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ui.R
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ui.R
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shinyUI(dashboardPage(
dashboardHeader(
title = "MetaboLink",
titleWidth = 400,
dropdownMenu(type = "notifications",
icon = icon("question-circle"),
badgeStatus = NULL,
headerText = "Help",
notificationItem("User manual", icon = icon("book"),
href = "https://github.com/anitamnd/MetaboLink/wiki"),
notificationItem("Source code and installation", icon = icon("file"),
href = "https://github.com/anitamnd/MetaboLink"),
notificationItem("Institution", icon = icon("university"),
href = "https://www.sdu.dk/en")
)
),
# Sidebar
dashboardSidebar(
width = "400",
useShinyjs(),
tags$style(HTML(".panel-primary {color: #000000;}")),
tags$style(HTML("#removeIS {
color: black;
text-decoration: underline;
}")),
tags$style(".skin-blue .sidebar .norm a { color: #444; }"),
tags$head(tags$script(src="CallShiny.js")),
extendShinyjs(script="CallShiny.js", functions=c("retrieve_results","send_message","run_button")),
fluidPage(
fluidRow(
selectizeInput("selectDataset", "Active dataset",
choices = NULL, width = "100%",
options = list(placeholder = "Please upload a file to start")
) %>%
bsTooltip("Switch between the different uploaded/saved datsets.", placement = "bottom", trigger = "hover")
),
bsCollapse(
id = "menu", multiple = FALSE, open = "Data input",
bsCollapsePanel("Data input",
style = "primary",
fluidRow(style = "padding: 0px;",
selectInput("fileType", "Select file format",
choices = c("Samples in columns", "Samples in rows"),
selected = "Samples in columns",
width = "100%"
)
),
fluidRow(style = "padding: 0px;",
fileInput("inputFile", "Upload file (.txt or .csv)",
accept = c("txt/csv", "text/comma-seperated-values, text/plain", ".csv"),
width = "100%"
)
),
fluidRow(
style = "margin-right: 0px;",
column(6, style = "padding-left:0px;",
bsButton("upload", "Upload", width = "100%")
),
column(6, style = "padding-left:0px;",
bsButton("example", "Load example", width = "100%") %>%
bsTooltip("Load example metabolomics datasets in positive and negative ion mode and respective metadata files. More examples available on GitHub.", placement = "bottom", trigger = "hover")
)
)
),
bsCollapsePanel("Blank filtration",
style = "primary",
fluidRow(
style = "padding: 0px;",
column(12,
sliderInput("signalStrength", "Signal strength above blank", 1, 10, 5, step = 0.1, width = "100%"),
style = "padding: 0px"
)
),
fluidRow(
style = "margin-right: 0px;",
column(12,
checkboxInput("discardBlank", "Discard blank", value = T, width = "100%"),
style = "padding: 0px; margin-top: -25px; margin-bottom: -15px; margin-left: 5px;"
),
column(12,
checkboxInput("keepIS", "Keep internal standards", value = T, width = "100%"),
style = "padding: 0px; margin-top: -15px; margin-bottom: -15px; margin-left: 5px;"
),
column(12,
checkboxInput("newFileBF", "Save as new file", value = T, width = "100%"),
style = "padding: 0px; margin-top: -15px; margin-bottom: -15px; margin-left: 5px;"
)
),
fluidRow(
style = "margin-right: 0px;",
column(6, bsButton("blankFiltrate", "Blank filtrate", width = "100%"),
style = "padding-left:0px; margin-top: 10px;"
),
column(6, bsButton("saveBF", "Save", width = "100%"),
style = "padding-left:0px; margin-top: 10px;"
)
)
) %>%
bsTooltip("Requires columns labeled 'Blank' and 'QC'.", placement = "bottom", trigger = "hover"),
bsCollapsePanel("Missing value filtration",
