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R/app_ui.R
In SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny
Defines functions
app_ui
app_ui <- function(){
shiny::addResourcePath("SEAHORS", system.file("R", package="SEAHORS"))
##### script R shiny
options(shiny.reactlog = TRUE)
css <- "
.radio-inline {
padding: 0 3px;
text-align: center;
margin-left: 0 !important;
line-height: 30px;
}
.radio-inline input {
top: 20px;
left: 50%;
margin-left: -6px !important;
line-height: 30px;
}"
ui <- shinyUI(
navbarPage(
windowTitle = "SEAHORS",
fluidPage(
useShinyjs(),
theme = shinytheme(theme = "journal"),
sidebarLayout(
sidebarPanel(span(img(src = "www/logo1.png", height = 110)),
tags$header(
tags$a(href = "https://github.com/AurelienRoyer/SEAHORS/",
"Spatial Exploration of ArcHaeological Objects in R Shiny")),
tags$hr(),
tags$style(HTML(css)),
column(12,
column(2,
shinyWidgets::actionBttn(
inputId = "save_load",
label = "save",
style = "stretch",
color = "danger",
size= "xs",
icon = icon("fas fa-save",lib = "font-awesome")
),
),
column(2,),
column(2,
shinyWidgets::actionBttn(
inputId = "save_load2",
label = "load",
style = "stretch",
color = "danger",
size= "xs",
icon = icon("fas fa-upload",lib = "font-awesome")
),)
),
radioButtons(
"bt2", h4("QUICK SIDEBAR"),
choices = c("Data" = 1,
"Point size" = 2,
"Point color" = 3,
"Point shape" = 4,
"Fig. options"=5),
selected = "1", inline=TRUE), style = "font-size:90%",
tags$hr(),
conditionalPanel(condition="input.bt2==1",
h4(style = "color: red;","Subsetting dataset"),
tags$br(),
uiOutput("Date"),
uiOutput("xlimits"),
uiOutput("ylimits"),
uiOutput("zlimits"),
uiOutput("liste.sector"),
uiOutput("liste.UAS"),
fluidRow(conditionalPanel("output.fileUploaded",
column(5,
actionButton("all_UAS_entry", label = "ALL"),),
column(2,
actionButton("reset_UAS_entry", label = "reset"),)
)),#end fluidrow
uiOutput("liste.Nature"),
fluidRow(conditionalPanel("output.fileUploaded",
column(5,
actionButton("all_artifact_entry", label = "ALL"),),
column(2,
actionButton("reset_artifact_entry", label = "reset"),))
), #end fluidrow
uiOutput("liste.passe"),
width=4,
), # end of conditionalPanel
conditionalPanel(condition="input.bt2==2",
h4(style = "color: red;","Modifying point size according to a variable"),
tags$br(),
fluidRow(column (6,numericInput("minsize", "Minimal point size", 0.25, min = 0.1, max=10, width="50%")),
column (6,numericInput("point.size", "Default point size", 2, min = 1, max=20, width="50%"), ), ),
tags$br(),
h5(style = "color: blue;","Only available with unique ID: "),
uiOutput("sectionXx2"),
uiOutput("sectionXy2"),
uiOutput("sectionXz2"),
uiOutput("var.gris.2D"),
uiOutput("var.gris.2D.1"),
), # end of conditionalPanel
conditionalPanel(condition="input.bt2==3",
h4(style = "color: red;","Modifying point color according to a variable"),
tags$h5(style = "color: blue;","you can import color ramp from panel 'additional settings'"),
tags$br(),
#fluidRow(column (7,checkboxInput("optioninfosfigplotly", "Show figure legend", TRUE))),
tags$br(),
uiOutput("liste.Colors"),
tags$hr(),
column(7,div(style = "height:2px"),
h4("Select colors"),
uiOutput("colors2")),
tags$br(),
tags$br(),
), # end of conditionalPanel
conditionalPanel(condition="input.bt2==4",
h4(style = "color: red;","Modifying point shape"),
tags$br(),
column(9,
column(6,selectInput("shape", "main shape",
choices= list("circle"='circle',
"square"= 'square',
"triangle"='triangle',
"diamond"='diamond',
"star"='star')),
),
column(6, style = "margin-top: 25px;", actionButton("do.shape1", "Set main shape ")),
),
column(10,
column(7, uiOutput("shape2"),),
column(6, style = "margin-top: 3px;",uiOutput("shape2.var1"),),
column(6, style = "margin-top: 3px;",uiOutput("shape2.var2"),),
br(),
column(6, actionButton("do.shape2", "Set secondary shape")),
tagAppendAttributes(textOutput("text.shape"), style="white-space:pre-wrap;"),
)
),# end of conditionalPanel
conditionalPanel(condition="input.bt2==5",
h4(style = "color: red;","Figure options"),
tags$br(),
fluidRow(column (7,checkboxInput("optioninfosfigplotly", "Show figure legend", TRUE))),
tags$br(),
column(10,column(5,numericInput("height.size.b", label = h5("Figure height"), value = 800),),
column(5,numericInput("width.size.b", label = h5("Figure width"), value = 1000),),
tags$hr(),),
tags$br(),
column(10,
column(4,numericInput("fontsizeaxis", "Axis font size",12, min = 1, max=40),),
column(4,numericInput("fontsizetick", "tick font size",12, min = 1, max=40),),),
column(10,
column(4,textInput("Name.X", label="Legends name of X",value = "X"),),
column(4,textInput("Name.Y", label="Legends name of Y",value = "Y"),),
column(4,textInput("Name.Z", label="Legends name of Z",value = "Z"),),),
column(10,
column(4,numericInput("Xtickmarks", "Position of X tick marks",1, min = 0, max=40),),
column(4,numericInput("Ytickmarks", "Position of Y tick marks",1, min = 0, max=40),),
column(4,numericInput("Ztickmarks", "Position of Z tick marks",1, min = 0, max=40),),),
column(10,
column(4,numericInput("Xminor.breaks", "Position of X minor breaks",1, min = 0, max=40),),
column(4,numericInput("Yminor.breaks", "Position of Y minor breaks",1, min = 0, max=40),),
column(4,numericInput("Zminor.breaks", "Position of Z minor breaks",1, min = 0, max=40),),),
column(10,
checkboxInput("checkbox.auto.limits", label = "Automatic limits", value = TRUE),
uiOutput("X.limx2"),
uiOutput("Y.limx2"),
),
column(12,br(),
hr(),),
uiOutput("themeforfigure"),
)# end of conditionalPanel
), #end sidebarpanel
mainPanel(
tabsetPanel(type = "tabs",id="mainpanel",
tabPanel("Overview",
tags$div(
h2(" Welcome to the", em("SEAHORS"), "application",align="center", style = "font-family: 'Times', serif;
font-weight: 500; font-size: 500; text-shadow: 3px 3px 3px #aaa; line-height: 1;
color: #404040;"),
tags$br(),
column(12,
column(3,),
column(6,span(img(src = "www/logo2.png", height = 200)),),
tags$br(),
tags$br(),
),
column(12, br(),
column(1,),
column(9,
br(),
HTML(
paste0(" <div style=width:100%;, align=left>
<font size=3>
<span style='text-transform:none'>
<i>SEAHORS</i> (v. ", packageVersion("SEAHORS"), ") is an application dedicated to the intra-site spatial analysis of archaeological piece-plotted objects.</p>
