geex/ui.R
In zhezhangsh/awsomics:
#####################
####### GeEx ########
#####################
print("loading UI");
print(system.time(source("/zhangz/awsomics/geex/preload.R")));
shinyUI(fluidPage(
tags$head(includeScript("google-analytics.js")),
navbarPage(
id="GeEx", collapsible = TRUE, title='GeEx',
############################################################################
################################ "Home" tab ################################
tabPanel(
"Home", htmlOutput('home.title'), hr(),
htmlOutput('home.message'), br(),
DT::dataTableOutput('home.table')
),
###############################################################################
################################ "Data" menu ##################################
{
navbarMenu(
"Data",
####################
############################################################################
############################# "Metadata" tab ###############################
tabPanel(
"Metadata", htmlOutput('meta.title'), br(),
wellPanel(h4("Select metadata table"), selectInput("meta.options", NULL, c(), width='150px')),
htmlOutput('meta.message'), br(),
DT::dataTableOutput('meta.table'), br(), br(),
wellPanel(htmlOutput('meta.detail'))
), # end of tabPanel
############################################################################
############################# "Data set" tab ###############################
tabPanel(
"Data set summary", htmlOutput('expr.title'), br(),
wellPanel(fluidRow(
column(3, wellPanel(
selectizeInput("expr.dataset", "Select data set", c(), width='100%'),
checkboxGroupInput("expr.group", label='Select group(s)', choices=c()),
checkboxGroupInput("expr.species", label='Select species', choices=c()),
selectizeInput("expr.scale", label='Select data scale', choices=c('logged', 'unlogged', 'percentile'),
selected='logged', width='80%'))),
column(3, wellPanel(
h5('Select table column(s)'),
checkboxGroupInput('expr.column', NULL, choice=expr_columns, selected=expr_columns[1], inline=FALSE),
checkboxGroupInput('expr.desc', h5('-Descriptive statistics'), choices=GetRowStatTypes(),
selected=GetRowStatTypes(), inline=TRUE),
checkboxGroupInput('expr.anno', h5('-Gene annotation'), choices=expr_anno_columns,
selected=expr_anno_columns[c(1, length(expr_anno_columns))], inline=TRUE), br(),
checkboxInput('expr.select.all', HTML(geex.html.msg('Select all')), FALSE))),
column(6, wellPanel(h5('Select gene subset(s)'),
fluidRow(
column(4, selectizeInput("expr.gs.source", "Source", names(geneset),
selected=names(geneset)[1])),
column(4, selectizeInput("expr.gs.coll", "Collection", names(geneset[[1]]),
selected=names(geneset[[1]])[1])),
column(4, selectizeInput("expr.gs.species", "Species", names(geneset[[1]][[1]]),
selected=names(geneset[[1]][[1]])[1])),
DT::dataTableOutput('expr.gs.table', width='100%'),
actionButton("expr.gs.clear", 'Clear selection')))))),
htmlOutput('expr.message'),
DT::dataTableOutput('expr.table')
), # end of tabPanel
############################################################################
############################# "Gene summary" tab ###########################
tabPanel(
"Gene summary", htmlOutput('gene.title'), br(),
wellPanel(
h4("Select the gene to show"),
fluidRow(column(2, checkboxInput('gene.filter', HTML(geex.html.msg('Filter by gene set')), value=FALSE)),
column(10, uiOutput("gene.ui"))),
wellPanel(DT::dataTableOutput('gene.table'))),
htmlOutput('gene.message'), br(),
DT::dataTableOutput('gene.stat.table')
), # end of tabPanel
############################################################################
############################# "Gene-data set " tab #########################
tabPanel(
"Gene-data set", htmlOutput('comb.title'), br(),
wellPanel(
fluidRow(column(2, checkboxInput('comb.filter', HTML(geex.html.msg('Filter by gene set')), value=FALSE)),
column(10, uiOutput("comb.ui"))), br(),
fluidRow(
column(4, wellPanel(