style = "primary",
fluidRow(
style = "padding: 0px;",
column(12,
sliderInput("cutoffNAs", "Minimum percentage of messured values", 0, 100, 80, step = 5, width = "100%"),
style = "padding: 0px"
)
),
fluidRow(
column(6,
prettyCheckboxGroup("filterNAmethod", "", choices = c("in QC", "in group", "entire data"))
)),
fluidRow(
column(6,
checkboxInput("mvf_newsave", "Save as new file", value = T, width = "100%")
)),
fluidRow(
style = "margin-right: 0px;",
column(6, bsButton("runFilterNA", "Run", width = "100%"), style = "padding-left:0px;"),
column(6, bsButton("saveFilterNA", "Save", width = "100%"), style = "padding-left:0px;")
)
),
bsCollapsePanel("Imputation",
style = "primary",
fluidRow(selectInput("imputationMethod", "Imputation method", choices = c("KNN", "Min/X", "Median"), width = "100%")),
fluidRow(hidden(div(id = "imp_remaining_hide", selectInput("remainingNAs", "Remaining missing values", choices = c("zero", "Min/X", "Median"), width = "100%")))),
fluidRow(hidden(div(id = "imp_minx_hide", sliderInput("imputationMinX", "Divide min by", min = 1, max = 10, value = 1, step = 1, width = "100%")))),
fluidRow(
style = "margin-right: 0px;",
column(6, prettyCheckbox("imp_onlyQC", "Only impute QC", value = TRUE)),
column(6)
),
fluidRow(
style = "margin-right: 0px;",
column(6,
checkboxInput("newFileImp", "Save as new file", value = T, width = "100%"),
style = "padding: 0px; margin-top: -10px; margin-left: 10px; margin-right: -10px;")
),
fluidRow(
style = "margin-right: 0px;",
column(6, bsButton("runImputation", "Run", width = "100%"), style = "padding-left:0px;"),
column(6, bsButton("saveImputation", "Save", width = "100%"), style = "padding-left:0px;")
)
),
bsCollapsePanel("Normalization",
style = "primary",
p("Expand options below to see all the normalization methods."),
div(class = "norm",
bsCollapse(
id = "norm2", multiple = FALSE, open = "Normalization",
bsCollapsePanel("Internal standards",
fluidRow(
selectInput("isMethod", "Method", choices = c("Nearest RT", "Same lipid structure"), selected = "Nearest RT", width = "100%")
),
fluidRow(
checkboxGroupInput("isChoose", NULL, choices = NULL, selected = NULL, inline = FALSE)
),
fluidRow(
style = "margin-right: 0px;",
column(12, actionLink("removeIS", "Remove IS", width = "50%") %>%
bsTooltip("Remove internal standards.", placement = "bottom", trigger = "hover")
)),
fluidRow(
style = "margin-right: 0px;",
column(6, checkboxInput("normalizeQC", "Normalize QC", value = T, width = "100%"), style = "padding: 0px; margin-top: 0px; margin-left: 10px; margin-right: -10px;"),
column(6, checkboxInput("newFileIS", "Save as new file", value = T, width = "100%"), style = "padding: 0px; margin-top: 0px; margin-left: 10px; margin-right: -10px;")
),
fluidRow(
style = "margin-right: 0px;",
column(6, bsButton("normalizeIS", "Normalize", width = "100%"), style = "padding-left:0px;"),
column(6, bsButton("saveIS", "Save", width = "100%"), style = "padding-left:0px;")
)
),
bsCollapsePanel("Drift correction",
fluidRow(
selectInput("driftMethod", "Signal correction method", choices = c("QC-RFSC (random forest)", "QC-RLSC (robust LOESS)"), width = "100%")
),
fluidRow(
conditionalPanel(
condition = "input.driftMethod == 'QC-RFSC (random forest)'",
div(id = "dc_ntree_hide",
sliderInput("driftTrees", "ntree", min = 100, max = 1000, value = 500, step = 100, width = "100%")
)
),
conditionalPanel(
condition = "input.driftMethod == 'QC-RLSC (robust LOESS)'",
