organizing maps</h3></td></tr></table>'),
br(),
wellPanel(
fluidRow(column(8, h4("Import Data")),
column(4, actionButton("help_filesize", "", width = NULL,
icon = icon("question")))),
selectInput('file_type', NULL,
choices = c("Text file (.csv, .txt)" = "csv_txt",
"OpenDocument (.ods)" = "ods",
"Microsoft Excel (.xls, .xlsx)" = "excel",
"SPSS (.sav, .por)" = "spss",
"SAS (.sas7bdat)" = "sas_data",
"Stata v5-v12 (.dta)" = "stata"),
selected = "csv_txt"
),
fileInput('dataFile', 'Choose File'),
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" = "auto",
"Header" = TRUE,
"No Header" = FALSE),
"Auto"))),
fluidRow(column(4, p('Separator')),
column(8, selectInput('sep', NULL,
c("Auto" = "auto",
"Comma ','" = ",",
"Semicolon ';'" = ";",
"Tab" = "\t",
"Space" = " "),
"Auto"))),
fluidRow(column(4, p('Quote')),
column(8, selectInput('quote', NULL,
c("Double Quote \"" = "\"",
"Single Quote '" = "'",
"None" = "None"),
"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", "Latin-1"),
"unknown")))),
## Options for ods files
conditionalPanel(
"input.file_type == 'ods'",
fluidRow(column(4, p('Sheet')),
column(8, numericInput('ods_sheet', NULL, 1, 1,
step = 1))),
checkboxInput("ods_col_names", "Column names", TRUE),
fluidRow(column(4, p('NA symbol')),
column(8, textInput('ods_na', NULL, value = ""))),
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('ods_skip', NULL, 0, 0,
step = 1))),
fluidRow(column(4, p('Specify range')),
column(8, textInput('ods_range', NULL, value = "")))
),
## Options for xls / xlsx files
conditionalPanel(
"input.file_type == 'excel'",
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, 0,
step = 1))),
fluidRow(column(4, p('Trim whitespaces')),
column(8, selectInput('trim_spaces', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
checkboxInput("worksheet_specified_bol",
"Specify Worksheet", FALSE),
conditionalPanel("input.worksheet_specified_bol",
textInput("worksheet_specs", NULL, "")),
checkboxInput("range_specified_bol", "Specify Range", FALSE),
conditionalPanel("input.range_specified_bol",
textInput("range_specs", NULL, "")
)),
## Options for SPSS files
conditionalPanel(
"input.file_type == 'spss'",
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('skip_spss', NULL, 0, 0,
step = 1))),
checkboxInput("user_na_spss", "User-defined NA", FALSE)),
## Options for SAS files
conditionalPanel(
"input.file_type == 'sas_data'",
fluidRow(column(4, p('Skip rows')),
column(8, numericInput("sas_skip", NULL, 0, 0,
step = 1))),
checkboxInput("sas_use_catalog", "Use catalog file", FALSE),
conditionalPanel(
"input.sas_use_catalog",
fileInput("sas_catalog_file", "Catalog file"))
),
## Options for STATA dta files
conditionalPanel(
"input.file_type == 'stata'",
checkboxInput("convert_factors_stata", "Convert factors", FALSE))
)
),
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"))
)),
############################################################################
#### Panel 'Train'
############################################################################
tabPanel(
"Train",
wellPanel(fluidRow(column(2, h3("Map info:")),
column(10, verbatimTextOutput("Message")))),
fluidRow(column(5, wellPanel(
h3("Train new map:"),
actionButton("trainbutton", HTML("<b>Train SOM</b>"), width= "100%", class = "btn-primary"),
hr(),
fluidRow(column(3, numericInput('kohDimy', "Rows", 4, min= 1)),
column(3, numericInput('kohDimx', "Cols", 4, min= 1)),
column(6, selectInput('kohTopo', "Topology",
c("hexagonal", "rectangular")))),
fluidRow(column(4, checkboxInput("trainscale", "Scale variables", T)),
column(2, actionButton("help_scale", "", icon = icon("question"),
width = NULL)),
column(3, actionLink("weightsToOne", "Weights to 1")),
column(3, actionLink("weightsToComp", "Balance weights"))),
br(),
fluidRow(column(10, checkboxInput("trainAdvanced", "Advanced options", F))),
conditionalPanel("input.trainAdvanced",
fluidRow(column(4, p("Random seed:")),
column(6, numericInput("trainSeed", NULL, sample(1e5, 1), 1, 1e9)),
column(2, actionButton("help_seed", "",
icon = icon("question"), width = NULL))),
fluidRow(column(4, p("Initialization")),
column(6, selectInput("kohInit", NULL,
c("PCA Obs"= "pca.sample",