fluidRow(column(5, h5('Select species')),
column(6, selectizeInput("comb.species", NULL, choices='human'))),
fluidRow(column(5, h5('Select data scale')),
column(6, selectizeInput("comb.scale", NULL, choices=c('logged', 'unlogged', 'percentile'),
selected='percentile'))))),
column(4, wellPanel(
checkboxGroupInput('comb.desc', 'Select descriptive statistics', choices=GetRowStatTypes(),
selected=GetRowStatTypes()[1:(length(GetRowStatTypes())-1)], inline=TRUE))),
column(4, wellPanel(
checkboxGroupInput('comb.anno', 'Select gene annotation', choices=expr_anno_columns,
selected=expr_anno_columns[1], inline=TRUE))))),
DT::dataTableOutput('comb.table')
) # end of tabPanel
) # end of navbarMenu
},
########################################################################################
################################ "Visualization" menu ##################################
{
####################
navbarMenu(
"Visualization",
####################
#######################################################################
############################# "PCA" tab ###############################
tabPanel(
"Principal components analysis", htmlOutput('pca.title'), hr(),
fluidRow(
column(8,
wellPanel( fluidRow (
column(4, wellPanel(
h5("Select principal components"),
column(6, selectizeInput("pca.x", NULL, c())),
column(6, selectizeInput("pca.y", NULL, c())),
h5("Select color range"),
selectizeInput("pca.color", NULL, GetColorTypes()))),
column(4, wellPanel(selectizeInput("pca.dataset", "Select data set", c(), width='100%'))),
column(4, wellPanel(checkboxGroupInput("pca.group", label='Select group(s)', choices=c()))))),
htmlOutput('pca.message'), br(),
plotOutput('pca.plot')),
column(4,
wellPanel(
h4('Select gene subset(s) to re-run PCA'),
column(3, h5("Source")),
column(8, selectizeInput("pca.geneset.source", NULL, names(geneset), selected=names(geneset)[1],
options=list('caption-side'='bottom'))),
column(3, h5("Collection")),
column(8, selectizeInput("pca.geneset.coll", NULL, names(geneset[[1]]),
selected=names(geneset[[1]])[1])),
column(3, h5("Species")),
column(8, selectizeInput("pca.geneset.species", NULL, names(geneset[[1]][[1]]),
selected=names(geneset[[1]][[1]])[1])),
DT::dataTableOutput('pca.geneset.table', width='100%'),
actionButton("pca.geneset.clear", 'Clear selection')),
wellPanel(
h5('Select sample(s) to highlight'),
DT::dataTableOutput('pca.table'),
actionButton("pca.clear", 'Clear selection'))))
), # end of tabPanel
##############################################################################
############################# "Barplot" tab ##################################
tabPanel(
"Single gene expression", htmlOutput('bar.title'), hr(),
fluidRow(
column(8,
wellPanel(fluidRow(
column(4, wellPanel(
selectizeInput("bar.scale", "Select data scale", c('logged', 'unlogged', 'percentile')),
selectizeInput("bar.color", "Select color range", GetColorTypes()))),
column(4, wellPanel(
selectizeInput("bar.dataset", "Select data set", c(), width='100%'),
uiOutput('bar.dataset.message'))),
column(4, wellPanel(
checkboxGroupInput("bar.group", label='Select group(s)', choices=c()),
checkboxInput("bar.mean", HTML(geex.html.msg("Plot group mean"))))))),
htmlOutput('bar.message'),
plotOutput('bar.plot', width='100%'),
DT::dataTableOutput('bar.stat'), br()),
column(4,
wellPanel(
h3('Select gene(s)'),
uiOutput('bar.table.message'),
DT::dataTableOutput('bar.table'),
actionButton("bar.clear", 'Clear selection'),
fluidRow(
column(6,
checkboxInput('lookup.option', HTML(geex.html.msg("Look up gene in dictionary")), FALSE),
uiOutput("lookup.key.ui"),
uiOutput("lookup.species.ui")
),
column(6, uiOutput("lookup.table.ui")
)))))
), # end of tabPanel
##############################################################################
############################### "Gene set" tab ###############################
tabPanel(
"Gene set expression", htmlOutput('geneset.title'), hr(),