div(id = "dc_qcspan_hide",
sliderInput("driftQCspan", "QCspan", min = 0.2, max = 0.75, value = 0.5, step = 0.05, width = "100%")
),
div(id = "dc_degree_hide",
sliderInput("driftDegree", "degree", min = 0, max = 2, value = 2, step = 1, width = "100%")
)
)
),
fluidRow(style = "margin-right: 0px;",
column(12, checkboxInput("newFileDrift", "Save as new file", value = T, width = "100%"), style = "padding: 0px; margin-top: -10px; margin-left: 10px; margin-right: -10px;"),
column(6, bsButton("runDrift", "Run", width = "100%"), style = "padding-left:0px;"),
column(6, bsButton("saveDrift", "Save", width = "100%"), style = "padding-left:0px;")
)
),
bsCollapsePanel("More",
fluidRow(
style = "margin-right: 0px;",
column(12, selectInput("normMethod", "Select normalization method", choices = c("QC (PQN)", "Sum", "Median", "Sample amount"), width = "100%"), style = "padding-left:0px;")
),
fluidRow(
style = "margin-right: 0px;",
column(12, checkboxInput("newFileNorm", "Save as new file", value = F, width = "100%"), style = "padding: 0px; margin-top: -10px; margin-left: 10px; margin-right: -10px;"),
column(6, bsButton("normalize", "Run", width = "100%"), style = "padding-left:0px;"),
column(6, bsButton("saveNormalization", "Save", width = "100%"), style = "padding-left:0px;")
)
) %>%
bsTooltip("Press for more normalization options.", placement = "bottom", trigger = "hover")
))
),
bsCollapsePanel("Log transform and scaling",
style = "primary",
fluidRow(
style = "margin-right: 0px;",
column(6, style = "padding-left:0px;",
selectInput("logTransform", "Log transform", choices = c("None", "log2", "log10", "ln"), width = "100%") %>%
bsTooltip("Do not use log transformation for negative values.", placement = "top", trigger = "hover")
),
column(6, selectInput("scaling", "Data scaling", choices = c("None", "Mean center", "Auto scale"), width = "100%"), style = "padding-left:0px;")
),
fluidRow(
column(6,
checkboxInput("newFileTransform", "Save as new file", value = T, width = "100%")
)),
fluidRow(
style = "margin-right: 0px;",
column(6, bsButton("transform", "Run", width = "100%"), style = "padding-left:0px;"),
column(6, bsButton("saveTransform", "Save", width = "100%"), style = "padding-left:0px;")
)
) %>% bsTooltip("Some features will be removed after transforming the data if Inf values are introduced.", placement = "bottom", trigger = "hover"),
bsCollapsePanel("Merge datasets",
style = "primary",
fluidRow(selectInput("mergeFile", "Select dataset to merge with", choices = NULL, width = "100%")),
fluidRow(
style = "margin-right: 0px;",
column(6, numericInput("merge_ppm", "M/z tolerance ppm", min = 0, value = 10, width = "100%"), style = "padding-left:0px;"),
column(6, numericInput("merge_rt", "RT tolerance", min = 0, value = 0.1, step = 0.01, width = "100%"), style = "padding-left:0px;")
),
fluidRow(
style = "margin-right: 0px;",
column(6, bsButton("editRankings", "Edit priorities", width = "100%"), style = "padding-left:0px;"),
column(6, bsButton("mergeDatasets", "Run", width = "100%"), style = "padding-left:0px;")
)
) %>% bsTooltip("Merge datasets with same samples and different ion mode. The datasets must have the same number of samples.", placement = "bottom", trigger = "hover"),
bsCollapsePanel("Remove files",
style = "primary",
fluidRow(
style = "margin-right: 0px;",
column(12, checkboxGroupInput("filesToRemove", "Select files to remove", choices = NULL, selected = NULL), style = "padding-left:0px;"),