<p>It makes it possible to explore the spatial organisation of coordinate points taken on archaeological fields and to visualise their distributions using interactive 3D and 2D plots.</p>
<p> Its functionalities are presented in: </p>
<p>
<ul>
<li>a <a href=https://nakala.fr/10.34847/nkl.3fdd6h8j target=_blank>video </a> tutorial</li>
<li>and papers:
<p> -Royer, A., E. Discamps, S. Plutniak, M. Thomas. (2023). 'SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny'. <a href=https://archaeo.peercommunityin.org/articles/rec?id=320 target=_blank> <i>PCI Archaeology</i> </a>, DOI: <a href=https://doi.org/10.5281/zenodo.7674698 target=_blank>10.5281/zenodo.7674698</a>.</li> </p>
<p> -Royer, A., E. Discamps, S. Plutniak, M. Thomas. (2023). 'SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny'. <a href=https://peercommunityjournal.org/articles/10.24072/pcjournal.289/ target=_blank> <i>Peer Community Journal</i> </a>, DOI: <a href=10.24072/pcjournal.289 target=_blank>10.24072/pcjournal.289</a>.</li> </p>
</ul>
</p>
<p>This is an open and free software,
<ul>
<li>it is available as an R package on the <a href=https://cran.r-project.org/package=SEAHORS target=_blank>CRAN</a>, and</li>
<li> its source code is published on a <a href=https://github.com/AurelienRoyer/SEAHORS/ target=_blank>github repository</a>.</li>
</ul>
</p>
<br>
<p>Try <i>SEAHORS</i> now with the <a href=https://hal.science/hal-02190243 target=_blank>Cassenade</a> Paleolithic site dataset:</p>
</span>
</font>" ))
),
actionButton("button_example",
"Click to load the Cassenade dataset", style="height:50%"),
br(), br(),
HTML("<p style = 'color:blue;'> <i>ENJOY IT !</i></color> </p> </div>"),
), #end of column
) # end div()
# column(12, column(2, HTML(
# " <div style=height:50%;, align=left>
# <font size=2>
# <p>Try <i>SEAHORS</i> with the <a href=https://hal.science/hal-02190243 target=_blank>Cassenade</a> Paleolithic site dataset:</p>
# </font size>
# </div>"),#end html
# actionButton("button_example","Click to load the Cassenade dataset",style="height:50%")),
# tags$br(),
# tags$br(),),
), #end of tabPanel
tabPanel("Load data",
tabsetPanel(type = "tabs",
tabPanel(tags$h5("Import xyz data"),
tags$br(),
tags$br(),
tags$hr(),
tags$h4(style = "color: red;","Loading file"),
#fluidRow(
# column(10,
# tags$h4(style = "color: red;","Options for loading file"),
# checkboxInput("header", "Header", TRUE),
# checkboxInput("set.dec", "Check this option to automatically correct for the presence of comma in decimal numbers", TRUE),
# numericInput("digit.number", "To control the number of significant digit", 11, min = 1, step=1, max=30, width="50%"),
#
# tags$hr(),
# ),#endcolumn
#),#end of fluidrow
fluidRow(column(9,
fileInput("file1", "Choose File (.csv/.xls/.xlsx)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values",
".csv",
".xlsx",".xls")),
selectInput(inputId = "worksheet", label="Worksheet Name", choices =''),
actionButton(inputId = "getData",label="Get Data"),
actionButton('reset.BDD', 'Reset Input')
),
column(3,
shinyWidgets::actionBttn(
inputId = "chr_setting",
label = "Options for loading file",
style = "unite",
color = "danger",
icon = icon("fas fa-cogs",lib = "font-awesome")
),
tags$style("#bsmodal_param .modal-dialog{ width:1200px}
.modal-backdrop {
display: none;
z-index: 1040 !important;
}
.modal-content {
margin: 2px auto;
z-index: 1100 !important;
}
"),
bsModal(
id = "bsmodal_param",
title = tags$h4(style = "color: red;","Options for loading file"),
trigger = "chr_setting",size = "large",
checkboxInput("header", "Header", TRUE),
checkboxInput("set.dec", "Check this option to automatically correct for the presence of comma in decimal numbers", TRUE),
numericInput("digit.number", "To control the number of significant digit", 11, min = 1, step=1, max=30)
),)
),
fluidRow(
tags$br(),
htmlOutput("nb6"),
column (7,
tags$hr(),
tags$h4(style = "color: red;","Basic data"),
tags$br(),
fluidRow(column(6,uiOutput("set.x"),),
column(2,checkboxInput("checkbox.invX", label = "Inversion of x", value = F),),),
fluidRow(column(6,uiOutput("set.y"),),
column(2,checkboxInput("checkbox.invY", label = "Inversion of y", value = F),),),
fluidRow(column(6,uiOutput("set.z"),),
column(2,checkboxInput("checkbox.invZ", label = "Inversion of z", value = F),),),
uiOutput("set.ID"),
tags$hr(),
tags$br(),
tags$br(),
tags$h4(style = "color: red;","Variable for quick sidebar selection"),
tags$br(),
uiOutput("set.date"),
uiOutput("set.sector"),
uiOutput("set.levels"),
uiOutput("set.nature"),
uiOutput("set.passe"),
), #endcolumn
),#end of fluidrow
tags$hr(),
tableOutput("contents")
), #end of tabPanel
tabPanel(tags$h5("Merge additional data"),
tags$br(),
tags$h5(style = "color: blue;","This allows you to merge additional data with the XYZ data, using a Unique object ID (recorded in a column in both datasets). First, load the additional data below:"),
tags$br(),
fileInput("file.extradata", "Choose File (.csv/.xls/.xlsx)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values",
".csv",
".xlsx",".xls")),
tags$h5(style = "color: blue;","Choose the column with the same Unique object ID, then press Merge "),
uiOutput("set.columnID"),
tags$br(),
actionButton("goButton.set.columnID", "Merge"),
tags$br(),
tags$br(),
tags$hr(),
tags$h5(style = "color: red;","Report on the merging"),
tags$h5(style = "color: blue;","IDs that are NOT unique in the XYZ dataset"),
verbatimTextOutput("notunique"),
tags$h5(style = "color: blue;","IDs that are NOT unique in the additional dataset"),
verbatimTextOutput("notunique2"),
tags$h5(style = "color: blue;","Objects present in the XYZ dataset that have no correspondence in the additional dataset"),
verbatimTextOutput("suppl.no.include"),
tags$h5(style = "color: blue;","Objects present in the additional dataset that have no correspondence in the XYZ dataset"),
verbatimTextOutput("ID.no.suppl.data"),
tags$br(),
),#end tabpanel
tabPanel(tags$h5("Import orthophoto "),
tags$br(),
tags$h5(style = "color: red;","Orthophoto file must be in .tiff format"),
tags$br(),
fluidRow(
fileInput("file2", "For x/y section",
multiple = F,
accept = c(".tif",".tiff")),
uiOutput("liste.ortho.file2"),
fileInput("file5", "For y/x section",
multiple = F,
accept = c(".tif",".tiff")),
uiOutput("liste.ortho.file5"),
fileInput("file3", "For x/z section",
multiple = F,
accept = c(".tif",".tiff")),
uiOutput("liste.ortho.file3"),