"PCA"= "pca",
"Random Obs"= "random"),
"pca.sample")),
column(2, actionButton("help_init", "",
icon = icon("question"), width = NULL))),
fluidRow(column(4, p("maxNA.fraction")),
column(6, numericInput("trainMaxNA", NULL, .25, 0, 1, .01)),
column(2, actionButton("help_maxNA", "",
icon = icon("question"), width = NULL))),
fluidRow(column(4, p("rlen")),
column(6, numericInput("trainRlen", NULL, 100, 1, 1e6)),
column(2, actionButton("help_rlen", "",
icon = icon("question"), width = NULL))),
fluidRow(column(4, p("Alpha (start,stop)")),
column(4, numericInput("trainAlpha1", NULL, .05, 0, 1e3, 1e-3)),
column(4, numericInput("trainAlpha2", NULL, .01, 0, 1e3, 1e-3))),
fluidRow(column(4, p("Radius (start,stop)")),
column(4, numericInput("trainRadius1", NULL, .05, step = 1e-3)),
column(4, numericInput("trainRadius2", NULL, .05, step = 1e-3)))))),
column(7, fluidRow(column(
5,
fluidRow(h3("Training variables:")),
fluidRow(actionButton("varNum", "Select numeric"),
actionButton("varAll", "All"),
actionButton("varNone", "None")),
fluidRow(uiOutput("trainVarSelect"),
HTML("<p><em>Use Shift and Ctrl to select several variables.</em></p>"))),
column(
7,
br(), br(),
HTML('<h5>Training <a id=help_types class="action-button" href="#">types</a>,
<a id=help_weights class="action-button" href="#">weights</a> and
<a id=help_levels class="action-button" href="#">levels</a>.</h5>'),
fluidRow(column(4, HTML("<p><b>Type</b></p>")),
column(3, HTML("<p><b>Weight</b></p>")),
column(5, HTML("<p><b>Variable</b></p>"))),
uiOutput("trainVarOptions")
))
))),
############################################################################
#### Panel 'Plot'
############################################################################
tabPanel("Plot", fluidRow(column(
4,
fluidRow(column(6, h4("Roll the dice:")),
column(6, actionButton('retrainButton', "Train new SOM", class = "btn-primary"))),
## 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("Observations Cloud"= "Cloud",
"Population map"= "Hitmap",
"Superclass Dendrogram"= "Dendrogram",
"Superclass Scree plot"= "Screeplot",
"Superclass Silhouette"= "Silhouette",
"Neighbour distance"= "UMatrix",
"Smooth distance"= "SmoothDist"
),
selected= "Cloud"))),
#question about that panel below
conditionalPanel(
'input.graphType == "Pie" | input.graphType == "CatBarplot" | input.graphType == "Color"',
fluidRow(column(4, p("Plot variable:")),
column(8, selectInput("plotVarOne", NULL, choices= NULL, selected= NULL)))),
conditionalPanel(
'input.graphType == "Cloud"',
fluidRow(column(4, p("Color variable:")),
column(8, selectInput("plotVarColor", NULL, choices= NULL, selected= NULL))),
checkboxInput("plotShowTooltip", "Tooltip obs. info", TRUE),
conditionalPanel(
'input.plotShowTooltip',
selectInput("plotVarTooltip", NULL, choices= NULL, selected= NULL, multiple = TRUE))),
conditionalPanel(
paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Radar"'),
# fluidRow(column(4, p("Plot variables:"),
# conditionalPanel("input.plotAdvanced",
# actionButton("plotArrange", "Reorder", class = "btn-primary"))),
# column(8, selectInput("plotVarMult", NULL, multiple= TRUE, choices= NULL, selected= NULL)))
fluidRow(column(4, p("Plot variables:")),
column(4, actionLink("plotSelectTrain", "Select training vars.")),
column(4, actionLink("plotArrange", "Reorder"))),
fluidRow(selectInput("plotVarMult", NULL, multiple= TRUE, choices= NULL, selected= NULL))),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist" & input.graphType != "Abstraction"',
uiOutput("plotNames")),
wellPanel(
checkboxInput("plotAdvanced", "Advanced options", FALSE),
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 == "CatBarplot" | ',
'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= TRUE)),
conditionalPanel(
'input.graphType == "Pie"',
checkboxInput("plotEqualSize", "Equal pie sizes", FALSE)),
conditionalPanel(
'input.graphType == "Color" | input.graphType == "UMatrix"',
checkboxInput("plotShowSC", "Show superclasses", TRUE)),
conditionalPanel(
'input.graphType == "Cloud"',
fluidRow(
column(4, p("Cloud type")),
column(5, selectInput("plotCloudType", NULL,
c("Cell-wise PCA" = "cellPCA",
"Cell-centered kPCA" = "kPCA",