fluidRow(
column(8, wellPanel( fluidRow(
column(4, wellPanel(
h4("Select plot"),
fluidRow(column(4, h5("Plot\ntype")),
column(8, selectizeInput("geneset.type", NULL, PlotMatrixGroupTypes()))),
fluidRow(column(4, h5("Data\nscale")),
column(8, selectizeInput("geneset.scale", NULL, c('logged', 'unlogged', 'percentile')))),
fluidRow(column(4, h5("Color\nrange")),
column(8, selectizeInput("geneset.color", NULL, GetColorTypes()))))),
column(4, wellPanel(
h4("Select data set"),
selectizeInput("geneset.dataset", NULL, c(), width='100%'),
checkboxInput("geneset.normalize", HTML(geex.html.msg("Normalize across samples")), TRUE))),
column(4, wellPanel( h4('Select group(s)'),
checkboxGroupInput("geneset.group", NULL, label=, choices=c())))),
column(12, br(), htmlOutput('geneset.message')),
column(12, plotOutput('geneset.plot', width='640px', height='640px')))),
column(4,
wellPanel(
h4('Select one gene set'),
column(3, h5("Source")),
column(8, selectizeInput("geneset.source", NULL, names(geneset), selected=names(geneset)[1],
options=list('caption-side'='bottom'))),
column(3, h5("Collection")),
column(8, selectizeInput("geneset.coll", NULL, names(geneset[[1]]),
selected=names(geneset[[1]])[1])),
column(3, h5("Species")),
column(8, selectizeInput("geneset.species", NULL, names(geneset[[1]][[1]]),
selected=names(geneset[[1]][[1]])[1])),
DT::dataTableOutput('geneset.table', width='100%'),
actionButton("geneset.clear", 'Clear selection'))))
), # end of tabPanel
##############################################################################
############################# "Compare" tab ###############################
tabPanel(
"Differential expression", htmlOutput('two.title'), hr(),
fluidRow(
column(8, wellPanel( fluidRow(
column(4, wellPanel(
h4("Select plot"),
fluidRow(column(4, h5("Plot\ntype")),
column(8, selectizeInput("two.type", NULL, PlotPairDiffTypes()))),
fluidRow(column(4, h5("Data\nscale")),
column(8, selectizeInput("two.scale", NULL, c('logged', 'unlogged', 'percentile')))),
fluidRow(column(4, h5("Color\nrange")),
column(8, selectizeInput("two.color", NULL, GetColorTypes()))),
fluidRow(column(4, h5("Use\nspecies")),
column(8, selectizeInput("two.select.species", NULL, c()))))),
column(4, wellPanel(
h4('Select X-axis'),
selectizeInput("x.dataset", "Data set", c(), width='100%'),
selectizeInput("x.group", "Sample group", c(), width='100%'),
selectizeInput("x.sample", "Single sample", c(), width='100%'))),
column(4, wellPanel(
h4('Select Y-axis'),
selectizeInput("y.dataset", "Data set", c(), width='100%'),
selectizeInput("y.group", "Sample group", c(), width='100%'),
selectizeInput("y.sample", "Single sample", c(), width='100%'))))),
column(12, htmlOutput('two.message')),
column(12, plotOutput('two.plot', width='640px', height='640px')),
column(12, wellPanel(DT::dataTableOutput('two.geneset.stat', width='90%')))),
column(4,
wellPanel(
h4('Highlight gene(s)'),
DT::dataTableOutput('two.table', width='100%'),
actionButton("two.clear", 'Clear selection')),
wellPanel(
h4('Highlight gene set(s)'),
column(3, h5("Source")),
column(8, selectizeInput("two.source", NULL, names(geneset),
selected=names(geneset)[1], options=list('caption-side'='bottom'))),
column(3, h5("Collection")),
column(8, selectizeInput("two.coll", NULL, names(geneset[[1]]),
selected=names(geneset[[1]])[1])),
column(3, h5("Species")),
column(8, selectizeInput("two.species", NULL, names(geneset[[1]][[1]]),
selected=names(geneset[[1]][[1]])[1])),
DT::dataTableOutput('two.table.geneset', width='100%'),
actionButton("two.clear.geneset", 'Clear selection'))))
), # end of tabPanel
############################################################################
############################# "Coexpression" tab ###########################
tabPanel(
"Two gene coexpression", htmlOutput('coex.title'), br(),
fluidRow(
column(8,
wellPanel( fluidRow(
column(4, wellPanel(