fileInput("file4", "For y/z section",
multiple = F,
accept = c(".tif",".tiff")),
uiOutput("liste.ortho.file4"),
)#end fluidrow
),#end tabpanel
tabPanel(tags$h5("Import refit data"),
tags$br(),
tags$br(),
tags$h5(style = "color: red;", "This allows you to import refit data, either directly from the XYZ dataset, or from another file using a Unique object ID (recorded in a column in both datasets). Recommended format for the refit data: a dataframe with two columns, one with the unique object ID and one with a unique number for each refit group"),
fileInput("file.fit", "Choose File (.csv/.xls/.xlsx)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values",
".csv",
".xlsx",".xls")),
tags$h5(style = "color: blue;","Choose the column with the Unique object ID, then press Import refit data"),
column(12,
column(8, uiOutput("set.columnID.for.fit"),),
tags$br(),
column(8, uiOutput("set.REM"),),
column(12,checkboxInput("Refit.data.from.XYZ.file", label = "Check this box if the refit data is included in the XYZ dataset", value = F),),
tags$br(),
), # end of column
actionButton("goButton.set.columnID.for.fit", "Import refit data"),
tags$br(),
tags$br(),
tags$h5(style = "color: blue;","Table of refits"),
verbatimTextOutput("Fit.table.output"),
downloadButton("downloadData_redata", "Download")
),#end tabpanel
tabPanel(tags$h5("Concatenate two columns"),
tags$br(),
column(12,textInput("Merge.groupe", "Choose the name of the new column",value = "new.concatenate.col"),),
tags$br(),
column(8, uiOutput("set.col1"),),
tags$br(),
column(8,radioButtons("separatormerge", "separator between the two names",
choices = c("." = ".",
"_" = "_",
"-" = "-",
"," =",",
"nospace"= ""),
selected = "_", inline=TRUE),),
tags$br(),
tags$br(),
column(8, uiOutput("set.col2"),),
tags$br(),
column(8,actionButton("Merge2", "Concatenate the two columns"),),
),
),#end tabSETPanel
),#end tabpanel
tabPanel("Table",
tabsetPanel(type = "tabs",
tabPanel(tags$h5("Raw table"),
fluidRow(
column(10,
br(),
downloadButton("downloadData_rawdata", "Download raw table"),
br(),br(),
DTOutput("table")
# column(10,)
))
),#end tabpanel
tabPanel(tags$h5("Pivot table"),
fluidRow(
uiOutput("liste.summary"),
column(5,
h4("Remains class "),
tableOutput("summary")),
column(11, downloadButton("downloadData_pivotdata", "Download")),
) #end fluidrow
), #end tabpanel
tabPanel(tags$h5("archeoViz exports"),
fluidRow(
column(10,
br(),
HTML("Like <i>SEAHORS</i>, <a href=https://analytics.huma-num.fr/archeoviz/en target=_blank><i>archeoViz </i> </a> is a web application to visualise spatial archaeological data. In addition, <i>archeoViz </i> allows to edit and communicate spatial datasets as <a href=https://analytics.huma-num.fr/archeoviz/home/ target=_blank>static web applications</a>.</p>
<p> Interoperability between archaeological software matters. So, here, you can:
</p>"),
br(),
downloadLink("download.archeoviz", "* Export your data in archeoViz format (CSV)"),
br(),
br(),
uiOutput("run.archeoviz")
))
),#end tabpanel
), #end tabset panel
), #end tabPanel
tabPanel("3D plot",
fluidRow(
tags$br(),
htmlOutput("nb"),
tags$br(),
tags$br(),
column(12,
uiOutput("plot3Dbox"),),
tags$br(),
tags$hr(),
tags$br(),
tags$hr(),),
fluidRow(
hr(style = "border-top: 1px solid #000000;"),
column(12,
column (8,fluidRow( column (4,numericInput("ratiox", "X ratio", 1, min = 1, max=10, width="50%")),
column (4,numericInput("ratioy", "Y ratio", 1, min = 1, max=10, width="50%")),
column (4,numericInput("ratioz", "Z ratio", 1, min = 1, max=10, width="50%")),),
),
),),
tags$br(),
tags$br(),
tags$br(),
column(8, downloadButton("downloadData3D", "Download as .HTML")),
tags$hr(),
tags$br(),
uiOutput("var.fit.3D"),
), #end tabPanel
tabPanel("2D plot",
tabsetPanel(type = "tabs",
tabPanel(tags$h5("Simple 2D plot"),
fluidRow(tags$br(),
htmlOutput("nb2.2"),
tags$br(),
tags$br(),
tags$br(),
column(12,
radioButtons("var1.simple", "section",
choices = c(xy = "xy",
yx = "yx",
yz = "yz",
xz = "xz"),
selected = "xy", inline=TRUE),
tags$br(),),
column(12,
uiOutput("plot2Dbox.simple"),),
tags$br(),),
fluidRow(
tags$br(),
tags$br(),
hr(style = "border-top: 1px solid #000000;"),
column(12,
column(2,numericInput("ratio.to.coord.simple", label = h5("Ratio figure"), value = 1),),
column(2),
),
),
column(12,
column(2,radioButtons("var.ortho.simple", "include ortho",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE), ),
column(2, radioButtons("var.fit.table.simple", "Include refits",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE),),
column(2),
column(6,downloadButton("downloadData2D.simple", "Download as .pdf")),
hr(style = "border-top: 0.5px solid #000000;"), ),
tags$br(),
),#end tabpanel
tabPanel(tags$h5("Advanced 2D plot"),
fluidRow(tags$br(),
htmlOutput("nb2"),
tags$br(),
column(1, actionButton("run_button", "Display/refresh", icon = icon("play")),),
tags$br(),
tags$br(),
tags$br(),
column(12,
radioButtons("var1", "section",
choices = c(xy = "xy",
yx = "yx",
yz = "yz",
xz = "xz"),
selected = "xy", inline=TRUE),
tags$br(),),
column(12,
uiOutput("plot2Dbox"),),
tags$br(),),
fluidRow(
tags$br(),
tags$br(),
hr(style = "border-top: 1px solid #000000;"),
column(7,
shinyWidgets::actionBttn(
inputId = "chr_settingbp",
label = "Bar plot display",
style = "unite",
color = "danger",
icon = icon("fas fa-chart-column",lib = "font-awesome")
),
),
radioButtons("var.ortho", "include ortho",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE),
tags$br(),
radioButtons("var.fit.table", "Include refits",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE),
column(2),
column(6,downloadButton("downloadData2D", "Download as .HTML")), ),
hr(style = "border-top: 0.5px solid #000000;"),
fluidRow(column(8,
tags$br(),
tags$h4(style = "color: red;","How to record a new variable in SEAHORS:"),
tags$h5(style = "color: blue;","Step1: go to the RECORD NEW GROUP subpanel in the ADDITIONAL SETTINGS panel"),
tags$h5(style = "color: blue;","Step2: choose a name for your new group variable and create it"),
tags$h5(style = "color: blue;","Step3: go back to 2D PLOT panel, and use the box or lasso tool to select points"),
tags$h5(style = "color: blue;","Step4: click on the button below to record group information for the selected points"),
),
column(12,actionButton('Change2','Change Group Assignment'),),