"Cell-centered PCA" = "PCA",
"Prototype Proximity" = "proximity",
"Random" = "random"))),
column(2, actionButton("help_cloud", "", icon = icon("question"), width = NULL)))),
conditionalPanel(
'input.graphType == "Cloud" & input.plotCloudType == "random"',
fluidRow(
column(4, p("Cloud seed")),
column(7, numericInput("plotCloudSeed", NULL, sample(1e5, 1), 1, step = 1)))),
## Show axes
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= TRUE)),
## Use transparency
conditionalPanel(
paste0('input.graphType == "Hitmap" | ',
'input.graphType == "Cloud" | ',
'input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "CatBarplot" | ',
'input.graphType == "Radar"'),
checkboxInput("plotTransparency", "Use transparency", value= TRUE)),
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")),
conditionalPanel(
'input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist"',
checkboxInput("plotShowNames", "Show obs. names", value= TRUE)),
conditionalPanel(
paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Color" | ',
'input.graphType == "UMatrix" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Cloud" | ',
'input.graphType == "CatBarplot" | ',
'input.graphType == "Pie" | ',
'input.graphType == "SmoothDist"'),
fluidRow(column(4, p("Legend")),
column(3, numericInput("legendFontsize", NULL, 14, 1, NA, .5)),
column(5, conditionalPanel(
'input.graphType != "SmoothDist"',
selectInput("legendPos", NULL,
c("Beside" = "beside", "Below" = "below",
"None" = "none"),
"beside")))))
)
),
hr(),
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"))),
column(4, conditionalPanel(
'input.sup_clust_method == "hierarchical"',
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()),
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"',
plotOutput("plotSmoothDist")),
## D3-based plots
conditionalPanel(
'input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist"',
HTML('<h4 id="theWidget-info"></h4>'),
HTML('<h4 id="theWidget-message"></h4>'),
aweSOM:::aweSOMoutput("theWidget"),
conditionalPanel(
"input.plotShowNames",
wellPanel(HTML('<p id="theWidget-names">Observation names will appear here.</p>'))),
conditionalPanel(
'input.graphType != "Radar" & input.graphType != "Line" & input.graphType != "Heat" & input.graphType != "Hitmap"',
HTML('<svg id="theWidget-newlegend", width="100%"></svg>'))
)
))),
############################################################################
#### Panel 'Export data'
############################################################################
tabPanel(
"Export data",
fluidRow(
column(4,
h4("Download full map"),
p("The rds file containing the trained map can be opened in R with readRDS."),
downloadButton("somDownload", "Download SOM (rds file)", class = "btn-primary"),
h4("Download clustered data (csv)"),
downloadButton("clustDownload", "Download Clustering (csv file)", class = "btn-primary"),
h5("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")))),
############################################################################
#### Panel 'R script'
############################################################################
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", class = "btn-primary"))),
verbatimTextOutput("codeTxt")),
############################################################################
#### Panel 'About'
############################################################################
tabPanel(
"About",
fluidRow(column(
6,
HTML('<table><tr>
<td width= "50%" height= "139" align="center" valign="middle"><img src="logo.png" alt="<aweSOM>" width="120"/></td>
<td width="50%" height="139" align="left" valign="middle"><h3>interactive self-organizing maps</h3></td>
</tr></table>'),
wellPanel(HTML('<p><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 visual inspection of the SOM easier.</p>'),
HTML("<p> Use this interface to train and visualize SOMs, 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</p>"),
HTML("<p> While standard SOM works on numeric data only, aweSOM handles
<strong>categorical variables</strong> through dummy-encoding and
appropriate scaling, so that each variable has the same total variance (as in MCA).