selectizeInput('coex.type', 'Select plot unit', rev(data.level.options), width='60%'),
selectizeInput("coex.scale", 'Select data scale', c('logged', 'unlogged', 'percentile'), width='60%'),
selectizeInput("coex.color", 'Select color range', GetColorTypes(), width='60%'),
fluidRow(
column(4,
checkboxInput('coex.lookup.option', HTML(geex.html.msg("Look up gene in dictionary")), FALSE),
uiOutput("coex.lookup.key.ui"),
uiOutput("coex.lookup.species.ui")
), column(8, uiOutput("coex.lookup.table.ui")))
)),
column(4, wellPanel(h4("Select gene 1"), DT::dataTableOutput('coex.gene1', width='100%'))),
column(4, wellPanel(h4("Select gene 2"), DT::dataTableOutput('coex.gene2', width='100%'))))),
column(12, fluidRow(
column(12, htmlOutput('coex.message')),
column(12, plotOutput('coex.plot', width='640px', height='640px'))))),
column(4, wellPanel(
h4("Highlight data set(s)"),
DT::dataTableOutput('coex.dataset', width='100%'),
actionButton('coex.clear.ds', 'Clear selection')))))
#####################################################################################################
#####################################################################################################
) # end of navbarMenu
},
########################################################################################
################################ "Advance" menu ########################################
{
####################
navbarMenu(
"Advance",
####################
############################################################################
############################# "Filter genes" tab ###########################
tabPanel(
"Filter genes", htmlOutput('filter.title'), br(),
wellPanel(
fluidRow(
column(6, wellPanel(
h3('Specify comparison'),
selectizeInput('filter.dataset', 'Select data set vs. other data sets', c(), width='75%'),
selectizeInput('filter.group', 'Select group vs. other groups in the same data set', c(), width='75%'),
selectizeInput('filter.sample', 'Select sample vs. other samples in the same data set', c(), width='75%')
)),
column(6, wellPanel(
h3('Specify cutoffs'),
sliderInput('filter.absolute', 'Range of absolute expression level in percentile', 0, 100, c(0, 100), 1),
sliderInput('filter.relative', 'Range of relative difference in percentile', 0, 100, c(0, 100), 1),
radioButtons('filter.direction', NULL, c('Higher', 'Lower'), inline=TRUE)
))
)),
htmlOutput('filter.msg'),
DT::dataTableOutput('filter.table')
),
############################################################################
############################# "Re-group" tab ###############################
tabPanel(
"Re-group samples", htmlOutput('regroup.title'), br(),
wellPanel(checkboxInput('regroup.check', 'Check box to activate sample re-grouping', FALSE)),
fluidRow(
column(6,
htmlOutput('regroup.ds.msg'),
DT::dataTableOutput('regroup.ds.tbl')),
column(6, wellPanel(
h4("Step 1: select sample feature(s) to define data set"),
DT::dataTableOutput('regroup.dataset'),
actionButton('regroup.clear.ds', 'Clear selection')))),
hr(),
fluidRow(
column(6,
htmlOutput('regroup.grp.msg'),
DT::dataTableOutput('regroup.grp.tbl')),
column(6, wellPanel(
h4("Step 2: select sample feature(s) to define group"),
DT::dataTableOutput('regroup.group'),
actionButton('regroup.clear.grp', 'Clear selection'))))
),
############################################################################
############################# "User data" tab ##############################
tabPanel("Upload user data", htmlOutput('upload.title')))
},
##############################################################################
################################# "About" tab ################################
# "About" tab
tab.home<-tabPanel("About", id = 'tab.home',
wellPanel(style = "background-color: #ffffff;", includeMarkdown('./intro.Rmd')))
) # end of navbarPage
)) # end of shinyUI