tags$br(),
column(8,
tags$br(),
tags$br(),
),
),#end fluidrow
fluidRow(
column(9,
verbatimTextOutput("brushed"))
) #end fluidrow
), #end sub-tabpanel
), #end tabset panel
), #end tabPanel
tabPanel("2D slice",
tags$br(),
htmlOutput("nb3"),
column(12,
column(6,radioButtons("var.2d.slice", "section",
choices = c(#xy = "xy",
#yx = "yx",
yz = "yz",
xz = "xz"),
selected = "yz", inline=TRUE),
tags$br(),),
column(2),
column(3,checkboxInput("advanced.slice",label="Advanced plot", value=FALSE)),
),
column(12, numericInput("step2dslice", HTML("Thickness of slices <br> (lower this parameter to get more slices)"), 4, min = 0.1, max=10,step = 1, width="50%")),
column(12, uiOutput("range.2d.slice")),
fluidRow(
tags$br(),
tags$br(),
tags$br(),
tags$br(),
column(12,
uiOutput("plot.2dslide")),
tags$br(),
),# end of fluidrow
hr(style = "border-top: 1px solid #000000;"),
fluidRow(column(12,
column(2, uiOutput("ratiotocoorsimple2"),),
# column(12, downloadButton("downloadData2d.slice", "Download as .HTML")),
tags$br(),
column(12, uiOutput("download.slice.output")),
),),#end of fluidrow
),#end tabPanel 2D slice
tabPanel("Rotated 2D plot",
tags$br(),
htmlOutput("nb4"),
tags$br(),
fluidRow(column(8,sliderInput('pi2','Angle of rotation:',1,min=-180,max=180,step=1, value=0),),
column(12,
uiOutput("plot2Drota"),
radioButtons("var.section2D", "section",
choices = c(xz = "xz",
yz = "yz"),
selected = "xz", inline=TRUE),
uiOutput("plot2Drota2"),),
tags$br(),
tags$br(),),
hr(style = "border-top: 1px solid #000000;"),
fluidRow(
tags$br(),
column(12,actionButton("transferxyz", "Replace XYZ data with the newly computed rotated XYZ coordinates"),),
),#end of fluidrow
tags$br(),
tags$br(),
fluidRow(
column(12, downloadButton("downloadData_rotateddata", "Download rotated coordinates in .csv")),
tags$br(),
tags$br(),
tags$br(),
column(12,
column(7,uiOutput("sectionXx3"),),
column(7,uiOutput("sectionXy3"),),
),#end of column
), #end of fluidrow
), #end tabPanel
tabPanel("Density plot",
fluidRow(tags$br(),
htmlOutput("nb5"),
tags$br(),
column(12,
uiOutput("plotdens"),),
tags$br(),
),#end of fluidrow
tags$br(),
hr(style = "border-top: 1px solid #000000;"),
fluidRow(column(12,
column(4,radioButtons("var3", "section",
choices = c(xy = "xy",
yx = "yx",
yz = "yz",
xz = "xz"), inline=TRUE),),
column(5, downloadButton("downloadDatadensity", "Download as .pdf")),
column(2,numericInput("ratio.to.coord", label = h5("Ratio figure"), value = 1),),
),
tags$hr(),
column(12,
column(6,radioButtons("var.ortho2", "Include ortho",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE),),
tags$hr(),
),
column(12,
column(4, radioButtons("var.plotlyg.lines", "include density lines",
choices = c(no = "no",
yes = "yes"),selected = "no"),),
column(4,radioButtons("var.density.curves", "include density curves",
choices = c(no = "no",
yes = "yes"),selected = "no"),),),
column(4, sliderInput("alpha.density", "Point transparency", min = 0, max=1, value=1, width="50%"),),
tags$br(),
tags$br(),
tags$hr(),
column(12,
tags$h5(style = "color: blue;","Density calculated by mass::ke2D package, using Kernel density"),),
) #end fluidrow
), #end tabPanel
tabPanel("Additional settings",
tabsetPanel(type = "tabs",
tabPanel(tags$h5("Color ramps"),
br(),
column(6,
column(6, downloadButton("save.col", "Save color ramp")),
br(),
br(),
br(),
br(),
column(6, fileInput("file.color", "Choose File to import color ramp (.csv)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")), ),
)#end of column
),
tabPanel(tags$h5("Refit customization"),
br(),
br(),
uiOutput("liste.Colors.refit"),
column(4, div(style = "height:2px"),
h4("Select a color for refit groups"),
uiOutput("colorsrefits")),
column(6, downloadButton("save.col.fit", "Save color ramp")),
br(),
br(),
br(),
br(),
column(6, fileInput("file.color.fit", "Choose File to import color ramp (.csv)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")), ),
column (6,numericInput("w2", "thickness of lines",2, min = 1, max=10, width="50%")),
br(),
column (12,tags$hr(),),
uiOutput("liste.var.refit"),
br(),
uiOutput("liste.varrefit"),
), #end of tabPanel
tabPanel(tags$h5("Slider parameters"),
br(),
tags$hr(),
fluidRow(column (7,numericInput("stepXsize", "Steps used for the X slider in the quick sidebar", 0.1, min = 0.1, step=0.1, max=100, width="50%")),
column (7,numericInput("stepYsize", "Steps used for the Y slider in the quick sidebar", 0.1, min = 0.1, step=0.1, max=100, width="50%")),
column (7,numericInput("stepZsize", "Steps used for the Z slider in the quick sidebar", 0.1, min = 0.1, step=0.1, max=100, width="50%")),
),
tags$hr(),
),
tabPanel(tags$h5("Information shown while hovering points"),
br(),
uiOutput("liste.infos"),
br(),
actionButton("listeinfos.go", "Update"),
),
tabPanel(tags$h5("Record new group"),
br(),
br(),
column (12,tags$h3("Record new group"),
br(),
textInput("text.new.group", label="Name of the new group variable",value = "new.group"),
uiOutput("liste.newgroup"),
actionButton("go.ng", "Create"),
br(),
br(),),
column (12,
hr(style = "border-top: 1px solid #000000;"),
br(),
tags$h3("Rename new group modality"),
uiOutput("liste.newgroup2"),
uiOutput("liste.newgroup4"),
textInput("text.new.group2", label=h5("New name of the modality"),value = "new.modality"),
actionButton("go.ng2", "Modify"),),
), #end tabpanel
tabPanel(tags$h5("Export settings"),
br(),
radioButtons("docpdfhtml", "Export format",
choices = c(html = "html"),
selected = "html", inline=TRUE),
br(),
fluidRow(
column(6, downloadButton("export.Rmarkdown", "Export settings as Rmarkdown document")),
),
br(),
hr(),
# br(),
# tags$h4("To save the settings as .csv"),
# fluidRow(
# column(7, downloadButton("export.settings", "Export settings as csv document")),
# br(),
# hr(),
# br(),),
# br(),
# tags$h4("To load settings"),
fluidRow(
# column(7, fileInput("file.color.set", "Choose File to import settings (.csv)",
# multiple = TRUE,
# accept = c("text/csv",
# "text/comma-separated-values,text/plain",
# ".csv")),
# actionButton("go.load.settings", "load it"))
)
), #end tabpanel
),#end tabsetpanel temp
), # end of tabpanel
) #end tabset panel
) #end main panel
,fluid=FALSE) #sidebarLayout
)#endfluidPage
) #end navbarPage
) #end shinyUI
}
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SEAHORS documentation built on June 8, 2025, 11:36 a.m.