As in <strong>specific</strong> MCA, chosen levels can be dropped from the training data.
The treatment of <strong>mixed data</strong> is equivalent to the one in FAMD (factorial analysis of mixed data).</p>")),
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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shinyUI(
navbarPage(
"aweSOM",
## Theme with bslib (requires shiny 1.6)
theme = bslib::bs_theme(bootswatch = "united",
primary = "#ff9733ff", secondary = "#ffc46dff",
"navbar-dark-color"= "#111"),
############################################################################
#### Panel 'Welcome, Import Data'
############################################################################
tabPanel(
"Import Data",
rclipboard::rclipboardSetup(),
includeHTML("js/svg_todataurl.js"),
fluidRow(
column(
4,
HTML('<table><tr>
<td width= "50%" height= "139" align="center" valign="middle">
<img src="logo.png" alt="<aweSOM>" width="120"/></td>
<td width="50%" height="139" align="left" valign="middle">
<h3>interactive self-organizing maps</h3></td></tr></table>'),
br(),
wellPanel(
fluidRow(column(8, h4("Import Data")),
column(4, actionButton("help_filesize", "", width = NULL,
icon = icon("question")))),
selectInput('file_type', NULL,
choices = c("Text file (.csv, .txt)" = "csv_txt",
"OpenDocument (.ods)" = "ods",
"Microsoft Excel (.xls, .xlsx)" = "excel",
"SPSS (.sav, .por)" = "spss",
"SAS (.sas7bdat)" = "sas_data",
"Stata v5-v12 (.dta)" = "stata"),
selected = "csv_txt"
),
fileInput('dataFile', 'Choose File'),
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" = "auto",
"Header" = TRUE,
"No Header" = FALSE),
"Auto"))),
fluidRow(column(4, p('Separator')),
column(8, selectInput('sep', NULL,
c("Auto" = "auto",
"Comma ','" = ",",
"Semicolon ';'" = ";",
"Tab" = "\t",
"Space" = " "),
"Auto"))),
fluidRow(column(4, p('Quote')),
column(8, selectInput('quote', NULL,
c("Double Quote \"" = "\"",
"Single Quote '" = "'",
"None" = "None"),
"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", "Latin-1"),
"unknown")))),
## Options for ods files
conditionalPanel(
"input.file_type == 'ods'",
fluidRow(column(4, p('Sheet')),
column(8, numericInput('ods_sheet', NULL, 1, 1,
step = 1))),
checkboxInput("ods_col_names", "Column names", TRUE),
fluidRow(column(4, p('NA symbol')),
column(8, textInput('ods_na', NULL, value = ""))),
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('ods_skip', NULL, 0, 0,
step = 1))),
fluidRow(column(4, p('Specify range')),
column(8, textInput('ods_range', NULL, value = "")))
),
## Options for xls / xlsx files
conditionalPanel(
"input.file_type == 'excel'",
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, 0,
step = 1))),
fluidRow(column(4, p('Trim whitespaces')),
column(8, selectInput('trim_spaces', NULL,
choices = c("Yes" = "TRUE",
"No" = "FALSE"),
selected = TRUE ))),
checkboxInput("worksheet_specified_bol",
"Specify Worksheet", FALSE),
conditionalPanel("input.worksheet_specified_bol",
textInput("worksheet_specs", NULL, "")),
checkboxInput("range_specified_bol", "Specify Range", FALSE),
conditionalPanel("input.range_specified_bol",
textInput("range_specs", NULL, "")
)),
## Options for SPSS files
conditionalPanel(
"input.file_type == 'spss'",
fluidRow(column(4, p('Skip rows')),
column(8, numericInput('skip_spss', NULL, 0, 0,
step = 1))),
checkboxInput("user_na_spss", "User-defined NA", FALSE)),
## Options for SAS files
conditionalPanel(
"input.file_type == 'sas_data'",
fluidRow(column(4, p('Skip rows')),
column(8, numericInput("sas_skip", NULL, 0, 0,