zhezhangsh/awsomics documentation built on May 4, 2019, 11:20 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#####################
####### GeEx ########
#####################
print("loading UI");
print(system.time(source("/zhangz/awsomics/geex/preload.R")));
shinyUI(fluidPage(
tags$head(includeScript("google-analytics.js")),
navbarPage(
id="GeEx", collapsible = TRUE, title='GeEx',
############################################################################
################################ "Home" tab ################################
tabPanel(
"Home", htmlOutput('home.title'), hr(),
htmlOutput('home.message'), br(),
DT::dataTableOutput('home.table')
),
###############################################################################
################################ "Data" menu ##################################
{
navbarMenu(
"Data",
####################
############################################################################
############################# "Metadata" tab ###############################
tabPanel(
"Metadata", htmlOutput('meta.title'), br(),
wellPanel(h4("Select metadata table"), selectInput("meta.options", NULL, c(), width='150px')),
htmlOutput('meta.message'), br(),
DT::dataTableOutput('meta.table'), br(), br(),
wellPanel(htmlOutput('meta.detail'))
), # end of tabPanel
############################################################################
############################# "Data set" tab ###############################
tabPanel(
"Data set summary", htmlOutput('expr.title'), br(),
wellPanel(fluidRow(
column(3, wellPanel(
selectizeInput("expr.dataset", "Select data set", c(), width='100%'),
checkboxGroupInput("expr.group", label='Select group(s)', choices=c()),
checkboxGroupInput("expr.species", label='Select species', choices=c()),
selectizeInput("expr.scale", label='Select data scale', choices=c('logged', 'unlogged', 'percentile'),
selected='logged', width='80%'))),
column(3, wellPanel(
h5('Select table column(s)'),
checkboxGroupInput('expr.column', NULL, choice=expr_columns, selected=expr_columns[1], inline=FALSE),
checkboxGroupInput('expr.desc', h5('-Descriptive statistics'), choices=GetRowStatTypes(),
selected=GetRowStatTypes(), inline=TRUE),
checkboxGroupInput('expr.anno', h5('-Gene annotation'), choices=expr_anno_columns,
selected=expr_anno_columns[c(1, length(expr_anno_columns))], inline=TRUE), br(),
checkboxInput('expr.select.all', HTML(geex.html.msg('Select all')), FALSE))),
column(6, wellPanel(h5('Select gene subset(s)'),
fluidRow(
column(4, selectizeInput("expr.gs.source", "Source", names(geneset),
selected=names(geneset)[1])),
column(4, selectizeInput("expr.gs.coll", "Collection", names(geneset[[1]]),
selected=names(geneset[[1]])[1])),
column(4, selectizeInput("expr.gs.species", "Species", names(geneset[[1]][[1]]),
selected=names(geneset[[1]][[1]])[1])),
DT::dataTableOutput('expr.gs.table', width='100%'),
actionButton("expr.gs.clear", 'Clear selection')))))),
htmlOutput('expr.message'),
DT::dataTableOutput('expr.table')
), # end of tabPanel
############################################################################
############################# "Gene summary" tab ###########################
tabPanel(
"Gene summary", htmlOutput('gene.title'), br(),
wellPanel(
h4("Select the gene to show"),
fluidRow(column(2, checkboxInput('gene.filter', HTML(geex.html.msg('Filter by gene set')), value=FALSE)),
column(10, uiOutput("gene.ui"))),
wellPanel(DT::dataTableOutput('gene.table'))),
htmlOutput('gene.message'), br(),
DT::dataTableOutput('gene.stat.table')
), # end of tabPanel
############################################################################
############################# "Gene-data set " tab #########################
tabPanel(
"Gene-data set", htmlOutput('comb.title'), br(),
wellPanel(
fluidRow(column(2, checkboxInput('comb.filter', HTML(geex.html.msg('Filter by gene set')), value=FALSE)),
column(10, uiOutput("comb.ui"))), br(),
fluidRow(
column(4, wellPanel(