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Defines functions app_ui
app_ui <- function(){
shiny::addResourcePath("SEAHORS", system.file("R", package="SEAHORS"))
##### script R shiny
options(shiny.reactlog = TRUE)
css <- "
.radio-inline {
padding: 0 3px;
text-align: center;
margin-left: 0 !important;
line-height: 30px;
}
.radio-inline input {
top: 20px;
left: 50%;
margin-left: -6px !important;
line-height: 30px;
}"
ui <- shinyUI(
navbarPage(
windowTitle = "SEAHORS",
fluidPage(
useShinyjs(),
theme = shinytheme(theme = "journal"),
sidebarLayout(
sidebarPanel(span(img(src = "www/logo1.png", height = 110)),
tags$header(
tags$a(href = "https://github.com/AurelienRoyer/SEAHORS/",
"Spatial Exploration of ArcHaeological Objects in R Shiny")),
tags$hr(),
tags$style(HTML(css)),
column(12,
column(2,
shinyWidgets::actionBttn(
inputId = "save_load",
label = "save",
style = "stretch",
color = "danger",
size= "xs",
icon = icon("fas fa-save",lib = "font-awesome")
),
),
column(2,),
column(2,
shinyWidgets::actionBttn(
inputId = "save_load2",
label = "load",
style = "stretch",
color = "danger",
size= "xs",
icon = icon("fas fa-upload",lib = "font-awesome")
),)
),
radioButtons(
"bt2", h4("QUICK SIDEBAR"),
choices = c("Data" = 1,
"Point size" = 2,
"Point color" = 3,
"Point shape" = 4,
"Fig. options"=5),
selected = "1", inline=TRUE), style = "font-size:90%",
tags$hr(),
conditionalPanel(condition="input.bt2==1",
h4(style = "color: red;","Subsetting dataset"),
tags$br(),
uiOutput("Date"),
uiOutput("xlimits"),
uiOutput("ylimits"),
uiOutput("zlimits"),
uiOutput("liste.sector"),
uiOutput("liste.UAS"),
fluidRow(conditionalPanel("output.fileUploaded",
column(5,
actionButton("all_UAS_entry", label = "ALL"),),
column(2,
actionButton("reset_UAS_entry", label = "reset"),)
)),#end fluidrow
uiOutput("liste.Nature"),
fluidRow(conditionalPanel("output.fileUploaded",
column(5,
actionButton("all_artifact_entry", label = "ALL"),),
column(2,
actionButton("reset_artifact_entry", label = "reset"),))
), #end fluidrow
uiOutput("liste.passe"),
width=4,
), # end of conditionalPanel
conditionalPanel(condition="input.bt2==2",
h4(style = "color: red;","Modifying point size according to a variable"),
tags$br(),
fluidRow(column (6,numericInput("minsize", "Minimal point size", 0.25, min = 0.1, max=10, width="50%")),
column (6,numericInput("point.size", "Default point size", 2, min = 1, max=20, width="50%"), ), ),
tags$br(),
h5(style = "color: blue;","Only available with unique ID: "),
uiOutput("sectionXx2"),
uiOutput("sectionXy2"),
uiOutput("sectionXz2"),
uiOutput("var.gris.2D"),
uiOutput("var.gris.2D.1"),
), # end of conditionalPanel
conditionalPanel(condition="input.bt2==3",
h4(style = "color: red;","Modifying point color according to a variable"),
tags$h5(style = "color: blue;","you can import color ramp from panel 'additional settings'"),
tags$br(),
#fluidRow(column (7,checkboxInput("optioninfosfigplotly", "Show figure legend", TRUE))),
tags$br(),
uiOutput("liste.Colors"),
tags$hr(),
column(7,div(style = "height:2px"),
h4("Select colors"),
uiOutput("colors2")),
tags$br(),
tags$br(),
), # end of conditionalPanel
conditionalPanel(condition="input.bt2==4",
h4(style = "color: red;","Modifying point shape"),
tags$br(),
column(9,
column(6,selectInput("shape", "main shape",
choices= list("circle"='circle',
"square"= 'square',
"triangle"='triangle',
"diamond"='diamond',
"star"='star')),
),
column(6, style = "margin-top: 25px;", actionButton("do.shape1", "Set main shape ")),
),
column(10,
column(7, uiOutput("shape2"),),
column(6, style = "margin-top: 3px;",uiOutput("shape2.var1"),),
column(6, style = "margin-top: 3px;",uiOutput("shape2.var2"),),
br(),
column(6, actionButton("do.shape2", "Set secondary shape")),
tagAppendAttributes(textOutput("text.shape"), style="white-space:pre-wrap;"),
)
),# end of conditionalPanel
conditionalPanel(condition="input.bt2==5",
h4(style = "color: red;","Figure options"),
tags$br(),
fluidRow(column (7,checkboxInput("optioninfosfigplotly", "Show figure legend", TRUE))),
tags$br(),
column(10,column(5,numericInput("height.size.b", label = h5("Figure height"), value = 800),),
column(5,numericInput("width.size.b", label = h5("Figure width"), value = 1000),),
tags$hr(),),
tags$br(),
column(10,
column(4,numericInput("fontsizeaxis", "Axis font size",12, min = 1, max=40),),
column(4,numericInput("fontsizetick", "tick font size",12, min = 1, max=40),),),
column(10,
column(4,textInput("Name.X", label="Legends name of X",value = "X"),),
column(4,textInput("Name.Y", label="Legends name of Y",value = "Y"),),
column(4,textInput("Name.Z", label="Legends name of Z",value = "Z"),),),
column(10,
column(4,numericInput("Xtickmarks", "Position of X tick marks",1, min = 0, max=40),),
column(4,numericInput("Ytickmarks", "Position of Y tick marks",1, min = 0, max=40),),
column(4,numericInput("Ztickmarks", "Position of Z tick marks",1, min = 0, max=40),),),
column(10,
column(4,numericInput("Xminor.breaks", "Position of X minor breaks",1, min = 0, max=40),),
column(4,numericInput("Yminor.breaks", "Position of Y minor breaks",1, min = 0, max=40),),
column(4,numericInput("Zminor.breaks", "Position of Z minor breaks",1, min = 0, max=40),),),
column(10,
checkboxInput("checkbox.auto.limits", label = "Automatic limits", value = TRUE),
uiOutput("X.limx2"),
uiOutput("Y.limx2"),
),
column(12,br(),
hr(),),
uiOutput("themeforfigure"),
)# end of conditionalPanel
), #end sidebarpanel
mainPanel(
tabsetPanel(type = "tabs",id="mainpanel",
tabPanel("Overview",
tags$div(
h2(" Welcome to the", em("SEAHORS"), "application",align="center", style = "font-family: 'Times', serif;
font-weight: 500; font-size: 500; text-shadow: 3px 3px 3px #aaa; line-height: 1;
color: #404040;"),
tags$br(),
column(12,
column(3,),
column(6,span(img(src = "www/logo2.png", height = 200)),),
tags$br(),
tags$br(),
),
column(12, br(),
column(1,),
column(9,
br(),
HTML(
paste0(" <div style=width:100%;, align=left>
<font size=3>
<span style='text-transform:none'>
<i>SEAHORS</i> (v. ", packageVersion("SEAHORS"), ") is an application dedicated to the intra-site spatial analysis of archaeological piece-plotted objects.</p>
<p>It makes it possible to explore the spatial organisation of coordinate points taken on archaeological fields and to visualise their distributions using interactive 3D and 2D plots.</p>
