inst/shiny-app/ui.r
In VCCRI/GEOracle: Georacle Shiny app
appCSS <- "
#loading-content {
position: absolute;
background: #000000;
opacity: 0.9;
z-index: 100;
left: 0;
right: 0;
height: 100%;
text-align: center;
color: #FFFFFF;
}
"
jscode <- "shinyjs.closeWindow = function() { window.close(); }"
########################################################################
# User Interface
########################################################################
shinyUI(fluidPage(
useShinyjs(),
inlineCSS(appCSS),
extendShinyjs(text = jscode, functions = c("closeWindow")),
# Loading message
div(
id = "loading-content",
h2("GEOracle is loading...")
),
tags$head(
tags$style(HTML("
.shiny-progress .progress {
position: absolute;
width: 100%;
top: 0px;
height: 20px;
margin: 0px;
}
.shiny-progress .bar {
opacity: 0.6;
transition-duration: 250ms;
height: 20px;
}
.shiny-progress .progress-text {
position: absolute;
right: 10px;
height: 50px;
width: 600px;
background-color: #eef8ff;
margin: 0px;
padding: 2px 3px;
opacity: 0.85;
}
.shiny-progress .progress-text .progress-message {
padding: 0px 3px;
font-weight: bold;
font-size: 200%;
}
.shiny-progress .progress-text .progress-detail {
padding: 0px 3px;
font-size: 200%;
}
"))
,
tags$head(tags$style("#curtab{color: white;
font-size: 5px;
font-style: italic;
}"
)
)
,
tags$head(tags$style("#curtabmessage{color: white;
font-size: 5px;
font-style: italic;
}"
)
)
),
sidebarPanel(
conditionalPanel("(output.curtab == 'Verify' || output.curtab == 'Add')",
#tags$div(title="GEOracle", img(src='http://georacle.victorchang.edu.au/georacle.png', align = "left", width="90%"))
imageOutput("GEoracleLogo", height = "auto")
,
hr()
,
uiOutput('analysis_select')
,
tabsetPanel(id = "inTabset",
tabPanel("Search GEO",
#renderText("You can search the GEO database for datasets to process here."),
textInput('searchTerm', label = "Enter a search term:"),
#bsTooltip(id = "searchTerm", title = "You can use & or | for multiple keywords.",
#placement = "bottom", trigger = "hover"),
div(id="species_select_search_div",
selectInput('selectSpecies', 'Species:', choices = c("A","C"), selectize = FALSE)
)
,
div(id="microarray_checkbox_div",
checkboxInput("GSE_platform_filter", label ="Show only microarray GSE", value=TRUE)#,
)
,
actionButton('find', "Search GEO",
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
hr(),
uiOutput("searchStatus"),
dataTableOutput(outputId="GEOtable"),
hr(),
div(id="keep_button_div", style="display:inline-block",
uiOutput('keep.button'))
,
div(id="remove_button_div", style="display:inline-block",
uiOutput('remove.button'))
,
hr()
,
div(id="download_GSE_button_div",
uiOutput('download.button'),
uiOutput('batch.download.button')
)
,
div(id="analyse_GSE_button_div",
uiOutput('direct.analyse.button')
)
)
,
tabPanel("Process GSE list",
hr()
,
fluidRow(
column(6,
textAreaInput('GSEtext', "Direct GSE input", placeholder = "GSE1234 GSE5678 GSE9123"), actionButton("submitGSETtext", "Submit")
)
,
column(6,
div(id="upload_file_div",
fileInput('uploadFile', "Upload list of GSE IDs")
)
,
bsTooltip(id = "uploadFile", title = "e.g. GSE123 GSE345 GSE567 ...",
placement = "bottom", trigger = "hover")
,
a(href="http://georacle.victorchang.edu.au/TGFB_Case_Study_GSE_IDs.txt", "Sample input file (Right click / save as)", target = "blank")
)
)
,
hr()
,
textOutput('numGSEs')
,
conditionalPanel("typeof output.numGSEs === 'string'",
h4('Set filters', align = "center")
,
uiOutput('filter_select')
,
### custom filter panel
conditionalPanel("input.filter == 'Custom'",
htmlOutput("speciesUI")
,
div(style="display:inline-block",
#sliderInput("clusterrange", "Cluster size ange:", min = 1, max = 15, value = c(2,5), width=150))
numericInput("minClusterSize", "Min. Cluster Size", value = 2, min = 1, step = 1, width = 100))
,
div(style="display:inline-block",
numericInput("maxClusterSize", "Max. Cluster Size", value = 5, min = 2, step = 1, width= 100))
,
div(style="display:inline-block",
checkboxInput("allbetween", "All clusters correct size", value = 0))
,
div(style="display:inline-block",
checkboxInput("simpleOnly", "Simple (2 clusters) only", value = 0))
,
div(style="display:inline-block",
numericInput("maxcomps", "Max. Comparisons", value = 10, min = 1, step = 1, width= 100))
,
div(style="display:inline-block",
checkboxInput("singlePlatformOnly", "1 platform only", value = 1))
,
div(style="display:inline-block",
