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ui.R
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ui.R
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library(shiny)
library(shinyFiles)
library(colourpicker)
#library(gdata)
options(shiny.maxRequestSize=500*1024^3)
# Define UI for slider demo application
shinyUI(pageWithSidebar(
# Application title
headerPanel("Wave-Crest"),
# Sidebar with sliders that demonstrate various available options
sidebarPanel(width=12,height=250,
# file
fileInput("filename", label = "Data file input (support .csv, .txt, .tab)"),
# grouping vector
fileInput("ConditionVector", label = "Condition vector \n file name (e.g. collection time. support .csv, .txt, .tab)"),
# List of key markers
fileInput("Markers", label = "List of marker genes \n file name (support .csv, .txt, .tab)"),
column(4,
# Num permutation
numericInput("Permu",
label = "The number of iteration for 2-opt",
value = 20000),
# Normalization
radioButtons("Norm_buttons",
label = "Do you need to normalize data?",
choices = list("Yes" = 1,
"No" = 2),
selected = 1),
#Log data for input
radioButtons("Log_InData",
label = "Use log data for input into WaveCrest?",
choices = list("Yes" = 1,
"No" = 2),
selected = 1),
# Mean Cutoff
numericInput("Meancut",
label = "Only analyze genes with a mean larger than:",
value = 10),
# Identify additional genes
radioButtons("Iden_buttons",
label = "Identify additional dynamic genes based on the recovered order ('fishing')?",
choices = list("Yes" = 1,
"No" = 2),
selected = 1),
# Identify additional genes
radioButtons("DF_buttons",
label = "What type of trend do you expect?",
choices = list("Linear" = 1,
"Quadratic" = 2,
"Cubic"=3,
"Quartic"=4),
selected = 3),
# set seed
numericInput("Seed",
label = "Set seed (for random number generator)",
value = 1),
# plot log-exp or not
radioButtons("log_whether",
label = "Plot in log scale?",
choices = list("No" = 1,
"log2(expression + 1)" = 2),
selected = 1),
radioButtons("MarkerPlot_buttons",
label = "Plot marker genes following recovered cell order?",
choices = list("Yes" = 1,
"No" = 2),
selected = 1)
),
column(width=4,
radioButtons("AddPlot_buttons",
label = "Plot additional dynamic genes following recovered cell order?",
choices = list("Yes" = 1,
"No" = 2),
selected = 1),
radioButtons("AddTrend_buttons",
label = "Add trendline to dynamic gene plots?",
choices = list("Yes" = 1,
"No" = 2),
selected = 1),
# num genes to plot
textInput("PlotNum",
label = "Number of additional genes to plot (if not specified, top 10 genes will be plotted)",
value = ""),
radioButtons("FlipOrder_buttons",
label = "Reverse the recovered cell order?",
choices = list("Yes" = 1,
"No" = 2),
selected = 2),
radioButtons("AddHeatMap_buttons",
label = "Plot heatmap of marker genes following recovered cell order?",
choices = list("Yes" = 1,
"No" = 2),
selected = 1),
tags$div(tags$b("Select colors for the heatmap :")),
checkboxInput("UseCols", "Use default green to red heatmap ? ", TRUE),
fluidPage(colourInput("col1", "Low values: ", "green")),
fluidPage(colourInput("col2", "Middle values:", "black")),
fluidPage(colourInput("col3", "High values:", "red")),
radioButtons("clusterRow",
label = "Cluster marker genes in heatmap (otherwise use original order) ? ",
choices = list("Yes" = 1,
"No" = 2),
selected = 1)
),
column(4,
# output dir
tags$div(tags$b("Please select a folder for output :")),
shinyDirButton('Outdir', label ='Select Output Folder', title = 'Please select a folder'),
tags$br(),
tags$br(),
# plot name
textInput("InfoFileName",
label = "Export file name - input parameters and version info",
value = "WaveCrest_info"),
# export normalzied matrix (original order)
textInput("exNormFileName",
label = "Export file name - normalized expression matrix (following original cell order)",
value = "normalized"),
# export normalzied matrix (recovered order)
textInput("exENINormFileName",
label = "Export file name - normalized expression matrix (following recovered cell order)",
value = "normalized_ENI"),
# export gene list with p-value (IdenRes)
textInput("exGListFileName",
label = "Export file name - genes sorted by fishing MSE",
value = "genes_by_dynamic"),
# plot name
textInput("exMarkerPlotFileName",
label = "Export file name for the plots? (marker genes following recovered order)",
value = "PlotMarkers"),
# plot name
textInput("exDynamicPlotFileName",
label = "Export file name for the plots? (additional genes following recovered order)",
value = "PlotDynamic"),
# plot name
textInput("exHeatMapPlotFileName",
label = "Export file name for the plots? (heatmap of key markers in recovered order)",
value = "PlotHeatMap")
),
br(),
br(),
actionButton("Submit","Submit for processing")
),
# Show a table summarizing the values entered
mainPanel(
h4(textOutput("print0")),
#tableOutput("values")
dataTableOutput("tab")
)
))