column(12, bsButton("removeFiles", "Remove", width = "50%"), style = "padding-left:0px;")
)
)
),
fluidRow(
column(12, div(style = "float: right;",
a(icon("book"), "User manual", href = "https://github.com/anitamnd/MetaboLink/wiki")
))
)
),
sidebarMenu()
),
# Main Body
dashboardBody(
tags$head(tags$style(".modal-sm{ width:300px}
.modal-lg{ width:1200px}")),
useShinyjs(),
fluidRow(hidden(div(
id = "buttons", style = "padding-bottom: 49px",
column(3, bsButton("sequence",
label = "Sequence",
icon = icon("tags"),
style = "default",
block = T
)),
column(3, bsButton("explore",
label = "Explore data",
icon = icon("table"),
style = "default",
block = T
)),
column(3, bsButton("statistics_button",
label = "Statistics",
icon = icon("clipboard"),
style = "default",
block = T
)),
tags$style(type = "text/css", "#plot2 {width:100%}"),
column(3, bsButton("export",
label = "Export",
icon = icon("download"),
style = "default",
block = TRUE
)),
))),
fluidRow(
hidden(
div(
id = "sequence_panel",
column(12, box(width = NULL, title = "Instructions", status = "primary", solidHeader = TRUE,
tagList(
list(
tags$li("Upload the sequence/metadata file."),
tags$li("The sample names in the metafile should match the sample names in the data file."),
tags$li("Make sure the columns are labeled correctly before proceeding."),
tags$li("If a sample (numeric) column is labeled '-', this usually means there are invalid characters in the column."),
tags$li("Labels cannot be edited in the app to avoid crashes. Please edit the file and re-upload.")
)
)
)),
column(
width = 8,
box(
title = textOutput("diboxtitle"), width = NULL,
DTOutput("seq_table") %>% withSpinner(color="#0A4F8F")
)
),
column(
width = 4,
box(
width = NULL, title = "Upload sequence file", status = "danger",
fileInput("inputSequence", "Select file", accept = c("txt/csv", "text/comma-seperated-values,text/plain", ".csv"), width = "100%"),
column(6, style = "padding-left: 0px;", actionButton("updateSequence", label = "Update", width = "100%")),
column(6, style = "padding-right: 0px;", actionButton("reuseSequence", label = "Re-use sequence", width = "100%"))
),
box(
width = NULL, title = "Edit data columns",
actionButton("editColumns", "Edit", width = "50%")
),
box(
width = NULL, title = "Group nicknames",
p("Only use letters and numbers."),
actionButton("editGroups", "Edit", width = "50%")
),
box(
width = NULL, title = "Download sequence file",
downloadButton("downloadSequence", " Download")
)
)
)
)
),
fluidRow(
hidden(
div(
id = "datatable_panel",
tabsetPanel(
tabPanel("Data table",
fluidRow(
column(12, box(width = NULL, DTOutput("dttable") %>% withSpinner(color="#0A4F8F")))
)
),
tabPanel("Sample distribution",
#TODO add specific panel for comparison?
fluidRow(
column(12,
box(width = NULL, title = "Median across samples",
plotlyOutput("histogram") %>% withSpinner(color="#0A4F8F")
)),
column(12,
box(width = NULL, title = "Median across QCs",
uiOutput("histogram_qc") %>% withSpinner(color="#0A4F8F")
)),
column(12,
box(width = NULL, title = "Median across groups",
column(6, selectInput("select_group", "Select group", choices = NULL, width = "100%")),
column(6),
plotlyOutput("histogram_group") %>% withSpinner(color="#0A4F8F")
))
)
),
tabPanel("PCA",
#TODO small guide/tooltips
fluidRow(
column(12, box(width = NULL, title = "Principal Component Analysis",
tagList(
list(
tags$li("Check log-transfomed checkbox if data is already log-transformed.")
