Nothing
inst/shiny/quant/ui.R
In powdR: Full Pattern Summation of X-Ray Powder Diffraction Data
shiny::shinyUI(
shiny::navbarPage("powdR",
#################################
# TAB 1: REFERENCE LIBRARY BUILDER
#################################
shiny::tabPanel("Reference Library Builder",
shiny::fluidRow(
shiny::column(4, shiny::wellPanel(
shiny::h3("1. File upload"),
shiny::h4("XRPD data"),
shiny::helpText(shiny::withMathJax("Choose a .csv file containing the 2\\(\\theta\\) scale
and the count intensities of all reference patterns.")),
shiny::div(style="display: inline-block;vertical-align:top; width: 300px;",
shiny::fileInput(inputId = "uploadXRD",
label = NULL,
multiple = FALSE,
accept = ".csv")),
shiny::div(style="display: inline-block;vertical-align:center; width: 0px;",
shinyWidgets::dropdownButton(
shiny::downloadLink(outputId = "download_xrd_eg",
label = "Download an example .csv file"),
circle = FALSE, status = "danger", icon = shiny::icon("question"),
width = "300px", size = "sm"
)),
shiny::h4("Phase information"),
shiny::helpText("Upload a .csv file containing the id's, names and reference
intensity ratios of all reference patterns."),
shiny::div(style="display: inline-block;vertical-align:top; width: 300px;",
shiny::fileInput(inputId = "uploadPHASE",
label = NULL,
multiple = FALSE,
accept = ".csv")),
shiny::div(style="display: inline-block;vertical-align:center; width: 0px;",
shinyWidgets::dropdownButton(
shiny::downloadLink(outputId = "download_phases_eg",
label = "Download an example .csv file"),
circle = FALSE, status = "danger", icon = shiny::icon("question"),
width = "300px", size = "sm"
)),
shiny::tags$hr(),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 100px;",
h3("2. Build")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 100px;",
shiny::actionButton("BuildLibButton", "Click to build library")),
shiny::tags$hr(),
shiny::h3("3. Download library"),
shiny::helpText("Provide a name for the new powdRlib object.
This is what the library will be called if it is
subsequently loaded into R (can be kept as the default
'RefLib'):"),
shiny::textInput("name", label = NULL, "RefLib"),
shiny::downloadButton(outputId = "download_lib",
label = "Download library as .Rdata binary file")
)),
shiny::column(8, shiny::wellPanel(
shiny::h3("Phases in your reference library"),
shiny::tags$hr(),
DT::dataTableOutput("minerals_table")
))
) # end fluidRow
),
#################################
## TAB 2: REFERENCE LIBRARY PLOTTER
#################################
shiny::tabPanel("Reference Library Viewer",
shiny::fluidRow(
shiny::column(4, shiny::wellPanel(
shiny::helpText("Choose a .Rdata reference library to load. Must be
a powdRlib object created using either the powdRlib function,
or via the Reference Library Builder in this application."),
shiny::fileInput(inputId = "loadLIB_plotter",
label = NULL,
multiple = FALSE,
accept = ".Rdata")
)),
shiny::column(4, shiny::wellPanel(
shiny::helpText("Select a wavelength to use when calculating d-spacings."),
shiny::selectInput(inputId = "selectWAVELENGTH",
label = NULL,
multiple = FALSE,
choices = list("Cu (1.54056 Angstroms)" = "Cu",
"Co (1.78897 Angstroms)" = "Co"))
)),
shiny::column(4, shiny::wellPanel(
shiny::helpText("Choose phases from the library to plot."),
shiny::selectInput(inputId = "selectPHASES_plotter",
label = NULL,
choices = c("Please upload a reference library"),
selected = "Please upload a reference library",
multiple = TRUE,
selectize = TRUE)
))
), # end fluidRow
shiny::fluidRow(
shiny::column(12, shiny::wellPanel(
plotly::plotlyOutput("lib_plot", width = "auto", height = 600),
shiny::tags$hr(),
DT::dataTableOutput("lib_table")
))
)
),