<p> Its functionalities are presented in: </p>
<p>
<ul>
<li>a <a href=https://nakala.fr/10.34847/nkl.3fdd6h8j target=_blank>video </a> tutorial</li>
<li>and papers:
<p> -Royer, A., E. Discamps, S. Plutniak, M. Thomas. (2023). 'SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny'. <a href=https://archaeo.peercommunityin.org/articles/rec?id=320 target=_blank> <i>PCI Archaeology</i> </a>, DOI: <a href=https://doi.org/10.5281/zenodo.7674698 target=_blank>10.5281/zenodo.7674698</a>.</li> </p>
<p> -Royer, A., E. Discamps, S. Plutniak, M. Thomas. (2023). 'SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny'. <a href=https://peercommunityjournal.org/articles/10.24072/pcjournal.289/ target=_blank> <i>Peer Community Journal</i> </a>, DOI: <a href=10.24072/pcjournal.289 target=_blank>10.24072/pcjournal.289</a>.</li> </p>
</ul>
</p>
<p>This is an open and free software,
<ul>
<li>it is available as an R package on the <a href=https://cran.r-project.org/package=SEAHORS target=_blank>CRAN</a>, and</li>
<li> its source code is published on a <a href=https://github.com/AurelienRoyer/SEAHORS/ target=_blank>github repository</a>.</li>
</ul>
</p>
<br>
<p>Try <i>SEAHORS</i> now with the <a href=https://hal.science/hal-02190243 target=_blank>Cassenade</a> Paleolithic site dataset:</p>
</span>
</font>" ))
),
actionButton("button_example",
"Click to load the Cassenade dataset", style="height:50%"),
br(), br(),
HTML("<p style = 'color:blue;'> <i>ENJOY IT !</i></color> </p> </div>"),
), #end of column
) # end div()
# column(12, column(2, HTML(
# " <div style=height:50%;, align=left>
# <font size=2>
# <p>Try <i>SEAHORS</i> with the <a href=https://hal.science/hal-02190243 target=_blank>Cassenade</a> Paleolithic site dataset:</p>
# </font size>
# </div>"),#end html
# actionButton("button_example","Click to load the Cassenade dataset",style="height:50%")),
# tags$br(),
# tags$br(),),
), #end of tabPanel
tabPanel("Load data",
tabsetPanel(type = "tabs",
tabPanel(tags$h5("Import xyz data"),
tags$br(),
tags$br(),
tags$hr(),
tags$h4(style = "color: red;","Loading file"),
#fluidRow(
# column(10,
# tags$h4(style = "color: red;","Options for loading file"),
# checkboxInput("header", "Header", TRUE),
# checkboxInput("set.dec", "Check this option to automatically correct for the presence of comma in decimal numbers", TRUE),
# numericInput("digit.number", "To control the number of significant digit", 11, min = 1, step=1, max=30, width="50%"),
#
# tags$hr(),
# ),#endcolumn
#),#end of fluidrow
fluidRow(column(9,
fileInput("file1", "Choose File (.csv/.xls/.xlsx)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values",
".csv",
".xlsx",".xls")),
selectInput(inputId = "worksheet", label="Worksheet Name", choices =''),
actionButton(inputId = "getData",label="Get Data"),
actionButton('reset.BDD', 'Reset Input')
),
column(3,
shinyWidgets::actionBttn(
inputId = "chr_setting",
label = "Options for loading file",
style = "unite",
color = "danger",
icon = icon("fas fa-cogs",lib = "font-awesome")
),
tags$style("#bsmodal_param .modal-dialog{ width:1200px}
.modal-backdrop {
display: none;
z-index: 1040 !important;
}
.modal-content {
margin: 2px auto;
z-index: 1100 !important;
}
"),
bsModal(
id = "bsmodal_param",
title = tags$h4(style = "color: red;","Options for loading file"),
trigger = "chr_setting",size = "large",
checkboxInput("header", "Header", TRUE),
checkboxInput("set.dec", "Check this option to automatically correct for the presence of comma in decimal numbers", TRUE),
numericInput("digit.number", "To control the number of significant digit", 11, min = 1, step=1, max=30)
),)
),
fluidRow(
tags$br(),
htmlOutput("nb6"),
column (7,
tags$hr(),
tags$h4(style = "color: red;","Basic data"),
tags$br(),
fluidRow(column(6,uiOutput("set.x"),),
column(2,checkboxInput("checkbox.invX", label = "Inversion of x", value = F),),),
fluidRow(column(6,uiOutput("set.y"),),
column(2,checkboxInput("checkbox.invY", label = "Inversion of y", value = F),),),
fluidRow(column(6,uiOutput("set.z"),),
column(2,checkboxInput("checkbox.invZ", label = "Inversion of z", value = F),),),
uiOutput("set.ID"),
tags$hr(),
tags$br(),
tags$br(),
tags$h4(style = "color: red;","Variable for quick sidebar selection"),
tags$br(),
uiOutput("set.date"),
uiOutput("set.sector"),
uiOutput("set.levels"),
uiOutput("set.nature"),
uiOutput("set.passe"),
), #endcolumn
),#end of fluidrow
tags$hr(),
tableOutput("contents")
), #end of tabPanel
tabPanel(tags$h5("Merge additional data"),
tags$br(),
tags$h5(style = "color: blue;","This allows you to merge additional data with the XYZ data, using a Unique object ID (recorded in a column in both datasets). First, load the additional data below:"),
tags$br(),
fileInput("file.extradata", "Choose File (.csv/.xls/.xlsx)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values",
".csv",
".xlsx",".xls")),
tags$h5(style = "color: blue;","Choose the column with the same Unique object ID, then press Merge "),
uiOutput("set.columnID"),
tags$br(),
actionButton("goButton.set.columnID", "Merge"),
tags$br(),
tags$br(),
tags$hr(),
tags$h5(style = "color: red;","Report on the merging"),
tags$h5(style = "color: blue;","IDs that are NOT unique in the XYZ dataset"),
verbatimTextOutput("notunique"),
tags$h5(style = "color: blue;","IDs that are NOT unique in the additional dataset"),
verbatimTextOutput("notunique2"),
tags$h5(style = "color: blue;","Objects present in the XYZ dataset that have no correspondence in the additional dataset"),
verbatimTextOutput("suppl.no.include"),
tags$h5(style = "color: blue;","Objects present in the additional dataset that have no correspondence in the XYZ dataset"),
verbatimTextOutput("ID.no.suppl.data"),
tags$br(),
),#end tabpanel
tabPanel(tags$h5("Import orthophoto "),
tags$br(),
tags$h5(style = "color: red;","Orthophoto file must be in .tiff format"),
tags$br(),
fluidRow(
fileInput("file2", "For x/y section",
multiple = F,
accept = c(".tif",".tiff")),
uiOutput("liste.ortho.file2"),
fileInput("file5", "For y/x section",
multiple = F,
accept = c(".tif",".tiff")),
uiOutput("liste.ortho.file5"),
fileInput("file3", "For x/z section",
multiple = F,
accept = c(".tif",".tiff")),
uiOutput("liste.ortho.file3"),
