inst/shiny/ui.R
In JinmiaoChenLab/cytofkit: cytofkit: an integrated mass cytometry data analysis pipeline
library(shiny)
library(shinyFiles)
#currently unused
shinyUI(fluidPage(
titlePanel("Interactive Exploration of cytofkit Analysis Results"),
hr(),
fluidRow(
## side panel--take 1/4 space
column(3,
h4('Load cytofkit RData:'),
wellPanel(
fileInput(inputId = 'cytofkitObj',
label = NULL,
multiple = FALSE,
accept = c('text/RData', '.RData')),
shinyFilesButton('serverObj', label = "Server File Select", title = "Please select your RData", multiple = FALSE),
textOutput("queryText"),
textOutput("rdata_desc"),
fluidRow(
column(6,
actionButton("goButton", "Submit", icon = icon("hand-o-right"))
),
column(6,
actionButton("reset", "Reset Data", icon = icon("repeat"))
)
)
),
hr(),
conditionalPanel(" input.main_panel == 'C_panel' && input.C_clusterTabs == 'C_tab1' ",
h4("Plot Control:"),
wellPanel(
checkboxInput(inputId = "C_addLabel", label = "Add Cluster Labels", value = TRUE),
checkboxInput(inputId = "C_labelRepel", label = "Repel Cluster Labels", value = FALSE),
checkboxInput(inputId = "C_facetPlot", label = "Separate Plot by Samples", value = FALSE)
),
actionButton("PDFClusterPlot", "Download Cluster Plot in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'M_panel' && input.M_markerTabs == 'M_tab1' ",
h4("Plot Control:"),
wellPanel(
selectInput('M_heatmap_dendrogram', strong('Heatmap Dendrogram:'),
choices = c("both","row","column","none"),
selected = "both", width = "100%"),
selectInput('M_heatmap_colorPalette', strong('Color Palette:'),
choices = c("bluered", "greenred", "spectral1", "spectral2"),
selected = "bluered", width = "100%")
),
actionButton("PDFHeatmap", "Download Marker Heatmap in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'M_panel' && input.M_markerTabs == 'M_tab2' ",
h4("Plot Control:"),
wellPanel(
actionButton("PDFExpPlot", "Download Exp Plot in PDF", icon = icon("download"))
)),
conditionalPanel(" input.main_panel == 'M_panel' && input.M_markerTabs == 'M_tab3' ",
h4("Plot Control:"),
wellPanel(
actionButton("PDFHistogram", "Download Histogram in PDF", icon = icon("download"))
)),
conditionalPanel(" input.main_panel == 'S_panel' && input.S_sampleTabs == 'S_tab1' ",
h4("Plot Control:"),
wellPanel(
selectInput('S_heatmap_dendrogram', strong('Heatmap Dendrogram:'),
choices = c("both","row","column","none"),
selected = "both", width = "100%"),
selectInput('S_heatmap_colorPalette', strong('Color Palette:'),
choices = c("bluered", "greenred", "spectral1", "spectral2"),
selected = "bluered", width = "100%")
),
actionButton("PDFSamHeat", "Download Sample Heatmap in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'S_panel' && input.S_sampleTabs == 'S_tab2' ",
h4("Plot Control:"),
actionButton("PDFrateChange", "Download Rate Change Plot in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'P_panel' && input.P_progressionTabs == 'P_tab1' ",
h4("Plot Control:"),
wellPanel(
checkboxInput(inputId = "P_addLabel", label = "Add Cluster Labels", value = TRUE),
checkboxInput(inputId = "P_labelRepel", label = "Repel Cluster Labels", value = FALSE),
checkboxInput(inputId = "P_facetPlot", label = "Separate Plot by Samples", value = FALSE)
),