step = 1))),
checkboxInput("sas_use_catalog", "Use catalog file", FALSE),
conditionalPanel(
"input.sas_use_catalog",
fileInput("sas_catalog_file", "Catalog file"))
),
## Options for STATA dta files
conditionalPanel(
"input.file_type == 'stata'",
checkboxInput("convert_factors_stata", "Convert factors", FALSE))
)
),
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"))
)),
############################################################################
#### Panel 'Train'
############################################################################
tabPanel(
"Train",
wellPanel(fluidRow(column(2, h3("Map info:")),
column(10, verbatimTextOutput("Message")))),
fluidRow(column(5, wellPanel(
h3("Train new map:"),
actionButton("trainbutton", HTML("<b>Train SOM</b>"), width= "100%", class = "btn-primary"),
hr(),
fluidRow(column(3, numericInput('kohDimy', "Rows", 4, min= 1)),
column(3, numericInput('kohDimx', "Cols", 4, min= 1)),
column(6, selectInput('kohTopo', "Topology",
c("hexagonal", "rectangular")))),
fluidRow(column(4, checkboxInput("trainscale", "Scale variables", T)),
column(2, actionButton("help_scale", "", icon = icon("question"),
width = NULL)),
column(3, actionLink("weightsToOne", "Weights to 1")),
column(3, actionLink("weightsToComp", "Balance weights"))),
br(),
fluidRow(column(10, checkboxInput("trainAdvanced", "Advanced options", F))),
conditionalPanel("input.trainAdvanced",
fluidRow(column(4, p("Random seed:")),
column(6, numericInput("trainSeed", NULL, sample(1e5, 1), 1, 1e9)),
column(2, actionButton("help_seed", "",
icon = icon("question"), width = NULL))),
fluidRow(column(4, p("Initialization")),
column(6, selectInput("kohInit", NULL,
c("PCA Obs"= "pca.sample",
"PCA"= "pca",
"Random Obs"= "random"),
"pca.sample")),
column(2, actionButton("help_init", "",
icon = icon("question"), width = NULL))),
fluidRow(column(4, p("maxNA.fraction")),
column(6, numericInput("trainMaxNA", NULL, .25, 0, 1, .01)),
column(2, actionButton("help_maxNA", "",
icon = icon("question"), width = NULL))),
fluidRow(column(4, p("rlen")),
column(6, numericInput("trainRlen", NULL, 100, 1, 1e6)),
column(2, actionButton("help_rlen", "",
icon = icon("question"), width = NULL))),
fluidRow(column(4, p("Alpha (start,stop)")),
column(4, numericInput("trainAlpha1", NULL, .05, 0, 1e3, 1e-3)),
column(4, numericInput("trainAlpha2", NULL, .01, 0, 1e3, 1e-3))),
fluidRow(column(4, p("Radius (start,stop)")),
column(4, numericInput("trainRadius1", NULL, .05, step = 1e-3)),
column(4, numericInput("trainRadius2", NULL, .05, step = 1e-3)))))),
column(7, fluidRow(column(
5,
fluidRow(h3("Training variables:")),
fluidRow(actionButton("varNum", "Select numeric"),
actionButton("varAll", "All"),
actionButton("varNone", "None")),
fluidRow(uiOutput("trainVarSelect"),
HTML("<p><em>Use Shift and Ctrl to select several variables.</em></p>"))),
column(
7,
br(), br(),
HTML('<h5>Training <a id=help_types class="action-button" href="#">types</a>,
<a id=help_weights class="action-button" href="#">weights</a> and
<a id=help_levels class="action-button" href="#">levels</a>.</h5>'),
fluidRow(column(4, HTML("<p><b>Type</b></p>")),
column(3, HTML("<p><b>Weight</b></p>")),
column(5, HTML("<p><b>Variable</b></p>"))),
uiOutput("trainVarOptions")
))
))),
############################################################################
#### Panel 'Plot'
############################################################################
tabPanel("Plot", fluidRow(column(
4,
fluidRow(column(6, h4("Roll the dice:")),