fluidRow(column(5, h5('Select species')),
column(6, selectizeInput("comb.species", NULL, choices='human'))),
fluidRow(column(5, h5('Select data scale')),
column(6, selectizeInput("comb.scale", NULL, choices=c('logged', 'unlogged', 'percentile'),
selected='percentile'))))),
column(4, wellPanel(
checkboxGroupInput('comb.desc', 'Select descriptive statistics', choices=GetRowStatTypes(),
selected=GetRowStatTypes()[1:(length(GetRowStatTypes())-1)], inline=TRUE))),
column(4, wellPanel(
checkboxGroupInput('comb.anno', 'Select gene annotation', choices=expr_anno_columns,
selected=expr_anno_columns[1], inline=TRUE))))),
DT::dataTableOutput('comb.table')
) # end of tabPanel
) # end of navbarMenu
},
########################################################################################
################################ "Visualization" menu ##################################
{
####################
navbarMenu(
"Visualization",
####################
#######################################################################
############################# "PCA" tab ###############################
tabPanel(
"Principal components analysis", htmlOutput('pca.title'), hr(),
fluidRow(
column(8,
wellPanel( fluidRow (
column(4, wellPanel(
h5("Select principal components"),
column(6, selectizeInput("pca.x", NULL, c())),
column(6, selectizeInput("pca.y", NULL, c())),
h5("Select color range"),
selectizeInput("pca.color", NULL, GetColorTypes()))),
column(4, wellPanel(selectizeInput("pca.dataset", "Select data set", c(), width='100%'))),
column(4, wellPanel(checkboxGroupInput("pca.group", label='Select group(s)', choices=c()))))),
htmlOutput('pca.message'), br(),
plotOutput('pca.plot')),
column(4,
wellPanel(
h4('Select gene subset(s) to re-run PCA'),
column(3, h5("Source")),
column(8, selectizeInput("pca.geneset.source", NULL, names(geneset), selected=names(geneset)[1],
options=list('caption-side'='bottom'))),
column(3, h5("Collection")),
column(8, selectizeInput("pca.geneset.coll", NULL, names(geneset[[1]]),
selected=names(geneset[[1]])[1])),
column(3, h5("Species")),
column(8, selectizeInput("pca.geneset.species", NULL, names(geneset[[1]][[1]]),
selected=names(geneset[[1]][[1]])[1])),
DT::dataTableOutput('pca.geneset.table', width='100%'),
actionButton("pca.geneset.clear", 'Clear selection')),
wellPanel(
h5('Select sample(s) to highlight'),
DT::dataTableOutput('pca.table'),
actionButton("pca.clear", 'Clear selection'))))
), # end of tabPanel
##############################################################################
############################# "Barplot" tab ##################################
tabPanel(
"Single gene expression", htmlOutput('bar.title'), hr(),
fluidRow(
column(8,
wellPanel(fluidRow(
column(4, wellPanel(
selectizeInput("bar.scale", "Select data scale", c('logged', 'unlogged', 'percentile')),
selectizeInput("bar.color", "Select color range", GetColorTypes()))),
column(4, wellPanel(
selectizeInput("bar.dataset", "Select data set", c(), width='100%'),
uiOutput('bar.dataset.message'))),
column(4, wellPanel(
checkboxGroupInput("bar.group", label='Select group(s)', choices=c()),
checkboxInput("bar.mean", HTML(geex.html.msg("Plot group mean"))))))),
htmlOutput('bar.message'),
plotOutput('bar.plot', width='100%'),
DT::dataTableOutput('bar.stat'), br()),
column(4,
wellPanel(
h3('Select gene(s)'),
uiOutput('bar.table.message'),
DT::dataTableOutput('bar.table'),
actionButton("bar.clear", 'Clear selection'),
fluidRow(
column(6,
checkboxInput('lookup.option', HTML(geex.html.msg("Look up gene in dictionary")), FALSE),
uiOutput("lookup.key.ui"),
uiOutput("lookup.species.ui")
),
column(6, uiOutput("lookup.table.ui")
)))))
), # end of tabPanel
##############################################################################
############################### "Gene set" tab ###############################
tabPanel(
"Gene set expression", htmlOutput('geneset.title'), hr(),