#################################
## TAB 3: REFERENCE LIBRARY EDITOR
#################################
shiny::tabPanel("Reference Library Editor",
shiny::fluidRow(
shiny::column(4, shiny::wellPanel(
shiny::h3("1. Load a library"),
shiny::helpText("Choose a .Rdata reference library to load. Must be
a powdRlib object created using either the powdRlib function,
or via the Reference Library Builder in this application."),
shiny::div(style="display: inline-block;vertical-align:top; width: 300px;",
shiny::fileInput(inputId = "loadLIB_editor",
label = NULL,
multiple = FALSE,
accept = ".Rdata")),
shiny::tags$hr(),
shiny::h3("2. Select the subset mode"),
shiny::selectInput(inputId = "selectMODE_editor",
label = NULL,
choices = c("keep", "remove"),
multiple = FALSE),
shiny::tags$hr(),
shiny::h3("3. Select reference patterns to subset"),
shiny::selectInput(inputId = "selectPHASES_editor",
label = NULL,
choices = c("Please upload a reference library"),
selected = "Please upload a reference library",
multiple = TRUE,
selectize = TRUE),
shiny::tags$hr(),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 120px;",
h3("4. Subset")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 100px;",
actionButton("SubsetLibButton", "Click to subset library")),
shiny::tags$hr(),
shiny::h3("5. Download library"),
shiny::helpText("Provide a name for the new powdRlib object.
This is what the library will be called if it is
subsequently loaded into R (can be kept as the default
'RefLib'):"),
shiny::textInput("name_editor", label = NULL, "RefLib"),
shiny::downloadButton(outputId = "download_subset_lib",
label = "Download library as .Rdata binary file")
)),
shiny::column(8, shiny::wellPanel(
shiny::h3("Phases in your subset reference library"),
shiny::tags$hr(),
DT::dataTableOutput("minerals_subset_table")
))
) #End fluid row
), #End tabpanel
######################################
# TAB 4: Full pattern summation
#####################################
shiny::tabPanel("Full Pattern Summation",
shiny::fluidRow(
shiny::column(3, shiny::wellPanel(
shiny::h3("1. Load samples for quantification"),
shiny::helpText("Must be .xy format (space separated)"),
shiny::div(style="display: inline-block;vertical-align:top; width: 225px;",
shiny::fileInput(inputId = "loadXY",
label = NULL,
multiple = FALSE,
accept = c(".xy", ".XY"))),
shiny::div(style="display: inline-block;vertical-align:center; width: 0px;",
shinyWidgets::dropdownButton(
shiny::downloadLink(outputId = "download_sandstone",
label = "sandstone_soil.xy "),
shiny::downloadLink(outputId = "download_limestone",
label = "limestone_soil.xy "),
shiny::downloadLink(outputId = "download_granite",
label = "granite_soil.xy "),
circle = FALSE, status = "danger", icon = shiny::icon("question"),
width = "300px", size = "sm")),
shiny::h3("2. Load a reference library"),
shiny::helpText("Must be a .Rdata powdRlib object"),
shiny::div(style="display: inline-block;vertical-align:top; width: 225px;",
shiny::fileInput(inputId = "loadLIB",
label = NULL,
multiple = FALSE,
accept = ".Rdata")),
shiny::div(style="display: inline-block;vertical-align:center; width: 0px;",
shinyWidgets::dropdownButton(
shiny::downloadLink(outputId = "download_rockjock",
label = "rockjock_powdRlib.Rdata"),
shiny::downloadLink(outputId = "download_mineral_library",
label = "example_powdRlib.Rdata"),
circle = FALSE, status = "danger", icon = shiny::icon("question"),
width = "300px", size = "sm")),
shiny::h3("3. Select mode"),
shiny::selectInput(inputId = "selectMode_fps",
label = NULL,
choices = c("Manual", "Automated"),
selected = "Manual"),
shiny::h3("4. Select a solver"),
shiny::helpText("Select the optimisation routine"),