column(6, actionButton('retrainButton', "Train new SOM", class = "btn-primary"))),
## 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("Observations Cloud"= "Cloud",
"Population map"= "Hitmap",
"Superclass Dendrogram"= "Dendrogram",
"Superclass Scree plot"= "Screeplot",
"Superclass Silhouette"= "Silhouette",
"Neighbour distance"= "UMatrix",
"Smooth distance"= "SmoothDist"
),
selected= "Cloud"))),
#question about that panel below
conditionalPanel(
'input.graphType == "Pie" | input.graphType == "CatBarplot" | input.graphType == "Color"',
fluidRow(column(4, p("Plot variable:")),
column(8, selectInput("plotVarOne", NULL, choices= NULL, selected= NULL)))),
conditionalPanel(
'input.graphType == "Cloud"',
fluidRow(column(4, p("Color variable:")),
column(8, selectInput("plotVarColor", NULL, choices= NULL, selected= NULL))),
checkboxInput("plotShowTooltip", "Tooltip obs. info", TRUE),
conditionalPanel(
'input.plotShowTooltip',
selectInput("plotVarTooltip", NULL, choices= NULL, selected= NULL, multiple = TRUE))),
conditionalPanel(
paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Radar"'),
# fluidRow(column(4, p("Plot variables:"),
# conditionalPanel("input.plotAdvanced",
# actionButton("plotArrange", "Reorder", class = "btn-primary"))),
# column(8, selectInput("plotVarMult", NULL, multiple= TRUE, choices= NULL, selected= NULL)))
fluidRow(column(4, p("Plot variables:")),
column(4, actionLink("plotSelectTrain", "Select training vars.")),
column(4, actionLink("plotArrange", "Reorder"))),
fluidRow(selectInput("plotVarMult", NULL, multiple= TRUE, choices= NULL, selected= NULL))),
conditionalPanel('input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist" & input.graphType != "Abstraction"',
uiOutput("plotNames")),
wellPanel(
checkboxInput("plotAdvanced", "Advanced options", FALSE),
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 == "CatBarplot" | ',
'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= TRUE)),
conditionalPanel(
'input.graphType == "Pie"',
checkboxInput("plotEqualSize", "Equal pie sizes", FALSE)),
conditionalPanel(
'input.graphType == "Color" | input.graphType == "UMatrix"',
checkboxInput("plotShowSC", "Show superclasses", TRUE)),
conditionalPanel(
'input.graphType == "Cloud"',
fluidRow(
column(4, p("Cloud type")),
column(5, selectInput("plotCloudType", NULL,
c("Cell-wise PCA" = "cellPCA",
"Cell-centered kPCA" = "kPCA",
"Cell-centered PCA" = "PCA",
"Prototype Proximity" = "proximity",
"Random" = "random"))),
column(2, actionButton("help_cloud", "", icon = icon("question"), width = NULL)))),
conditionalPanel(
'input.graphType == "Cloud" & input.plotCloudType == "random"',
fluidRow(
column(4, p("Cloud seed")),
column(7, numericInput("plotCloudSeed", NULL, sample(1e5, 1), 1, step = 1)))),
## Show axes
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= TRUE)),
## Use transparency
conditionalPanel(
paste0('input.graphType == "Hitmap" | ',
'input.graphType == "Cloud" | ',
'input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "CatBarplot" | ',
'input.graphType == "Radar"'),
checkboxInput("plotTransparency", "Use transparency", value= TRUE)),
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")),
conditionalPanel(
'input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist"',
checkboxInput("plotShowNames", "Show obs. names", value= TRUE)),
conditionalPanel(
paste0('input.graphType == "Circular" | ',
'input.graphType == "Barplot" | ',
'input.graphType == "Color" | ',
'input.graphType == "UMatrix" | ',