checkboxInput("onechannel", "1 channel array", value = 1))
,
div(style="display:inline-block",
checkboxInput("predpert", "Predicted perturbation", value = 1))
,
div(style="display:inline-block",
checkboxInput("gene_symbols_only", "Pre-annotated genes only", value = 0))
,
checkboxInput("see_all_GSE", "Let every GSE through", value = F)
)
,
actionButton("go", " COMPUTE", icon("wrench"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
)
)
,
conditionalPanel("input.go > 0",
hr()
,
h4('Processed GSEs', align = "center")
,
h5("Click the GSE IDs below to verify results before proceeding\n")
,
hr()
,
DT::dataTableOutput('processedGSEs')
,
tags$script(HTML(
"Shiny.addCustomMessageHandler('pager',function(page) {
$('#'+'processedGSEs').find('table').DataTable().page(page).draw(false);
})"
)),
hr()
,
conditionalPanel("input.processedGSEs_row_last_clicked > 0",
h5("Once you have renamed and verified all comparisons click here to create a GRN\n")
,
actionButton("finished", "NEXT STEP", icon("play"), style="color: #fff; background-color: #29C28A; border-color: #2e6da4")
)
)
)
,
conditionalPanel("output.curtab == 'GRN'",
imageOutput("GEoracleLogo2", height = "auto")
,
hr()
,
actionButton("goback", "GO BACK", icon("step-backward"), style="color: #fff; background-color: rgb(156, 5, 5); border-color: #2e6da4")
,
hr()
,
textInput("folder", "Output Folder Name", value = gsub("[: -]","_",Sys.time()))
,
hr()
,
h2("Set differential expression significance thresholds:")
,
selectInput("logfc", "Absolute log2 FC", choices = c(0.5,1,2), selected = 1, selectize = FALSE)
,
selectInput("pval", "B.H. adjusted P-value", choices = c(0.1,0.05,0.01,0.001), selected = 0.05, selectize = FALSE)
,
actionButton("process", "Calculate D.E.", icon("object-align-bottom"), style="color: #fff; background-color: rgb(18, 88, 24); border-color: rgb(141, 252, 0)")
)
,
uiOutput("curtabs")
),
mainPanel(
conditionalPanel("output.curtab == 'Verify'",
uiOutput('matchedPairs')
)
,
conditionalPanel("input.process > 0",
uiOutput('makeGRN')
)
,
conditionalPanel("output.curtab == 'Add'",
uiOutput('addComp')
)
)
))
VCCRI/GEOracle documentation built on May 10, 2019, 1:15 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
appCSS <- "
#loading-content {
position: absolute;
background: #000000;
opacity: 0.9;
z-index: 100;
left: 0;
right: 0;
height: 100%;
text-align: center;
color: #FFFFFF;
}
"
jscode <- "shinyjs.closeWindow = function() { window.close(); }"
########################################################################
# User Interface
########################################################################
shinyUI(fluidPage(
useShinyjs(),
inlineCSS(appCSS),
extendShinyjs(text = jscode, functions = c("closeWindow")),
# Loading message
div(
id = "loading-content",
h2("GEOracle is loading...")
),
tags$head(
tags$style(HTML("
.shiny-progress .progress {
position: absolute;
width: 100%;
top: 0px;
height: 20px;
margin: 0px;
}
.shiny-progress .bar {
opacity: 0.6;
transition-duration: 250ms;
height: 20px;
}
.shiny-progress .progress-text {
position: absolute;
right: 10px;
height: 50px;
width: 600px;
background-color: #eef8ff;
margin: 0px;
padding: 2px 3px;
opacity: 0.85;
}
.shiny-progress .progress-text .progress-message {
padding: 0px 3px;
font-weight: bold;
font-size: 200%;
}
.shiny-progress .progress-text .progress-detail {
padding: 0px 3px;
font-size: 200%;
}
"))
,
tags$head(tags$style("#curtab{color: white;
font-size: 5px;
font-style: italic;
}"
)
)
,
tags$head(tags$style("#curtabmessage{color: white;
font-size: 5px;
font-style: italic;
}"
)
)
),
sidebarPanel(
conditionalPanel("(output.curtab == 'Verify' || output.curtab == 'Add')",
#tags$div(title="GEOracle", img(src='http://georacle.victorchang.edu.au/georacle.png', align = "left", width="90%"))
imageOutput("GEoracleLogo", height = "auto")
,
hr()
,
uiOutput('analysis_select')
,
tabsetPanel(id = "inTabset",
tabPanel("Search GEO",
#renderText("You can search the GEO database for datasets to process here."),
textInput('searchTerm', label = "Enter a search term:"),
#bsTooltip(id = "searchTerm", title = "You can use & or | for multiple keywords.",
#placement = "bottom", trigger = "hover"),
div(id="species_select_search_div",
selectInput('selectSpecies', 'Species:', choices = c("A","C"), selectize = FALSE)
)
,
div(id="microarray_checkbox_div",