shiny::selectInput(inputId = "selectSolver_fps",
label = NULL,
choices = c("BFGS", "Nelder-Mead", "CG", "NNLS"),
selected = "BFGS"),
shiny::helpText("Select the objective function to minimise"),
shiny::selectInput(inputId = "selectOBJ_fps",
label = NULL,
choices = c("Rwp", "R", "Delta"),
selected = "Rwp"),
shiny::tags$hr(),
shiny::h3("5. Select phases"),
shiny::helpText("Select the phases to use in the fitting."),
shiny::selectInput(inputId = "selectPHASES_fps",
choices = c("Upload a powdRlib object in section 2"),
label = NULL,
multiple = TRUE,
selectize = TRUE,
selected = "Upload a powdRlib object in section 2"),
shiny::helpText("Choose an internal standard that may be used for peak
alignment or estimation of limits of detection."),
shiny::selectInput(inputId = "selectINT_fps",
label = NULL,
choices = c("")),
shiny::checkboxInput("std_conc_check_fps",
label = "Is the internal standard concentration known?",
value = FALSE),
shiny::uiOutput("std_conc_help_ui"),
shiny::uiOutput("std_conc_box_fps_ui"),
shiny::uiOutput("amorph_help_ui"),
shiny::uiOutput("selectAMORPH_ui"),
shiny::uiOutput("force_help_ui"),
shiny::uiOutput("selectFORCE_ui"),
shiny::tags$hr(),
shiny::h3("6. Adjust fit parameters"),
shiny::helpText("Adjust the alignment parameter"),
shiny::checkboxInput("align_man_fps", label = "Manual alignment?",
value = FALSE),
shiny::sliderInput("align_fps", label = NULL, min = 0,
max = 0.5, value = c(0.1)),
shiny::helpText("Adjust the shifting parameter"),
shiny::sliderInput("shift_fps", label = NULL, min = 0,
max = 0.5, value = c(0)),
shiny::helpText(withMathJax("Adjust the 2\\(\\theta\\) range
for full pattern summation")),
shiny::sliderInput("tth_fps_slide", label = NULL,
min = 2, max = 75,
value = c(2, 75), step = 0.1),
uiOutput("slide_help_ui"),
shiny::sliderInput("lod_slide", label = NULL,
min = 0, max = 3,
value = 0, step = 0.01),
shiny::helpText("Select a wavelength to use when calculating d-spacings."),
shiny::selectInput(inputId = "selectWAVELENGTHfps",
label = NULL,
multiple = FALSE,
choices = list("Cu (1.54056 Angstroms)" = "Cu",
"Co (1.78897 Angstroms)" = "Co"))
)),
shiny::column(9, shiny::wellPanel(
shiny::div(style="display: inline-block;vertical-align:bottom; width: 300px;",
h3("7. Full pattern summation")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 300px;",
shiny::actionButton("goButton_fps", "Click to start computation")),
shiny::tags$hr(),
shiny::h5("Once computation has finished, the results will be tabulated and
plotted below. Results can then be exported using download buttons at the
bottom of this page."),
shiny::tags$hr(),
DT::dataTableOutput("contents_fps"),
shiny::tags$hr(),
plotly::plotlyOutput("line_fps", width = "auto", height = 550),
shiny::tags$hr(),
shiny::h3("8. Download computed fit"),
shiny::downloadButton(outputId = "download_meas",
label = "Download measured pattern (.xy)"),
shiny::downloadButton(outputId = "download_calc",
label = "Download fitted pattern (.xy)"),
shiny::downloadButton(outputId = "download_concs",
label = "Download concentrations (.csv)"),
shiny::downloadButton(outputId = "download_fps",
label = "Download powdRfps object (.Rdata)")
))
) # end fluidRow
),
#################################
## TAB 5: RESULTS VIEWER EDITOR
#################################
shiny::tabPanel("Results Viewer/Editor",
shiny::fluidRow(
shiny::column(3, shiny::wellPanel(
shiny::h3("1. Load results to edit"),
shiny::helpText("Must be .Rdata powdRfps or powdRafps object"),
shiny::div(style="display: inline-block;vertical-align:top; width: 225px;",
shiny::fileInput(inputId = "loadResults_editor",
label = NULL,
multiple = FALSE,
accept = c(".Rdata"))),
shiny::h3("2. Load the reference library"),