fileInput("file4", "For y/z section",
multiple = F,
accept = c(".tif",".tiff")),
uiOutput("liste.ortho.file4"),
)#end fluidrow
),#end tabpanel
tabPanel(tags$h5("Import refit data"),
tags$br(),
tags$br(),
tags$h5(style = "color: red;", "This allows you to import refit data, either directly from the XYZ dataset, or from another file using a Unique object ID (recorded in a column in both datasets). Recommended format for the refit data: a dataframe with two columns, one with the unique object ID and one with a unique number for each refit group"),
fileInput("file.fit", "Choose File (.csv/.xls/.xlsx)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values",
".csv",
".xlsx",".xls")),
tags$h5(style = "color: blue;","Choose the column with the Unique object ID, then press Import refit data"),
column(12,
column(8, uiOutput("set.columnID.for.fit"),),
tags$br(),
column(8, uiOutput("set.REM"),),
column(12,checkboxInput("Refit.data.from.XYZ.file", label = "Check this box if the refit data is included in the XYZ dataset", value = F),),
tags$br(),
), # end of column
actionButton("goButton.set.columnID.for.fit", "Import refit data"),
tags$br(),
tags$br(),
tags$h5(style = "color: blue;","Table of refits"),
verbatimTextOutput("Fit.table.output"),
downloadButton("downloadData_redata", "Download")
),#end tabpanel
tabPanel(tags$h5("Concatenate two columns"),
tags$br(),
column(12,textInput("Merge.groupe", "Choose the name of the new column",value = "new.concatenate.col"),),
tags$br(),
column(8, uiOutput("set.col1"),),
tags$br(),
column(8,radioButtons("separatormerge", "separator between the two names",
choices = c("." = ".",
"_" = "_",
"-" = "-",
"," =",",
"nospace"= ""),
selected = "_", inline=TRUE),),
tags$br(),
tags$br(),
column(8, uiOutput("set.col2"),),
tags$br(),
column(8,actionButton("Merge2", "Concatenate the two columns"),),
),
),#end tabSETPanel
),#end tabpanel
tabPanel("Table",
tabsetPanel(type = "tabs",
tabPanel(tags$h5("Raw table"),
fluidRow(
column(10,
br(),
downloadButton("downloadData_rawdata", "Download raw table"),
br(),br(),
DTOutput("table")
# column(10,)
))
),#end tabpanel
tabPanel(tags$h5("Pivot table"),
fluidRow(
uiOutput("liste.summary"),
column(5,
h4("Remains class "),
tableOutput("summary")),
column(11, downloadButton("downloadData_pivotdata", "Download")),
) #end fluidrow
), #end tabpanel
tabPanel(tags$h5("archeoViz exports"),
fluidRow(
column(10,
br(),
HTML("Like <i>SEAHORS</i>, <a href=https://analytics.huma-num.fr/archeoviz/en target=_blank><i>archeoViz </i> </a> is a web application to visualise spatial archaeological data. In addition, <i>archeoViz </i> allows to edit and communicate spatial datasets as <a href=https://analytics.huma-num.fr/archeoviz/home/ target=_blank>static web applications</a>.</p>
<p> Interoperability between archaeological software matters. So, here, you can:
</p>"),
br(),
downloadLink("download.archeoviz", "* Export your data in archeoViz format (CSV)"),
br(),
br(),
uiOutput("run.archeoviz")
))
),#end tabpanel
), #end tabset panel
), #end tabPanel
tabPanel("3D plot",
fluidRow(
tags$br(),
htmlOutput("nb"),
tags$br(),
tags$br(),
column(12,
uiOutput("plot3Dbox"),),
tags$br(),
tags$hr(),
tags$br(),
tags$hr(),),
fluidRow(
hr(style = "border-top: 1px solid #000000;"),
column(12,
column (8,fluidRow( column (4,numericInput("ratiox", "X ratio", 1, min = 1, max=10, width="50%")),
column (4,numericInput("ratioy", "Y ratio", 1, min = 1, max=10, width="50%")),
column (4,numericInput("ratioz", "Z ratio", 1, min = 1, max=10, width="50%")),),
),
),),
tags$br(),
tags$br(),
tags$br(),
column(8, downloadButton("downloadData3D", "Download as .HTML")),
tags$hr(),
tags$br(),
uiOutput("var.fit.3D"),
), #end tabPanel
tabPanel("2D plot",
tabsetPanel(type = "tabs",
tabPanel(tags$h5("Simple 2D plot"),
fluidRow(tags$br(),
htmlOutput("nb2.2"),
tags$br(),
tags$br(),
tags$br(),
column(12,
radioButtons("var1.simple", "section",
choices = c(xy = "xy",
yx = "yx",
yz = "yz",
xz = "xz"),
selected = "xy", inline=TRUE),
tags$br(),),
column(12,
uiOutput("plot2Dbox.simple"),),
tags$br(),),
fluidRow(
tags$br(),
tags$br(),
hr(style = "border-top: 1px solid #000000;"),
column(12,
column(2,numericInput("ratio.to.coord.simple", label = h5("Ratio figure"), value = 1),),
column(2),
),
),
column(12,
column(2,radioButtons("var.ortho.simple", "include ortho",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE), ),
column(2, radioButtons("var.fit.table.simple", "Include refits",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE),),
column(2),
column(6,downloadButton("downloadData2D.simple", "Download as .pdf")),
hr(style = "border-top: 0.5px solid #000000;"), ),
tags$br(),
),#end tabpanel
tabPanel(tags$h5("Advanced 2D plot"),
fluidRow(tags$br(),
htmlOutput("nb2"),
tags$br(),
column(1, actionButton("run_button", "Display/refresh", icon = icon("play")),),
tags$br(),
tags$br(),
tags$br(),
column(12,
radioButtons("var1", "section",
choices = c(xy = "xy",
yx = "yx",
yz = "yz",
xz = "xz"),
selected = "xy", inline=TRUE),
tags$br(),),
column(12,
uiOutput("plot2Dbox"),),
tags$br(),),
fluidRow(
tags$br(),
tags$br(),
hr(style = "border-top: 1px solid #000000;"),
column(7,
shinyWidgets::actionBttn(
inputId = "chr_settingbp",
label = "Bar plot display",
style = "unite",
color = "danger",
icon = icon("fas fa-chart-column",lib = "font-awesome")
),
),
radioButtons("var.ortho", "include ortho",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE),
tags$br(),
radioButtons("var.fit.table", "Include refits",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE),
column(2),
column(6,downloadButton("downloadData2D", "Download as .HTML")), ),
hr(style = "border-top: 0.5px solid #000000;"),
fluidRow(column(8,
tags$br(),
tags$h4(style = "color: red;","How to record a new variable in SEAHORS:"),
tags$h5(style = "color: blue;","Step1: go to the RECORD NEW GROUP subpanel in the ADDITIONAL SETTINGS panel"),
tags$h5(style = "color: blue;","Step2: choose a name for your new group variable and create it"),
tags$h5(style = "color: blue;","Step3: go back to 2D PLOT panel, and use the box or lasso tool to select points"),
tags$h5(style = "color: blue;","Step4: click on the button below to record group information for the selected points"),
),
column(12,actionButton('Change2','Change Group Assignment'),),