actionButton("PDFScatter", "Download Scatterplot in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'P_panel' && input.P_progressionTabs == 'P_tab2' ",
h4("Plot Control:"),
wellPanel(
checkboxInput(inputId = "P_addLabel2", label = "Add Cluster Labels", value = TRUE)
),
actionButton("PDFmarkerPlot", "Download Marker Plot in PDF", icon = icon("download"))
),
br(),
fluidRow(
column(6,
sliderInput(inputId="tab_w", label = "PDF width(in):",
min=3, max=20, value=8, width=100, ticks=FALSE)
),
column(6,
sliderInput(inputId="tab_h", label = "PDF height(in):",
min=3, max=20, value=8, width=100, ticks=FALSE)
)),
actionButton("OpenDir", "Open download folder", icon = icon("folder")),
hr(),
h4("Sample Filter:"),
wellPanel(uiOutput("selectAll"),
uiOutput("sampleSelect")),
hr(),
h4("Data Summary:"),
wellPanel(
h5("Expression Data:"),
textOutput("summaryText1"),
h5("Markers used for dimension reduction and clustering:"),
textOutput("summaryText5"),
h5("Cluster Method(s):"),
textOutput("summaryText2"),
h5("Visualization Method(s):"),
textOutput("summaryText3"),
h5("Progression Method(s):"),
textOutput("summaryText4")
),
hr(),
h4("Save results:"),
h5("Outputs to save"),
fluidRow(
column(4,
checkboxInput(inputId = "saveFCS", label = "FCS", value = TRUE)
),
column(4,
checkboxInput(inputId = "saveRData", label = "RData", value = TRUE)
),
column(4,
checkboxInput(inputId = "saveCsv", label = "csv", value = FALSE)
)
),
actionButton("saveButton", "Save Data", icon = icon("download")),
hr(),
h4(tags$a(href="mailto:jinmiao@gmail.com,a0124008@u.nus.edu?subject=[cytofkit-question]",
"Contact Us")),
imageOutput("logo", height = "60px")
),
## main panel--take 3/4 space
column(9,
tabsetPanel(id="main_panel", type = "pills",
tabPanel(title="Cluster Panel", value="C_panel", fluidPage(
hr(),
tabsetPanel(id="C_clusterTabs", type = "tabs",
tabPanel(title="Cluster Plot", value="C_tab1",
br(),
fluidRow(
column(3,
uiOutput("C_PlotMethod")
),
column(3,
uiOutput("C_PlotFunction")
),
column(3,
numericInput("C_PointSize", "Point Size:", value = 1)
),
column(3,
numericInput("C_LabelSize", "Label Size:", value = 12)
)
),
uiOutput("C_clusterSelect"),
hr(),
plotOutput("C_ScatterPlot", width = "100%")
),
tabPanel(title="Change Cluster Color", value="C_tab2",
br(),
wellPanel(
uiOutput("C_colourCluster")
),
hr(),
lapply(1:100, function(i) {
uiOutput(paste0('Cluster_', i, '_col'))
}),
hr(),
fluidRow(
column(3,
actionButton("C_updateClusterColor", "Update Cluster Color",
icon = icon("hand-o-right"), width = "100%")
),
column(3,
actionButton("C_revertClusterColor", "Revert to default",
icon = icon("hand-o-right"), width = "100%")
),
column(6)
),
hr()),
tabPanel(title="Annotate Clusters", value="C_tab3",
br(),
wellPanel(
uiOutput("C_labelCluster"),
uiOutput("C_labelCluster_name")
),
hr(),
lapply(1:100, function(i) {
uiOutput(paste0('Cluster', i))
}),
hr(),
actionButton("updatelabel", "Submit Cluster Label", icon = icon("hand-o-right")),
hr()),
tabPanel(title="Run FlowSOM", value="C_tab4",
br(),
h4("FlowSOM Clustering Setup:"),
hr(),
wellPanel(
numericInput("C_FlowSOM_k", "Cluster k", value = 10, width = "30%"),
uiOutput("C_markerSelect")
),
hr(),
actionButton("C_runFlowSOM", "Run FlowSOM", icon = icon("hand-pointer-o")))
)
)),