shiny::helpText("Must be a .Rdata powdRlib object of the library used to
produce the original results"),
shiny::div(style="display: inline-block;vertical-align:top; width: 225px;",
shiny::fileInput(inputId = "loadLIB_fps_editor",
label = NULL,
multiple = FALSE,
accept = ".Rdata")),
shiny::h3("3. Select a solver"),
shiny::helpText("Choose the optimisation routine"),
shiny::selectInput(inputId = "selectSolver_editor",
label = NULL,
choices = c("BFGS", "Nelder-Mead", "CG", "NNLS"),
selected = "BFGS"),
shiny::helpText("Choose the objective function to minimise"),
shiny::selectInput(inputId = "selectOBJ_editor",
label = NULL,
choices = c("Rwp", "R", "Delta")),
shiny::tags$hr(),
shiny::h3("4. Select phases"),
shiny::helpText("Select phases to remove from the original analysis"),
shiny:: selectInput(inputId = "selectREMOVE_editor",
label = NULL,
multiple = TRUE,
selectize = TRUE,
choices = c("")),
shiny::helpText("Select phases from the library to add to the analysis"),
shiny::selectInput(inputId = "selectADD_editor",
label = NULL,
multiple = TRUE,
selectize = TRUE,
choices = c("")),
shiny::helpText("Select an internal standard"),
shiny::selectInput(inputId = "selectSTD_editor",
label = NULL,
multiple = FALSE,
selectize = TRUE,
choices = c("")),
shiny::checkboxInput("std_conc_check_editor",
label = "Is the internal standard concentration known?",
value = FALSE),
shiny::uiOutput("std_conc_box_editor_ui"),
shiny::tags$hr(),
shiny::h3("5. Adjust fit parameters"),
shiny::helpText("Adjust the alignment parameter"),
shiny::checkboxInput("align_man_editor", label = "Manual alignment?",
value = FALSE),
shiny::uiOutput("align_editor_ui"),
shiny::helpText("Adjust the shifting parameter"),
shiny::sliderInput("shift_editor", label = NULL, min = 0,
max = 0.5,
value = c(0)),
shiny::helpText(shiny::withMathJax("Adjust the 2\\(\\theta\\) range for
full pattern summation")),
shiny::sliderInput("tth_editor", label = NULL,
min = 2, max = 75,
value = c(2, 75), step = 0.1),
shiny::helpText("Select a wavelength to use when calculating d-spacings."),
shiny::selectInput(inputId = "selectWAVELENGTHeditor",
label = NULL,
multiple = FALSE,
choices = list("Cu (1.54056 Angstroms)" = "Cu",
"Co (1.78897 Angstroms)" = "Co"))
)),
shiny::column(9, shiny::wellPanel(
shiny::h3("6. Full pattern summation"),
shiny::selectInput(inputId = "selectPLOTeditor",
label = "Select whether the original results or new
results are plotted",
multiple = FALSE,
choices = list("Original results", "New results")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 225px;",
shiny::actionButton("goButton_editor", "Click to Recompute results")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 325px;",
shiny::helpText("Note: Computation may take several minutes.")),
shiny::tags$hr(),
DT::dataTableOutput("contents_editor"),
plotly::plotlyOutput("line_editor", width = "auto", height = 550),
shiny::tags$hr(),
shiny::h3("7. Download computed fit"),
shiny::downloadButton(outputId = "download_meas_editor",
label = "Download edited measured pattern (.xy)"),
shiny::downloadButton(outputId = "download_calc_editor",
label = "Download edited fitted pattern (.xy)"),
shiny::downloadButton(outputId = "download_mins_editor",
label = "Download edited phase concentrations (.csv)"),
shiny::downloadButton(outputId = "download_editor",
label = "Download edited powdRfps object (.Rdata)")
))
) # end fluidRow
),
#################################
## TAB 6: HELP
#################################
shiny::tabPanel("Help",
shiny::fluidRow(
shiny::column(12, align = "center",
shiny::h1("Video tutorial"),
shiny::uiOutput("video")
)
) # end fluidRow
)
) # end navbarPage
)# end shinyUI