'input.graphType == "Boxplot" | ',
'input.graphType == "Line" | ',
'input.graphType == "Cloud" | ',
'input.graphType == "CatBarplot" | ',
'input.graphType == "Pie" | ',
'input.graphType == "SmoothDist"'),
fluidRow(column(4, p("Legend")),
column(3, numericInput("legendFontsize", NULL, 14, 1, NA, .5)),
column(5, conditionalPanel(
'input.graphType != "SmoothDist"',
selectInput("legendPos", NULL,
c("Beside" = "beside", "Below" = "below",
"None" = "none"),
"beside")))))
)
),
hr(),
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"))),
column(4, conditionalPanel(
'input.sup_clust_method == "hierarchical"',
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()),
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"',
plotOutput("plotSmoothDist")),
## D3-based plots
conditionalPanel(
'input.graphType != "Silhouette" & input.graphType != "Dendrogram" & input.graphType != "Screeplot" & input.graphType != "SmoothDist"',
HTML('<h4 id="theWidget-info"></h4>'),
HTML('<h4 id="theWidget-message"></h4>'),
aweSOM:::aweSOMoutput("theWidget"),
conditionalPanel(
"input.plotShowNames",
wellPanel(HTML('<p id="theWidget-names">Observation names will appear here.</p>'))),
conditionalPanel(
'input.graphType != "Radar" & input.graphType != "Line" & input.graphType != "Heat" & input.graphType != "Hitmap"',
HTML('<svg id="theWidget-newlegend", width="100%"></svg>'))
)
))),
############################################################################
#### Panel 'Export data'
############################################################################
tabPanel(
"Export data",
fluidRow(
column(4,
h4("Download full map"),
p("The rds file containing the trained map can be opened in R with readRDS."),
downloadButton("somDownload", "Download SOM (rds file)", class = "btn-primary"),
h4("Download clustered data (csv)"),
downloadButton("clustDownload", "Download Clustering (csv file)", class = "btn-primary"),
h5("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")))),
############################################################################
#### Panel 'R script'
############################################################################
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", class = "btn-primary"))),
verbatimTextOutput("codeTxt")),
############################################################################
#### Panel 'About'
############################################################################
tabPanel(
"About",
fluidRow(column(
6,
HTML('<table><tr>
<td width= "50%" height= "139" align="center" valign="middle"><img src="logo.png" alt="<aweSOM>" width="120"/></td>
<td width="50%" height="139" align="left" valign="middle"><h3>interactive self-organizing maps</h3></td>
</tr></table>'),
wellPanel(HTML('<p><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 visual inspection of the SOM easier.</p>'),
HTML("<p> Use this interface to train and visualize SOMs, 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</p>"),
HTML("<p> While standard SOM works on numeric data only, aweSOM handles
<strong>categorical variables</strong> through dummy-encoding and
appropriate scaling, so that each variable has the same total variance (as in MCA).
As in <strong>specific</strong> MCA, chosen levels can be dropped from the training data.
The treatment of <strong>mixed data</strong> is equivalent to the one in FAMD (factorial analysis of mixed data).</p>")),
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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