tabPanel(title = "Marker Panel", value = "M_panel", fluidPage(
hr(),
tabsetPanel(id="M_markerTabs", type = "tabs",
tabPanel(title="Expression Heat Map", value="M_tab1",
br(),
fluidRow(
column(4,
uiOutput("M_plotCluster")
),
column(2,
selectInput('M_plotMethod', strong('Heatmap Type:'),
choices = c("mean", "median"),
selected = "mean", width = "100%")
),
column(2,
selectInput('M_scaleMethod', strong('Scale Data:'),
choices = c("none", "row", "column"),
selected = "none", width = "100%")
),
column(2,
numericInput("M_rowLabelSize", "Row Label Size:", value = 1, step = 0.5)
),
column(2,
numericInput("M_colLabelSize", "Col Label Size:", value = 1, step = 0.5)
)
),
fluidRow(
column(10,
uiOutput("M_heatmapmarkerSelect")
),
column(2,
actionButton("M_heatmapSelectAll", "All Markers"),
actionButton("M_updateHeatmap", "Update Plot")
)
),
hr(),
plotOutput("M_heatmapPlot", width = "100%")),
tabPanel(title="Expression Level Plot", value="M_tab2",
br(),
fluidRow(
column(3,
uiOutput("M_PlotMethod")
),
column(3,
numericInput("M_PointSize", "Point Size:", value = 1),
sliderInput("M_Alpha", "Transparency:", value = 1, min = 0, max = 1, step = 0.1)
),
column(3,
selectInput('M_colorPalette', label = "Color Palette:",
choices = c("bluered", "spectral1", "spectral2", "heat"),
selected = "bluered", width = "100%")
),
column(3,
selectInput('M_ScaleOptions', label = "Scaling Range:",
choices = c("Local", "Global"),
selected = "Local", width = "100%"),
selectInput('M_scaledData', label = "Centering:",
choices = c("Un-centered", "Centered"),
selected = "Un-centered", width = "100%")
)
),
fluidRow(
column(10,
uiOutput("M_PlotMarker")
),
column(2,
actionButton("M_chooseAllMarker", "All Markers"),
actionButton("M_updateExPlot", "Update Plot")
)
),
hr(),
plotOutput("M_markerExpressionPlot", width = "100%")),
tabPanel(title="Expression Histogram", value="M_tab3",
br(),
fluidRow(
column(4,
uiOutput("M_stackFactor")
),
column(2,
numericInput("M_markerTextSize", "Marker Text Size:",
value = 12, step = 1, min=1, max=15)
),
column(2,
numericInput("M_xlab_size", "x Label Size:",
value = 2, step = 1, min=1, max=10)
),
column(2,
numericInput("M_legendTextSize", "Legend Size:",
value = 1, step = 0.5, min=1, max=10)
),
column(2,
numericInput("M_legendRow", "Legend Row:",
value = 2, step = 1, min=1, max=10)
)
),
fluidRow(
column(10,
uiOutput("M_markerSelect")
),
column(2,
actionButton("M_histSelectAll", "All Markers")
)
),
hr(),
actionButton("M_updateDensityPlot", "Update Plot", icon = icon("hand-pointer-o")),
plotOutput("M_stackDensityPlot", width = "100%")),
tabPanel(title="Update Marker Names", value="M_tab4",
h5('Type in Your New Name for Each Marker:'),
hr(),
lapply(1:100, function(i) {
uiOutput(paste0('Marker_', i, "_name"))
}),
hr(),
actionButton("C_updateMarkerNames", "Update Marker Name", icon = icon("hand-pointer-o")))
)
)),
tabPanel(title = "Sample Panel", value = "S_panel", fluidPage(
hr(),
tabsetPanel(id="S_sampleTabs", type = "tabs",
tabPanel(title="Cell Percentage Heatmap", value="S_tab1",
br(),
fluidRow(
column(4,
uiOutput("S_plotCluster")
),
column(2,
selectInput('S_plotMethod', strong('Heatmap Type:'),
choices = c("percentage"),
selected = "percentage", width = "100%")
),
column(2,