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shiny::shinyUI(
shiny::navbarPage("powdR",
#################################
# TAB 1: REFERENCE LIBRARY BUILDER
#################################
shiny::tabPanel("Reference Library Builder",
shiny::fluidRow(
shiny::column(4, shiny::wellPanel(
shiny::h3("1. File upload"),
shiny::h4("XRPD data"),
shiny::helpText(shiny::withMathJax("Choose a .csv file containing the 2\\(\\theta\\) scale
and the count intensities of all reference patterns.")),
shiny::div(style="display: inline-block;vertical-align:top; width: 300px;",
shiny::fileInput(inputId = "uploadXRD",
label = NULL,
multiple = FALSE,
accept = ".csv")),
shiny::div(style="display: inline-block;vertical-align:center; width: 0px;",
shinyWidgets::dropdownButton(
shiny::downloadLink(outputId = "download_xrd_eg",
label = "Download an example .csv file"),
circle = FALSE, status = "danger", icon = shiny::icon("question"),
width = "300px", size = "sm"
)),
shiny::h4("Phase information"),
shiny::helpText("Upload a .csv file containing the id's, names and reference
intensity ratios of all reference patterns."),
shiny::div(style="display: inline-block;vertical-align:top; width: 300px;",
shiny::fileInput(inputId = "uploadPHASE",
label = NULL,
multiple = FALSE,
accept = ".csv")),
shiny::div(style="display: inline-block;vertical-align:center; width: 0px;",
shinyWidgets::dropdownButton(
shiny::downloadLink(outputId = "download_phases_eg",
label = "Download an example .csv file"),
circle = FALSE, status = "danger", icon = shiny::icon("question"),
width = "300px", size = "sm"
)),
shiny::tags$hr(),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 100px;",
h3("2. Build")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 100px;",
shiny::actionButton("BuildLibButton", "Click to build library")),
shiny::tags$hr(),
shiny::h3("3. Download library"),
shiny::helpText("Provide a name for the new powdRlib object.
This is what the library will be called if it is
subsequently loaded into R (can be kept as the default
'RefLib'):"),
shiny::textInput("name", label = NULL, "RefLib"),
shiny::downloadButton(outputId = "download_lib",
label = "Download library as .Rdata binary file")
)),
shiny::column(8, shiny::wellPanel(
shiny::h3("Phases in your reference library"),
shiny::tags$hr(),
DT::dataTableOutput("minerals_table")
))
) # end fluidRow
),
#################################
## TAB 2: REFERENCE LIBRARY PLOTTER
#################################
shiny::tabPanel("Reference Library Viewer",
shiny::fluidRow(
shiny::column(4, shiny::wellPanel(
shiny::helpText("Choose a .Rdata reference library to load. Must be
a powdRlib object created using either the powdRlib function,
or via the Reference Library Builder in this application."),
shiny::fileInput(inputId = "loadLIB_plotter",
label = NULL,
multiple = FALSE,
accept = ".Rdata")
)),
shiny::column(4, shiny::wellPanel(
shiny::helpText("Select a wavelength to use when calculating d-spacings."),
shiny::selectInput(inputId = "selectWAVELENGTH",
label = NULL,
multiple = FALSE,
choices = list("Cu (1.54056 Angstroms)" = "Cu",
"Co (1.78897 Angstroms)" = "Co"))
)),
shiny::column(4, shiny::wellPanel(
shiny::helpText("Choose phases from the library to plot."),
shiny::selectInput(inputId = "selectPHASES_plotter",
label = NULL,
choices = c("Please upload a reference library"),
selected = "Please upload a reference library",
multiple = TRUE,
selectize = TRUE)
))
), # end fluidRow
shiny::fluidRow(
shiny::column(12, shiny::wellPanel(
plotly::plotlyOutput("lib_plot", width = "auto", height = 600),
shiny::tags$hr(),
DT::dataTableOutput("lib_table")
))
)
),
#################################