fluidRow(
column(8, wellPanel( fluidRow(
column(4, wellPanel(
h4("Select plot"),
fluidRow(column(4, h5("Plot\ntype")),
column(8, selectizeInput("geneset.type", NULL, PlotMatrixGroupTypes()))),
fluidRow(column(4, h5("Data\nscale")),
column(8, selectizeInput("geneset.scale", NULL, c('logged', 'unlogged', 'percentile')))),
fluidRow(column(4, h5("Color\nrange")),
column(8, selectizeInput("geneset.color", NULL, GetColorTypes()))))),
column(4, wellPanel(
h4("Select data set"),
selectizeInput("geneset.dataset", NULL, c(), width='100%'),
checkboxInput("geneset.normalize", HTML(geex.html.msg("Normalize across samples")), TRUE))),
column(4, wellPanel( h4('Select group(s)'),
checkboxGroupInput("geneset.group", NULL, label=, choices=c())))),
column(12, br(), htmlOutput('geneset.message')),
column(12, plotOutput('geneset.plot', width='640px', height='640px')))),
column(4,
wellPanel(
h4('Select one gene set'),
column(3, h5("Source")),
column(8, selectizeInput("geneset.source", NULL, names(geneset), selected=names(geneset)[1],
options=list('caption-side'='bottom'))),
column(3, h5("Collection")),
column(8, selectizeInput("geneset.coll", NULL, names(geneset[[1]]),
selected=names(geneset[[1]])[1])),
column(3, h5("Species")),
column(8, selectizeInput("geneset.species", NULL, names(geneset[[1]][[1]]),
selected=names(geneset[[1]][[1]])[1])),
DT::dataTableOutput('geneset.table', width='100%'),
actionButton("geneset.clear", 'Clear selection'))))
), # end of tabPanel
##############################################################################
############################# "Compare" tab ###############################
tabPanel(
"Differential expression", htmlOutput('two.title'), hr(),
fluidRow(
column(8, wellPanel( fluidRow(
column(4, wellPanel(
h4("Select plot"),
fluidRow(column(4, h5("Plot\ntype")),
column(8, selectizeInput("two.type", NULL, PlotPairDiffTypes()))),
fluidRow(column(4, h5("Data\nscale")),
column(8, selectizeInput("two.scale", NULL, c('logged', 'unlogged', 'percentile')))),
fluidRow(column(4, h5("Color\nrange")),
column(8, selectizeInput("two.color", NULL, GetColorTypes()))),
fluidRow(column(4, h5("Use\nspecies")),
column(8, selectizeInput("two.select.species", NULL, c()))))),
column(4, wellPanel(
h4('Select X-axis'),
selectizeInput("x.dataset", "Data set", c(), width='100%'),
selectizeInput("x.group", "Sample group", c(), width='100%'),
selectizeInput("x.sample", "Single sample", c(), width='100%'))),
column(4, wellPanel(
h4('Select Y-axis'),
selectizeInput("y.dataset", "Data set", c(), width='100%'),
selectizeInput("y.group", "Sample group", c(), width='100%'),
selectizeInput("y.sample", "Single sample", c(), width='100%'))))),
column(12, htmlOutput('two.message')),
column(12, plotOutput('two.plot', width='640px', height='640px')),
column(12, wellPanel(DT::dataTableOutput('two.geneset.stat', width='90%')))),
column(4,
wellPanel(
h4('Highlight gene(s)'),
DT::dataTableOutput('two.table', width='100%'),
actionButton("two.clear", 'Clear selection')),
wellPanel(
h4('Highlight gene set(s)'),
column(3, h5("Source")),
column(8, selectizeInput("two.source", NULL, names(geneset),
selected=names(geneset)[1], options=list('caption-side'='bottom'))),
column(3, h5("Collection")),
column(8, selectizeInput("two.coll", NULL, names(geneset[[1]]),
selected=names(geneset[[1]])[1])),
column(3, h5("Species")),
column(8, selectizeInput("two.species", NULL, names(geneset[[1]][[1]]),
selected=names(geneset[[1]][[1]])[1])),
DT::dataTableOutput('two.table.geneset', width='100%'),
actionButton("two.clear.geneset", 'Clear selection'))))
), # end of tabPanel
############################################################################
############################# "Coexpression" tab ###########################
tabPanel(
"Two gene coexpression", htmlOutput('coex.title'), br(),
fluidRow(
column(8,
wellPanel( fluidRow(
column(4, wellPanel(