selectInput('S_scaleMethod', strong('Scale Data:'),
choices = c("none", "row", "column"),
selected = "none", width = "100%")
),
column(2,
numericInput("S_rowLabelSize", "Row Label Size:", value = 1, step = 0.5)
),
column(2,
numericInput("S_colLabelSize", "Col Label Size:", value = 1, step = 0.5)
)
),
hr(),
plotOutput("S_heatmapPlot", width = "100%")
),
tabPanel(title="Cell Percentage Line Chart", value="S_tab2",
br(),
uiOutput("S_clusterMethod2"),
uiOutput("S_clusterFilter"),
hr(),
plotOutput("S_rateChangePlot", width = "100%")
),
tabPanel(title="Regroup Samples", value="S_tab3",
br(),
h4("Type in the Group Name for Each Sample:"),
lapply(1:100, function(i) {
uiOutput(paste0('S_sample', i))
}),
hr(),
textInput("sampleGroupLevels", "Group Name Levels: (to order the group names)",
value = "", width = "100%",
placeholder = "Type in group names in order, seperated by semicolon(;)"),
hr(),
fluidRow(
column(3,
actionButton("updateSampleGroups", "Submit New Sample Groups", icon = icon("hand-o-right"))
),
column(3,
actionButton("revertSampleNames", "Revert to Old Sample Names", icon = icon("hand-o-right"))
),
column(6)
),
hr())
)
)),
tabPanel(title="Progression Panel", value = "P_panel", fluidPage(
hr(),
tabsetPanel(id="P_progressionTabs", type = "tabs",
tabPanel(title="Subset Relationship Plot", value="P_tab1",
br(),
fluidRow(
column(3,
uiOutput("P_xlab")
),
column(3,
uiOutput("P_ylab")
),
column(3,
numericInput("P_PointSize", "Point Size:", value = 3)
),
column(3,
numericInput("P_LabelSize", "Label Size:", value = 8)
)
),
plotOutput("P_scatterPlot", width = "80%")),
tabPanel(title="Marker Expression Profile", value="P_tab2",
br(),
fluidRow(
column(3,
uiOutput("P_orderBy")
),
column(2,
numericInput("P_LabelSize2", "Label Size:", value = 5)
),
column(7,
uiOutput("P_clusterSelect")
)
),
hr(),
uiOutput("P_markerSelect"),
hr(),
fluidRow(
column(3,
actionButton("P_updateRegressionPlot", "Update Plot", icon = icon("hand-pointer-o"))
),
column(2,
checkboxInput("P_reverseOrder", label = "Reverse Order", value = FALSE)
),
column(3,
checkboxInput("P_combineTrends", label = "Combine Trend Lines", value = FALSE)
),
column(4)
),
plotOutput("P_markerPlot", width = "100%")),
tabPanel(title="Run Diffusion Map", value="P_tab3",
br(),
h4("Diffusionmap Setup:"),
wellPanel(
h5("Cluster-based down-sampling to remove subset aboundance heterogeneity"),
fluidRow(
column(4,
uiOutput("P_clusterMethod")
),
column(4,
numericInput("P_clusterSampleSize", "Cluster Sample Size", value = 500,
min = 10, max = 1000, step = 5, width = "100%")
),
column(4,
selectInput('P_sampleMethod', 'Downsample Method:', choices = c("ceil", "all", "fixed", "min"),
selected = "ceil", width = "100%")
)
),
tableOutput('P_clusterTable'),
uiOutput("P_clusterFilter"),
hr(),
h5("Diffusionmap Parameters"),
fluidRow(
column(6,
selectInput('P_distMethod', 'Distance calculation Method:', choices = c("euclidean"),
selected = "euclidean", width = "100%")
),
column(6,
numericInput("P_outDim", "Output Dimensionality:", value = 4,
min = 1, max = 6, step = 1, width = "100%")
)
)
),
hr(),
actionButton("P_runDiffusionmap", "Run Diffusionmap", icon = icon("hand-pointer-o")))
)
))
)
)
)
))
JinmiaoChenLab/cytofkit documentation built on Dec. 20, 2020, 8:52 p.m.