tags$br(),
column(8,
tags$br(),
tags$br(),
),
),#end fluidrow
fluidRow(
column(9,
verbatimTextOutput("brushed"))
) #end fluidrow
), #end sub-tabpanel
), #end tabset panel
), #end tabPanel
tabPanel("2D slice",
tags$br(),
htmlOutput("nb3"),
column(12,
column(6,radioButtons("var.2d.slice", "section",
choices = c(#xy = "xy",
#yx = "yx",
yz = "yz",
xz = "xz"),
selected = "yz", inline=TRUE),
tags$br(),),
column(2),
column(3,checkboxInput("advanced.slice",label="Advanced plot", value=FALSE)),
),
column(12, numericInput("step2dslice", HTML("Thickness of slices <br> (lower this parameter to get more slices)"), 4, min = 0.1, max=10,step = 1, width="50%")),
column(12, uiOutput("range.2d.slice")),
fluidRow(
tags$br(),
tags$br(),
tags$br(),
tags$br(),
column(12,
uiOutput("plot.2dslide")),
tags$br(),
),# end of fluidrow
hr(style = "border-top: 1px solid #000000;"),
fluidRow(column(12,
column(2, uiOutput("ratiotocoorsimple2"),),
# column(12, downloadButton("downloadData2d.slice", "Download as .HTML")),
tags$br(),
column(12, uiOutput("download.slice.output")),
),),#end of fluidrow
),#end tabPanel 2D slice
tabPanel("Rotated 2D plot",
tags$br(),
htmlOutput("nb4"),
tags$br(),
fluidRow(column(8,sliderInput('pi2','Angle of rotation:',1,min=-180,max=180,step=1, value=0),),
column(12,
uiOutput("plot2Drota"),
radioButtons("var.section2D", "section",
choices = c(xz = "xz",
yz = "yz"),
selected = "xz", inline=TRUE),
uiOutput("plot2Drota2"),),
tags$br(),
tags$br(),),
hr(style = "border-top: 1px solid #000000;"),
fluidRow(
tags$br(),
column(12,actionButton("transferxyz", "Replace XYZ data with the newly computed rotated XYZ coordinates"),),
),#end of fluidrow
tags$br(),
tags$br(),
fluidRow(
column(12, downloadButton("downloadData_rotateddata", "Download rotated coordinates in .csv")),
tags$br(),
tags$br(),
tags$br(),
column(12,
column(7,uiOutput("sectionXx3"),),
column(7,uiOutput("sectionXy3"),),
),#end of column
), #end of fluidrow
), #end tabPanel
tabPanel("Density plot",
fluidRow(tags$br(),
htmlOutput("nb5"),
tags$br(),
column(12,
uiOutput("plotdens"),),
tags$br(),
),#end of fluidrow
tags$br(),
hr(style = "border-top: 1px solid #000000;"),
fluidRow(column(12,
column(4,radioButtons("var3", "section",
choices = c(xy = "xy",
yx = "yx",
yz = "yz",
xz = "xz"), inline=TRUE),),
column(5, downloadButton("downloadDatadensity", "Download as .pdf")),
column(2,numericInput("ratio.to.coord", label = h5("Ratio figure"), value = 1),),
),
tags$hr(),
column(12,
column(6,radioButtons("var.ortho2", "Include ortho",
choices = c(no = "no",
yes = "yes"),
selected = "no", inline=TRUE),),
tags$hr(),
),
column(12,
column(4, radioButtons("var.plotlyg.lines", "include density lines",
choices = c(no = "no",
yes = "yes"),selected = "no"),),
column(4,radioButtons("var.density.curves", "include density curves",
choices = c(no = "no",
yes = "yes"),selected = "no"),),),
column(4, sliderInput("alpha.density", "Point transparency", min = 0, max=1, value=1, width="50%"),),
tags$br(),
tags$br(),
tags$hr(),
column(12,
tags$h5(style = "color: blue;","Density calculated by mass::ke2D package, using Kernel density"),),
) #end fluidrow
), #end tabPanel
tabPanel("Additional settings",
tabsetPanel(type = "tabs",
tabPanel(tags$h5("Color ramps"),
br(),
column(6,
column(6, downloadButton("save.col", "Save color ramp")),
br(),
br(),
br(),
br(),
column(6, fileInput("file.color", "Choose File to import color ramp (.csv)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")), ),
)#end of column
),
tabPanel(tags$h5("Refit customization"),
br(),
br(),
uiOutput("liste.Colors.refit"),
column(4, div(style = "height:2px"),
h4("Select a color for refit groups"),
uiOutput("colorsrefits")),
column(6, downloadButton("save.col.fit", "Save color ramp")),
br(),
br(),
br(),
br(),
column(6, fileInput("file.color.fit", "Choose File to import color ramp (.csv)",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")), ),
column (6,numericInput("w2", "thickness of lines",2, min = 1, max=10, width="50%")),
br(),
column (12,tags$hr(),),
uiOutput("liste.var.refit"),
br(),
uiOutput("liste.varrefit"),
), #end of tabPanel
tabPanel(tags$h5("Slider parameters"),
br(),
tags$hr(),
fluidRow(column (7,numericInput("stepXsize", "Steps used for the X slider in the quick sidebar", 0.1, min = 0.1, step=0.1, max=100, width="50%")),
column (7,numericInput("stepYsize", "Steps used for the Y slider in the quick sidebar", 0.1, min = 0.1, step=0.1, max=100, width="50%")),
column (7,numericInput("stepZsize", "Steps used for the Z slider in the quick sidebar", 0.1, min = 0.1, step=0.1, max=100, width="50%")),
),
tags$hr(),
),
tabPanel(tags$h5("Information shown while hovering points"),
br(),
uiOutput("liste.infos"),
br(),
actionButton("listeinfos.go", "Update"),
),
tabPanel(tags$h5("Record new group"),
br(),
br(),
column (12,tags$h3("Record new group"),
br(),
textInput("text.new.group", label="Name of the new group variable",value = "new.group"),
uiOutput("liste.newgroup"),
actionButton("go.ng", "Create"),
br(),
br(),),
column (12,
hr(style = "border-top: 1px solid #000000;"),
br(),
tags$h3("Rename new group modality"),
uiOutput("liste.newgroup2"),
uiOutput("liste.newgroup4"),
textInput("text.new.group2", label=h5("New name of the modality"),value = "new.modality"),
actionButton("go.ng2", "Modify"),),
), #end tabpanel
tabPanel(tags$h5("Export settings"),
br(),
radioButtons("docpdfhtml", "Export format",
choices = c(html = "html"),
selected = "html", inline=TRUE),
br(),
fluidRow(
column(6, downloadButton("export.Rmarkdown", "Export settings as Rmarkdown document")),
),
br(),
hr(),
# br(),
# tags$h4("To save the settings as .csv"),
# fluidRow(
# column(7, downloadButton("export.settings", "Export settings as csv document")),
# br(),
# hr(),
# br(),),
# br(),
# tags$h4("To load settings"),
fluidRow(
# column(7, fileInput("file.color.set", "Choose File to import settings (.csv)",
# multiple = TRUE,
# accept = c("text/csv",
# "text/comma-separated-values,text/plain",
# ".csv")),
# actionButton("go.load.settings", "load it"))
)
), #end tabpanel
),#end tabsetpanel temp
), # end of tabpanel
) #end tabset panel
) #end main panel
,fluid=FALSE) #sidebarLayout
)#endfluidPage
) #end navbarPage
) #end shinyUI
}
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