checkboxInput("GSE_platform_filter", label ="Show only microarray GSE", value=TRUE)#,
)
,
actionButton('find', "Search GEO",
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
hr(),
uiOutput("searchStatus"),
dataTableOutput(outputId="GEOtable"),
hr(),
div(id="keep_button_div", style="display:inline-block",
uiOutput('keep.button'))
,
div(id="remove_button_div", style="display:inline-block",
uiOutput('remove.button'))
,
hr()
,
div(id="download_GSE_button_div",
uiOutput('download.button'),
uiOutput('batch.download.button')
)
,
div(id="analyse_GSE_button_div",
uiOutput('direct.analyse.button')
)
)
,
tabPanel("Process GSE list",
hr()
,
fluidRow(
column(6,
textAreaInput('GSEtext', "Direct GSE input", placeholder = "GSE1234 GSE5678 GSE9123"), actionButton("submitGSETtext", "Submit")
)
,
column(6,
div(id="upload_file_div",
fileInput('uploadFile', "Upload list of GSE IDs")
)
,
bsTooltip(id = "uploadFile", title = "e.g. GSE123 GSE345 GSE567 ...",
placement = "bottom", trigger = "hover")
,
a(href="http://georacle.victorchang.edu.au/TGFB_Case_Study_GSE_IDs.txt", "Sample input file (Right click / save as)", target = "blank")
)
)
,
hr()
,
textOutput('numGSEs')
,
conditionalPanel("typeof output.numGSEs === 'string'",
h4('Set filters', align = "center")
,
uiOutput('filter_select')
,
### custom filter panel
conditionalPanel("input.filter == 'Custom'",
htmlOutput("speciesUI")
,
div(style="display:inline-block",
#sliderInput("clusterrange", "Cluster size ange:", min = 1, max = 15, value = c(2,5), width=150))
numericInput("minClusterSize", "Min. Cluster Size", value = 2, min = 1, step = 1, width = 100))
,
div(style="display:inline-block",
numericInput("maxClusterSize", "Max. Cluster Size", value = 5, min = 2, step = 1, width= 100))
,
div(style="display:inline-block",
checkboxInput("allbetween", "All clusters correct size", value = 0))
,
div(style="display:inline-block",
checkboxInput("simpleOnly", "Simple (2 clusters) only", value = 0))
,
div(style="display:inline-block",
numericInput("maxcomps", "Max. Comparisons", value = 10, min = 1, step = 1, width= 100))
,
div(style="display:inline-block",
checkboxInput("singlePlatformOnly", "1 platform only", value = 1))
,
div(style="display:inline-block",
checkboxInput("onechannel", "1 channel array", value = 1))
,
div(style="display:inline-block",
checkboxInput("predpert", "Predicted perturbation", value = 1))
,
div(style="display:inline-block",
checkboxInput("gene_symbols_only", "Pre-annotated genes only", value = 0))
,
checkboxInput("see_all_GSE", "Let every GSE through", value = F)
)
,
actionButton("go", " COMPUTE", icon("wrench"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
)
)
,
conditionalPanel("input.go > 0",
hr()
,
h4('Processed GSEs', align = "center")
,
h5("Click the GSE IDs below to verify results before proceeding\n")
,
hr()
,
DT::dataTableOutput('processedGSEs')
,
tags$script(HTML(
"Shiny.addCustomMessageHandler('pager',function(page) {
$('#'+'processedGSEs').find('table').DataTable().page(page).draw(false);
})"
)),
hr()
,
conditionalPanel("input.processedGSEs_row_last_clicked > 0",
h5("Once you have renamed and verified all comparisons click here to create a GRN\n")
,
actionButton("finished", "NEXT STEP", icon("play"), style="color: #fff; background-color: #29C28A; border-color: #2e6da4")
)
)
)
,
conditionalPanel("output.curtab == 'GRN'",
imageOutput("GEoracleLogo2", height = "auto")
,
hr()
,
actionButton("goback", "GO BACK", icon("step-backward"), style="color: #fff; background-color: rgb(156, 5, 5); border-color: #2e6da4")
,
hr()
,
textInput("folder", "Output Folder Name", value = gsub("[: -]","_",Sys.time()))
,
hr()
,
h2("Set differential expression significance thresholds:")
,
selectInput("logfc", "Absolute log2 FC", choices = c(0.5,1,2), selected = 1, selectize = FALSE)
,
selectInput("pval", "B.H. adjusted P-value", choices = c(0.1,0.05,0.01,0.001), selected = 0.05, selectize = FALSE)
,
actionButton("process", "Calculate D.E.", icon("object-align-bottom"), style="color: #fff; background-color: rgb(18, 88, 24); border-color: rgb(141, 252, 0)")
)
,
uiOutput("curtabs")
),
mainPanel(
conditionalPanel("output.curtab == 'Verify'",
uiOutput('matchedPairs')
)
,
conditionalPanel("input.process > 0",
uiOutput('makeGRN')
)
,
conditionalPanel("output.curtab == 'Add'",
uiOutput('addComp')
)
)
))
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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