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library(shiny)
library(shinyFiles)
#currently unused
shinyUI(fluidPage(
titlePanel("Interactive Exploration of cytofkit Analysis Results"),
hr(),
fluidRow(
## side panel--take 1/4 space
column(3,
h4('Load cytofkit RData:'),
wellPanel(
fileInput(inputId = 'cytofkitObj',
label = NULL,
multiple = FALSE,
accept = c('text/RData', '.RData')),
shinyFilesButton('serverObj', label = "Server File Select", title = "Please select your RData", multiple = FALSE),
textOutput("queryText"),
textOutput("rdata_desc"),
fluidRow(
column(6,
actionButton("goButton", "Submit", icon = icon("hand-o-right"))
),
column(6,
actionButton("reset", "Reset Data", icon = icon("repeat"))
)
)
),
hr(),
conditionalPanel(" input.main_panel == 'C_panel' && input.C_clusterTabs == 'C_tab1' ",
h4("Plot Control:"),
wellPanel(
checkboxInput(inputId = "C_addLabel", label = "Add Cluster Labels", value = TRUE),
checkboxInput(inputId = "C_labelRepel", label = "Repel Cluster Labels", value = FALSE),
checkboxInput(inputId = "C_facetPlot", label = "Separate Plot by Samples", value = FALSE)
),
actionButton("PDFClusterPlot", "Download Cluster Plot in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'M_panel' && input.M_markerTabs == 'M_tab1' ",
h4("Plot Control:"),
wellPanel(
selectInput('M_heatmap_dendrogram', strong('Heatmap Dendrogram:'),
choices = c("both","row","column","none"),
selected = "both", width = "100%"),
selectInput('M_heatmap_colorPalette', strong('Color Palette:'),
choices = c("bluered", "greenred", "spectral1", "spectral2"),
selected = "bluered", width = "100%")
),
actionButton("PDFHeatmap", "Download Marker Heatmap in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'M_panel' && input.M_markerTabs == 'M_tab2' ",
h4("Plot Control:"),
wellPanel(
actionButton("PDFExpPlot", "Download Exp Plot in PDF", icon = icon("download"))
)),
conditionalPanel(" input.main_panel == 'M_panel' && input.M_markerTabs == 'M_tab3' ",
h4("Plot Control:"),
wellPanel(
actionButton("PDFHistogram", "Download Histogram in PDF", icon = icon("download"))
)),
conditionalPanel(" input.main_panel == 'S_panel' && input.S_sampleTabs == 'S_tab1' ",
h4("Plot Control:"),
wellPanel(
selectInput('S_heatmap_dendrogram', strong('Heatmap Dendrogram:'),
choices = c("both","row","column","none"),
selected = "both", width = "100%"),
selectInput('S_heatmap_colorPalette', strong('Color Palette:'),
choices = c("bluered", "greenred", "spectral1", "spectral2"),
selected = "bluered", width = "100%")
),
actionButton("PDFSamHeat", "Download Sample Heatmap in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'S_panel' && input.S_sampleTabs == 'S_tab2' ",
h4("Plot Control:"),
actionButton("PDFrateChange", "Download Rate Change Plot in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'P_panel' && input.P_progressionTabs == 'P_tab1' ",
h4("Plot Control:"),
wellPanel(
checkboxInput(inputId = "P_addLabel", label = "Add Cluster Labels", value = TRUE),
checkboxInput(inputId = "P_labelRepel", label = "Repel Cluster Labels", value = FALSE),
checkboxInput(inputId = "P_facetPlot", label = "Separate Plot by Samples", value = FALSE)
),
actionButton("PDFScatter", "Download Scatterplot in PDF", icon = icon("download"))