selectizeInput('coex.type', 'Select plot unit', rev(data.level.options), width='60%'),
selectizeInput("coex.scale", 'Select data scale', c('logged', 'unlogged', 'percentile'), width='60%'),
selectizeInput("coex.color", 'Select color range', GetColorTypes(), width='60%'),
fluidRow(
column(4,
checkboxInput('coex.lookup.option', HTML(geex.html.msg("Look up gene in dictionary")), FALSE),
uiOutput("coex.lookup.key.ui"),
uiOutput("coex.lookup.species.ui")
), column(8, uiOutput("coex.lookup.table.ui")))
)),
column(4, wellPanel(h4("Select gene 1"), DT::dataTableOutput('coex.gene1', width='100%'))),
column(4, wellPanel(h4("Select gene 2"), DT::dataTableOutput('coex.gene2', width='100%'))))),
column(12, fluidRow(
column(12, htmlOutput('coex.message')),
column(12, plotOutput('coex.plot', width='640px', height='640px'))))),
column(4, wellPanel(
h4("Highlight data set(s)"),
DT::dataTableOutput('coex.dataset', width='100%'),
actionButton('coex.clear.ds', 'Clear selection')))))
#####################################################################################################
#####################################################################################################
) # end of navbarMenu
},
########################################################################################
################################ "Advance" menu ########################################
{
####################
navbarMenu(
"Advance",
####################
############################################################################
############################# "Filter genes" tab ###########################
tabPanel(
"Filter genes", htmlOutput('filter.title'), br(),
wellPanel(
fluidRow(
column(6, wellPanel(
h3('Specify comparison'),
selectizeInput('filter.dataset', 'Select data set vs. other data sets', c(), width='75%'),
selectizeInput('filter.group', 'Select group vs. other groups in the same data set', c(), width='75%'),
selectizeInput('filter.sample', 'Select sample vs. other samples in the same data set', c(), width='75%')
)),
column(6, wellPanel(
h3('Specify cutoffs'),
sliderInput('filter.absolute', 'Range of absolute expression level in percentile', 0, 100, c(0, 100), 1),
sliderInput('filter.relative', 'Range of relative difference in percentile', 0, 100, c(0, 100), 1),
radioButtons('filter.direction', NULL, c('Higher', 'Lower'), inline=TRUE)
))
)),
htmlOutput('filter.msg'),
DT::dataTableOutput('filter.table')
),
############################################################################
############################# "Re-group" tab ###############################
tabPanel(
"Re-group samples", htmlOutput('regroup.title'), br(),
wellPanel(checkboxInput('regroup.check', 'Check box to activate sample re-grouping', FALSE)),
fluidRow(
column(6,
htmlOutput('regroup.ds.msg'),
DT::dataTableOutput('regroup.ds.tbl')),
column(6, wellPanel(
h4("Step 1: select sample feature(s) to define data set"),
DT::dataTableOutput('regroup.dataset'),
actionButton('regroup.clear.ds', 'Clear selection')))),
hr(),
fluidRow(
column(6,
htmlOutput('regroup.grp.msg'),
DT::dataTableOutput('regroup.grp.tbl')),
column(6, wellPanel(
h4("Step 2: select sample feature(s) to define group"),
DT::dataTableOutput('regroup.group'),
actionButton('regroup.clear.grp', 'Clear selection'))))
),
############################################################################
############################# "User data" tab ##############################
tabPanel("Upload user data", htmlOutput('upload.title')))
},
##############################################################################
################################# "About" tab ################################
# "About" tab
tab.home<-tabPanel("About", id = 'tab.home',
wellPanel(style = "background-color: #ffffff;", includeMarkdown('./intro.Rmd')))
) # end of navbarPage
)) # end of shinyUI
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