## TAB 3: REFERENCE LIBRARY EDITOR
#################################
shiny::tabPanel("Reference Library Editor",
shiny::fluidRow(
shiny::column(4, shiny::wellPanel(
shiny::h3("1. Load a library"),
shiny::helpText("Choose a .Rdata reference library to load. Must be
a powdRlib object created using either the powdRlib function,
or via the Reference Library Builder in this application."),
shiny::div(style="display: inline-block;vertical-align:top; width: 300px;",
shiny::fileInput(inputId = "loadLIB_editor",
label = NULL,
multiple = FALSE,
accept = ".Rdata")),
shiny::tags$hr(),
shiny::h3("2. Select the subset mode"),
shiny::selectInput(inputId = "selectMODE_editor",
label = NULL,
choices = c("keep", "remove"),
multiple = FALSE),
shiny::tags$hr(),
shiny::h3("3. Select reference patterns to subset"),
shiny::selectInput(inputId = "selectPHASES_editor",
label = NULL,
choices = c("Please upload a reference library"),
selected = "Please upload a reference library",
multiple = TRUE,
selectize = TRUE),
shiny::tags$hr(),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 120px;",
h3("4. Subset")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 100px;",
actionButton("SubsetLibButton", "Click to subset library")),
shiny::tags$hr(),
shiny::h3("5. Download library"),
shiny::helpText("Provide a name for the new powdRlib object.
This is what the library will be called if it is
subsequently loaded into R (can be kept as the default
'RefLib'):"),
shiny::textInput("name_editor", label = NULL, "RefLib"),
shiny::downloadButton(outputId = "download_subset_lib",
label = "Download library as .Rdata binary file")
)),
shiny::column(8, shiny::wellPanel(
shiny::h3("Phases in your subset reference library"),
shiny::tags$hr(),
DT::dataTableOutput("minerals_subset_table")
))
) #End fluid row
), #End tabpanel
######################################
# TAB 4: Full pattern summation
#####################################
shiny::tabPanel("Full Pattern Summation",
shiny::fluidRow(
shiny::column(3, shiny::wellPanel(
shiny::h3("1. Load samples for quantification"),
shiny::helpText("Must be .xy format (space separated)"),
shiny::div(style="display: inline-block;vertical-align:top; width: 225px;",
shiny::fileInput(inputId = "loadXY",
label = NULL,
multiple = FALSE,
accept = c(".xy", ".XY"))),
shiny::div(style="display: inline-block;vertical-align:center; width: 0px;",
shinyWidgets::dropdownButton(
shiny::downloadLink(outputId = "download_sandstone",
label = "sandstone_soil.xy "),
shiny::downloadLink(outputId = "download_limestone",
label = "limestone_soil.xy "),
shiny::downloadLink(outputId = "download_granite",
label = "granite_soil.xy "),
circle = FALSE, status = "danger", icon = shiny::icon("question"),
width = "300px", size = "sm")),
shiny::h3("2. Load a reference library"),
shiny::helpText("Must be a .Rdata powdRlib object"),
shiny::div(style="display: inline-block;vertical-align:top; width: 225px;",
shiny::fileInput(inputId = "loadLIB",
label = NULL,
multiple = FALSE,
accept = ".Rdata")),
shiny::div(style="display: inline-block;vertical-align:center; width: 0px;",
shinyWidgets::dropdownButton(
shiny::downloadLink(outputId = "download_rockjock",
label = "rockjock_powdRlib.Rdata"),
shiny::downloadLink(outputId = "download_mineral_library",
label = "example_powdRlib.Rdata"),
circle = FALSE, status = "danger", icon = shiny::icon("question"),
width = "300px", size = "sm")),
shiny::h3("3. Select mode"),
shiny::selectInput(inputId = "selectMode_fps",
label = NULL,
choices = c("Manual", "Automated"),
selected = "Manual"),
shiny::h3("4. Select a solver"),
shiny::helpText("Select the optimisation routine"),
shiny::selectInput(inputId = "selectSolver_fps",
label = NULL,