)
)
))
),
fluidRow(
column(6, box(width = NULL,
selectInput("selectpca1", "", choices = NULL, width = "100%"),
checkboxInput("pca1_islog", "Data is log-transformed.", value = FALSE, width = "100%"),
actionButton("run_pca1", "Run PCA", width = "50%") %>%
bsTooltip("Check box if the data is log-transformed!", placement = "bottom", trigger = "hover"),
plotlyOutput("plotpca1", width = "100%"), br(),
htmlOutput("pca1Details")
)),
column(6, box(width = NULL,
selectInput("selectpca2", "", choices = NULL, width = "100%"),
checkboxInput("pca2_islog", "Data is log-transformed.", value = FALSE, width = "100%"),
actionButton("run_pca2", "Run PCA", width = "50%"),
plotlyOutput("plotpca2"), br(),
htmlOutput("pca2Details")
)),
#TODO boxplots (see normalization)
column(6, box(width = NULL,
plotOutput("boxplot_1", width = "100%")
)),
column(6, box(width = NULL,
plotOutput("boxplot_2", width = "100%")
))
),
),
tabPanel("Feature drift",
fluidRow(
column(3, box(width = NULL, DTOutput("dt_drift_panel"))),
column(9,
box(
width = NULL,
fluidRow(
column(4, selectizeInput("drift_select", "Select dataset to compare with", choices = NULL, width = "100%", options = list(placeholder = "Select file"))),
column(2, style = "margin-top: 25px;", bsButton("drift_1", label = "Individual", block = TRUE)),
column(2, style = "margin-top: 25px;", bsButton("drift_2", label = "CV variation", block = TRUE)),
column(2, style = "margin-top: 25px;", bsButton("drift_3", label = "CV distribution", block = TRUE))
),
),
uiOutput("drift_ui")
)
)
),
tabPanel("Feature viewer",
fluidRow(
column(3, box(
width = NULL,
title = "Select feature",
DTOutput("dt_boxplot_panel")
)),
column(9, box(width = NULL, title = "Settings",
fluidRow(
column(6,
textInput("boxplot_title", "Title", value = NULL),
radioButtons(
inputId = "bloxplot_log",
label = "Log",
choices = c("None", "ln", "log2", "log10"),
selected = "None",
inline = TRUE
)
),
column(6, radioButtons(
inputId = "bloxplot_ylog",
label = "Y axis log",
choices = c("None", "log2", "log10"),
selected = "None",
inline = TRUE
))
)),
uiOutput("boxplot_ui")
)
)
),
tabPanel("Summary",
box(width = NULL,
fluidRow(
column(12,htmlOutput("title")),
),
fluidRow(
column(6, uiOutput("info_ui")),
column(6, htmlOutput("cvinfo_ui"))
)
)
)
)
)
)
),
fluidRow(
hidden(
div(
id = "statistics_panel",
fluidPage(
fluidRow(
column(12, box(width = NULL, title = "Guide", status = "primary", solidHeader = TRUE,
collapsible = TRUE, collapsed = TRUE,
strong("Local test"),
p("Start by selecting the test type:"),
tags$ul(
tags$li("2 groups (unpaired): compare the means of two independent or unrelated groups to determine if there is a statistically significant difference between them."),
tags$li("2 groups (paired): compare the means of two related groups to see if their average difference is significantly different from zero. Used when the same subjects are tested under two different conditions (e.g., before and after a treatment)."),
tags$li("2 groups with time (paired): used to analyze the changes within the same group over different times or conditions, assessing if there is a consistent effect across these points."),
tags$li("Compare to reference group: compare the mean of all groups against a reference group. Can be used to determine if the groups significantly differ from the expected performance or baseline.")
),
br(),
strong("PolySTest"),
p("Usage of PolySTest is recommended for data with few replicates and high amounts of missing values."),
tagList(
list(
tags$li("Select groups (required) and time (optional)."),
tags$li("Options such as 'paired' analysis are available in PolySTest."),
tags$li("To export the entire dataset to PolySTest, go to the Export panel.")