),
conditionalPanel(" input.main_panel == 'P_panel' && input.P_progressionTabs == 'P_tab2' ",
h4("Plot Control:"),
wellPanel(
checkboxInput(inputId = "P_addLabel2", label = "Add Cluster Labels", value = TRUE)
),
actionButton("PDFmarkerPlot", "Download Marker Plot in PDF", icon = icon("download"))
),
br(),
fluidRow(
column(6,
sliderInput(inputId="tab_w", label = "PDF width(in):",
min=3, max=20, value=8, width=100, ticks=FALSE)
),
column(6,
sliderInput(inputId="tab_h", label = "PDF height(in):",
min=3, max=20, value=8, width=100, ticks=FALSE)
)),
actionButton("OpenDir", "Open download folder", icon = icon("folder")),
hr(),
h4("Sample Filter:"),
wellPanel(uiOutput("selectAll"),
uiOutput("sampleSelect")),
hr(),
h4("Data Summary:"),
wellPanel(
h5("Expression Data:"),
textOutput("summaryText1"),
h5("Markers used for dimension reduction and clustering:"),
textOutput("summaryText5"),
h5("Cluster Method(s):"),
textOutput("summaryText2"),
h5("Visualization Method(s):"),
textOutput("summaryText3"),
h5("Progression Method(s):"),
textOutput("summaryText4")
),
hr(),
h4("Save results:"),
h5("Outputs to save"),
fluidRow(
column(4,
checkboxInput(inputId = "saveFCS", label = "FCS", value = TRUE)
),
column(4,
checkboxInput(inputId = "saveRData", label = "RData", value = TRUE)
),
column(4,
checkboxInput(inputId = "saveCsv", label = "csv", value = FALSE)
)
),
actionButton("saveButton", "Save Data", icon = icon("download")),
hr(),
h4(tags$a(href="mailto:jinmiao@gmail.com,a0124008@u.nus.edu?subject=[cytofkit-question]",
"Contact Us")),
imageOutput("logo", height = "60px")
),
## main panel--take 3/4 space
column(9,
tabsetPanel(id="main_panel", type = "pills",
tabPanel(title="Cluster Panel", value="C_panel", fluidPage(
hr(),
tabsetPanel(id="C_clusterTabs", type = "tabs",
tabPanel(title="Cluster Plot", value="C_tab1",
br(),
fluidRow(
column(3,
uiOutput("C_PlotMethod")
),
column(3,
uiOutput("C_PlotFunction")
),
column(3,
numericInput("C_PointSize", "Point Size:", value = 1)
),
column(3,
numericInput("C_LabelSize", "Label Size:", value = 12)
)
),
uiOutput("C_clusterSelect"),
hr(),
plotOutput("C_ScatterPlot", width = "100%")
),
tabPanel(title="Change Cluster Color", value="C_tab2",
br(),
wellPanel(
uiOutput("C_colourCluster")
),
hr(),
lapply(1:100, function(i) {
uiOutput(paste0('Cluster_', i, '_col'))
}),
hr(),
fluidRow(
column(3,
actionButton("C_updateClusterColor", "Update Cluster Color",
icon = icon("hand-o-right"), width = "100%")
),
column(3,
actionButton("C_revertClusterColor", "Revert to default",
icon = icon("hand-o-right"), width = "100%")
),
column(6)
),
hr()),
tabPanel(title="Annotate Clusters", value="C_tab3",
br(),
wellPanel(
uiOutput("C_labelCluster"),
uiOutput("C_labelCluster_name")
),
hr(),
lapply(1:100, function(i) {
uiOutput(paste0('Cluster', i))
}),
hr(),
actionButton("updatelabel", "Submit Cluster Label", icon = icon("hand-o-right")),
hr()),
tabPanel(title="Run FlowSOM", value="C_tab4",
br(),
h4("FlowSOM Clustering Setup:"),
hr(),
wellPanel(
numericInput("C_FlowSOM_k", "Cluster k", value = 10, width = "30%"),
uiOutput("C_markerSelect")
),
hr(),
actionButton("C_runFlowSOM", "Run FlowSOM", icon = icon("hand-pointer-o")))
)
)),