choices = c("BFGS", "Nelder-Mead", "CG", "NNLS"),
selected = "BFGS"),
shiny::helpText("Select the objective function to minimise"),
shiny::selectInput(inputId = "selectOBJ_fps",
label = NULL,
choices = c("Rwp", "R", "Delta"),
selected = "Rwp"),
shiny::tags$hr(),
shiny::h3("5. Select phases"),
shiny::helpText("Select the phases to use in the fitting."),
shiny::selectInput(inputId = "selectPHASES_fps",
choices = c("Upload a powdRlib object in section 2"),
label = NULL,
multiple = TRUE,
selectize = TRUE,
selected = "Upload a powdRlib object in section 2"),
shiny::helpText("Choose an internal standard that may be used for peak
alignment or estimation of limits of detection."),
shiny::selectInput(inputId = "selectINT_fps",
label = NULL,
choices = c("")),
shiny::checkboxInput("std_conc_check_fps",
label = "Is the internal standard concentration known?",
value = FALSE),
shiny::uiOutput("std_conc_help_ui"),
shiny::uiOutput("std_conc_box_fps_ui"),
shiny::uiOutput("amorph_help_ui"),
shiny::uiOutput("selectAMORPH_ui"),
shiny::uiOutput("force_help_ui"),
shiny::uiOutput("selectFORCE_ui"),
shiny::tags$hr(),
shiny::h3("6. Adjust fit parameters"),
shiny::helpText("Adjust the alignment parameter"),
shiny::checkboxInput("align_man_fps", label = "Manual alignment?",
value = FALSE),
shiny::sliderInput("align_fps", label = NULL, min = 0,
max = 0.5, value = c(0.1)),
shiny::helpText("Adjust the shifting parameter"),
shiny::sliderInput("shift_fps", label = NULL, min = 0,
max = 0.5, value = c(0)),
shiny::helpText(withMathJax("Adjust the 2\\(\\theta\\) range
for full pattern summation")),
shiny::sliderInput("tth_fps_slide", label = NULL,
min = 2, max = 75,
value = c(2, 75), step = 0.1),
uiOutput("slide_help_ui"),
shiny::sliderInput("lod_slide", label = NULL,
min = 0, max = 3,
value = 0, step = 0.01),
shiny::helpText("Select a wavelength to use when calculating d-spacings."),
shiny::selectInput(inputId = "selectWAVELENGTHfps",
label = NULL,
multiple = FALSE,
choices = list("Cu (1.54056 Angstroms)" = "Cu",
"Co (1.78897 Angstroms)" = "Co"))
)),
shiny::column(9, shiny::wellPanel(
shiny::div(style="display: inline-block;vertical-align:bottom; width: 300px;",
h3("7. Full pattern summation")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 300px;",
shiny::actionButton("goButton_fps", "Click to start computation")),
shiny::tags$hr(),
shiny::h5("Once computation has finished, the results will be tabulated and
plotted below. Results can then be exported using download buttons at the
bottom of this page."),
shiny::tags$hr(),
DT::dataTableOutput("contents_fps"),
shiny::tags$hr(),
plotly::plotlyOutput("line_fps", width = "auto", height = 550),
shiny::tags$hr(),
shiny::h3("8. Download computed fit"),
shiny::downloadButton(outputId = "download_meas",
label = "Download measured pattern (.xy)"),
shiny::downloadButton(outputId = "download_calc",
label = "Download fitted pattern (.xy)"),
shiny::downloadButton(outputId = "download_concs",
label = "Download concentrations (.csv)"),
shiny::downloadButton(outputId = "download_fps",
label = "Download powdRfps object (.Rdata)")
))
) # end fluidRow
),
#################################
## TAB 5: RESULTS VIEWER EDITOR
#################################
shiny::tabPanel("Results Viewer/Editor",
shiny::fluidRow(
shiny::column(3, shiny::wellPanel(
shiny::h3("1. Load results to edit"),
shiny::helpText("Must be .Rdata powdRfps or powdRafps object"),
shiny::div(style="display: inline-block;vertical-align:top; width: 225px;",
shiny::fileInput(inputId = "loadResults_editor",
label = NULL,
multiple = FALSE,
accept = c(".Rdata"))),
shiny::h3("2. Load the reference library"),
shiny::helpText("Must be a .Rdata powdRlib object of the library used to