)
)
)
)
),
fluidRow(
column(6, box(width = NULL,
h4("Local test"),
fluidRow(
column(12,
selectInput("testType", "Select test", width = "100%",
choices = c("2 groups (unpaired)" = "GroupsUnpaired",
"2 groups (paired)" = "GroupsPaired",
"2 groups with time (unpaired)" = "GroupsTimeUnpaired",
"2 groups with time (paired)" = "GroupsMultipleTime",
"Compare to reference group" = "CompareToReference"), selected = NULL
))
),
conditionalPanel(
condition = "input.testType == 'GroupsUnpaired' || input.testType == 'GroupsPaired'",
fluidRow(
column(6, selectInput("group1", "Group 1", choices = NULL, width = "100%")),
column(6, selectInput("group2", "Group 2", choices = NULL, width = "100%"))
)
),
conditionalPanel(
condition = "input.testType == 'GroupsTimeUnpaired'",
fluidRow(
column(6, selectInput("group1_time", "Group", choices = NULL, width = "100%")),
column(6, selectInput("time1_time", "Time", choices = NULL, width = "100%"))
),
fluidRow(
column(6, selectInput("group2_time", "Group", choices = NULL, width = "100%")),
column(6, selectInput("time2_time", "Time", choices = NULL, width = "100%"))
),
),
conditionalPanel(
condition = "input.testType == 'CompareToReference'",
fluidRow(
column(12, selectInput("referenceGroup", "Select reference group", choices = NULL, width = "100%"))
)
),
conditionalPanel(
condition = "input.testType == 'GroupsMultipleTime'",
fluidRow(
column(12, checkboxGroupInput("contrasts", "Select contrasts", choices = NULL, selected = NULL, inline = FALSE))
)
),
fluidRow(
column(6, actionButton("selectTest", "Run test", width = "100%"))
)
)),
column(6, box(width = NULL,
h4("Export to PolySTest"),
fluidRow(
column(6, selectInput("group1_polystest", "Group", choices = NULL, width = "100%")),
column(6, selectInput("time1_polystest", "Time", choices = NULL, width = "100%"))
),
fluidRow(
column(6, selectInput("group2_polystest", "Group", choices = NULL, width = "100%")),
column(6, selectInput("time2_polystest", "Time", choices = NULL, width = "100%"))
),
fluidRow(
column(6, actionButton("export_polystest", "Send to PolySTest", width = "100%"))
)
))
),
fluidRow(
column(12, box(title = "Results", width = NULL,
uiOutput("results_ui")
))
)
)
)
)
),
fluidRow(
hidden(
div(
id = "export_panel",
box(title = ".csv and .xlsx", status = "primary", solidHeader = TRUE, width = 6,
column(12,
h4(".csv"),
uiOutput("export_ui")
),
column(12, style = "margin-top: 20px;",
h4(".xlsx"),
checkboxGroupInput("export_xml_list", "Choose sheets", choices = NULL, selected = NULL),
downloadButton("export_xml", "Export combined .xlsx")
),
column(12, style = "margin-top: 20px;",
h4("Statistics results"),
uiOutput("export_stats")
),
column(12, style = "margin-top: 20px;",
h4("Settings used in app"),
uiOutput("export_settings")
)
),
box(title = "Export to other apps", status = "primary", solidHeader = TRUE, width = 6,
column(12,
h4("Statistical testing"),
actionButton("send_polystest", "Send to PolySTest"),
span(textOutput("connection_polystest"), style="color:#33DD33;")
),
column(12, style = "margin-top: 20px;",
h4("Clustering"),
actionButton("send_vsclust", "Send to VSClust"),
span(textOutput("connection_vsclust"), style="color:#33DD33;")
),
column(12, style = "margin-top: 20px;",
h4(".csv for MetaboAnalyst"),
uiOutput("export_metabo")
)
)
)
)
),
fluidRow(
div(
id = "welcome_panel",
column(12, box(width = NULL, includeHTML("intro_text.html")))
)
)
)
))