tabPanel(title = "Marker Panel", value = "M_panel", fluidPage(
hr(),
tabsetPanel(id="M_markerTabs", type = "tabs",
tabPanel(title="Expression Heat Map", value="M_tab1",
br(),
fluidRow(
column(4,
uiOutput("M_plotCluster")
),
column(2,
selectInput('M_plotMethod', strong('Heatmap Type:'),
choices = c("mean", "median"),
selected = "mean", width = "100%")
),
column(2,
selectInput('M_scaleMethod', strong('Scale Data:'),
choices = c("none", "row", "column"),
selected = "none", width = "100%")
),
column(2,
numericInput("M_rowLabelSize", "Row Label Size:", value = 1, step = 0.5)
),
column(2,
numericInput("M_colLabelSize", "Col Label Size:", value = 1, step = 0.5)
)
),
fluidRow(
column(10,
uiOutput("M_heatmapmarkerSelect")
),
column(2,
actionButton("M_heatmapSelectAll", "All Markers"),
actionButton("M_updateHeatmap", "Update Plot")
)
),
hr(),
plotOutput("M_heatmapPlot", width = "100%")),
tabPanel(title="Expression Level Plot", value="M_tab2",
br(),
fluidRow(
column(3,
uiOutput("M_PlotMethod")
),
column(3,
numericInput("M_PointSize", "Point Size:", value = 1),
sliderInput("M_Alpha", "Transparency:", value = 1, min = 0, max = 1, step = 0.1)
),
column(3,
selectInput('M_colorPalette', label = "Color Palette:",
choices = c("bluered", "spectral1", "spectral2", "heat"),
selected = "bluered", width = "100%")
),
column(3,
selectInput('M_ScaleOptions', label = "Scaling Range:",
choices = c("Local", "Global"),
selected = "Local", width = "100%"),
selectInput('M_scaledData', label = "Centering:",
choices = c("Un-centered", "Centered"),
selected = "Un-centered", width = "100%")
)
),
fluidRow(
column(10,
uiOutput("M_PlotMarker")
),
column(2,
actionButton("M_chooseAllMarker", "All Markers"),
actionButton("M_updateExPlot", "Update Plot")
)
),
hr(),
plotOutput("M_markerExpressionPlot", width = "100%")),
tabPanel(title="Expression Histogram", value="M_tab3",
br(),
fluidRow(
column(4,
uiOutput("M_stackFactor")
),
column(2,
numericInput("M_markerTextSize", "Marker Text Size:",
value = 12, step = 1, min=1, max=15)
),
column(2,
numericInput("M_xlab_size", "x Label Size:",
value = 2, step = 1, min=1, max=10)
),
column(2,
numericInput("M_legendTextSize", "Legend Size:",
value = 1, step = 0.5, min=1, max=10)
),
column(2,
numericInput("M_legendRow", "Legend Row:",
value = 2, step = 1, min=1, max=10)
)
),
fluidRow(
column(10,
uiOutput("M_markerSelect")
),
column(2,
actionButton("M_histSelectAll", "All Markers")
)
),
hr(),
actionButton("M_updateDensityPlot", "Update Plot", icon = icon("hand-pointer-o")),
plotOutput("M_stackDensityPlot", width = "100%")),
tabPanel(title="Update Marker Names", value="M_tab4",
h5('Type in Your New Name for Each Marker:'),
hr(),
lapply(1:100, function(i) {
uiOutput(paste0('Marker_', i, "_name"))
}),
hr(),
actionButton("C_updateMarkerNames", "Update Marker Name", icon = icon("hand-pointer-o")))
)
)),
tabPanel(title = "Sample Panel", value = "S_panel", fluidPage(
hr(),
tabsetPanel(id="S_sampleTabs", type = "tabs",
tabPanel(title="Cell Percentage Heatmap", value="S_tab1",
br(),
fluidRow(
column(4,
uiOutput("S_plotCluster")
),
column(2,
selectInput('S_plotMethod', strong('Heatmap Type:'),
choices = c("percentage"),
selected = "percentage", width = "100%")
),
column(2,