produce the original results"),
shiny::div(style="display: inline-block;vertical-align:top; width: 225px;",
shiny::fileInput(inputId = "loadLIB_fps_editor",
label = NULL,
multiple = FALSE,
accept = ".Rdata")),
shiny::h3("3. Select a solver"),
shiny::helpText("Choose the optimisation routine"),
shiny::selectInput(inputId = "selectSolver_editor",
label = NULL,
choices = c("BFGS", "Nelder-Mead", "CG", "NNLS"),
selected = "BFGS"),
shiny::helpText("Choose the objective function to minimise"),
shiny::selectInput(inputId = "selectOBJ_editor",
label = NULL,
choices = c("Rwp", "R", "Delta")),
shiny::tags$hr(),
shiny::h3("4. Select phases"),
shiny::helpText("Select phases to remove from the original analysis"),
shiny:: selectInput(inputId = "selectREMOVE_editor",
label = NULL,
multiple = TRUE,
selectize = TRUE,
choices = c("")),
shiny::helpText("Select phases from the library to add to the analysis"),
shiny::selectInput(inputId = "selectADD_editor",
label = NULL,
multiple = TRUE,
selectize = TRUE,
choices = c("")),
shiny::helpText("Select an internal standard"),
shiny::selectInput(inputId = "selectSTD_editor",
label = NULL,
multiple = FALSE,
selectize = TRUE,
choices = c("")),
shiny::checkboxInput("std_conc_check_editor",
label = "Is the internal standard concentration known?",
value = FALSE),
shiny::uiOutput("std_conc_box_editor_ui"),
shiny::tags$hr(),
shiny::h3("5. Adjust fit parameters"),
shiny::helpText("Adjust the alignment parameter"),
shiny::checkboxInput("align_man_editor", label = "Manual alignment?",
value = FALSE),
shiny::uiOutput("align_editor_ui"),
shiny::helpText("Adjust the shifting parameter"),
shiny::sliderInput("shift_editor", label = NULL, min = 0,
max = 0.5,
value = c(0)),
shiny::helpText(shiny::withMathJax("Adjust the 2\\(\\theta\\) range for
full pattern summation")),
shiny::sliderInput("tth_editor", label = NULL,
min = 2, max = 75,
value = c(2, 75), step = 0.1),
shiny::helpText("Select a wavelength to use when calculating d-spacings."),
shiny::selectInput(inputId = "selectWAVELENGTHeditor",
label = NULL,
multiple = FALSE,
choices = list("Cu (1.54056 Angstroms)" = "Cu",
"Co (1.78897 Angstroms)" = "Co"))
)),
shiny::column(9, shiny::wellPanel(
shiny::h3("6. Full pattern summation"),
shiny::selectInput(inputId = "selectPLOTeditor",
label = "Select whether the original results or new
results are plotted",
multiple = FALSE,
choices = list("Original results", "New results")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 225px;",
shiny::actionButton("goButton_editor", "Click to Recompute results")),
shiny::div(style="display: inline-block;vertical-align:bottom; width: 325px;",
shiny::helpText("Note: Computation may take several minutes.")),
shiny::tags$hr(),
DT::dataTableOutput("contents_editor"),
plotly::plotlyOutput("line_editor", width = "auto", height = 550),
shiny::tags$hr(),
shiny::h3("7. Download computed fit"),
shiny::downloadButton(outputId = "download_meas_editor",
label = "Download edited measured pattern (.xy)"),
shiny::downloadButton(outputId = "download_calc_editor",
label = "Download edited fitted pattern (.xy)"),
shiny::downloadButton(outputId = "download_mins_editor",
label = "Download edited phase concentrations (.csv)"),
shiny::downloadButton(outputId = "download_editor",
label = "Download edited powdRfps object (.Rdata)")
))
) # end fluidRow
),
#################################
## TAB 6: HELP
#################################
shiny::tabPanel("Help",
shiny::fluidRow(
shiny::column(12, align = "center",
shiny::h1("Video tutorial"),
shiny::uiOutput("video")
)
) # end fluidRow
)
) # end navbarPage
)# end shinyUI
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