selectInput('S_scaleMethod', strong('Scale Data:'),
choices = c("none", "row", "column"),
selected = "none", width = "100%")
),
column(2,
numericInput("S_rowLabelSize", "Row Label Size:", value = 1, step = 0.5)
),
column(2,
numericInput("S_colLabelSize", "Col Label Size:", value = 1, step = 0.5)
)
),
hr(),
plotOutput("S_heatmapPlot", width = "100%")
),
tabPanel(title="Cell Percentage Line Chart", value="S_tab2",
br(),
uiOutput("S_clusterMethod2"),
uiOutput("S_clusterFilter"),
hr(),
plotOutput("S_rateChangePlot", width = "100%")
),
tabPanel(title="Regroup Samples", value="S_tab3",
br(),
h4("Type in the Group Name for Each Sample:"),
lapply(1:100, function(i) {
uiOutput(paste0('S_sample', i))
}),
hr(),
textInput("sampleGroupLevels", "Group Name Levels: (to order the group names)",
value = "", width = "100%",
placeholder = "Type in group names in order, seperated by semicolon(;)"),
hr(),
fluidRow(
column(3,
actionButton("updateSampleGroups", "Submit New Sample Groups", icon = icon("hand-o-right"))
),
column(3,
actionButton("revertSampleNames", "Revert to Old Sample Names", icon = icon("hand-o-right"))
),
column(6)
),
hr())
)
)),
tabPanel(title="Progression Panel", value = "P_panel", fluidPage(
hr(),
tabsetPanel(id="P_progressionTabs", type = "tabs",
tabPanel(title="Subset Relationship Plot", value="P_tab1",
br(),
fluidRow(
column(3,
uiOutput("P_xlab")
),
column(3,
uiOutput("P_ylab")
),
column(3,
numericInput("P_PointSize", "Point Size:", value = 3)
),
column(3,
numericInput("P_LabelSize", "Label Size:", value = 8)
)
),
plotOutput("P_scatterPlot", width = "80%")),
tabPanel(title="Marker Expression Profile", value="P_tab2",
br(),
fluidRow(
column(3,
uiOutput("P_orderBy")
),
column(2,
numericInput("P_LabelSize2", "Label Size:", value = 5)
),
column(7,
uiOutput("P_clusterSelect")
)
),
hr(),
uiOutput("P_markerSelect"),
hr(),
fluidRow(
column(3,
actionButton("P_updateRegressionPlot", "Update Plot", icon = icon("hand-pointer-o"))
),
column(2,
checkboxInput("P_reverseOrder", label = "Reverse Order", value = FALSE)
),
column(3,
checkboxInput("P_combineTrends", label = "Combine Trend Lines", value = FALSE)
),
column(4)
),
plotOutput("P_markerPlot", width = "100%")),
tabPanel(title="Run Diffusion Map", value="P_tab3",
br(),
h4("Diffusionmap Setup:"),
wellPanel(
h5("Cluster-based down-sampling to remove subset aboundance heterogeneity"),
fluidRow(
column(4,
uiOutput("P_clusterMethod")
),
column(4,
numericInput("P_clusterSampleSize", "Cluster Sample Size", value = 500,
min = 10, max = 1000, step = 5, width = "100%")
),
column(4,
selectInput('P_sampleMethod', 'Downsample Method:', choices = c("ceil", "all", "fixed", "min"),
selected = "ceil", width = "100%")
)
),
tableOutput('P_clusterTable'),
uiOutput("P_clusterFilter"),
hr(),
h5("Diffusionmap Parameters"),
fluidRow(
column(6,
selectInput('P_distMethod', 'Distance calculation Method:', choices = c("euclidean"),
selected = "euclidean", width = "100%")
),
column(6,
numericInput("P_outDim", "Output Dimensionality:", value = 4,
min = 1, max = 6, step = 1, width = "100%")
)
)
),
hr(),
actionButton("P_runDiffusionmap", "Run Diffusionmap", icon = icon("hand-pointer-o")))
)
))
)
)
)
))
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