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ui.R
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ui.R
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options(rgl.useNULL = TRUE)
library(shiny)
library(Biobase)
library("RNASeqPower")
library("ComplexHeatmap")
library("circlize")
library("edgeR")
library(shinyjs)
library(shinyBS)
library(shinycssloaders)
library("rgl")
library("rsconnect")
library("shinyRGL")
library(Rtsne)
library("rglwidget")
library("RColorBrewer")
library("pairsD3")
library("data.table")
library("feather")
library("plotly")
library("ggplot2")
library("reshape2")
library(DT)
library("iheatmapr")
source("R/dropdownButton.R", local = TRUE)
shinyUI(
navbarPage(
inverse=TRUE, windowTitle = 'GREIN'
,title= tags$a(href='https://shiny.ilincs.org/grein',target="_blank", tags$img(src='images/logo1c.png', height="40px",width="100px", style='margin: -20px 0px;'))
,id='grin', selected="datasets"
,tabPanel(tags$b('Help'), value='help'
,tags$style(
'.navbar-nav {width: 90%;}
.navbar-nav :first-child{float:right}'
)
,column(1
)
,column(10
,div(style="color:#337ab7; text-align:center;", titlePanel(h2("Step-by-step guide of GREIN"))), br()
,htmlOutput('help_pdf')
)
,column(1
)
)
,tabPanel(tags$b('About'), value='about',
tags$head(
tags$style(type="text/css", "
#loadmessage {
position: fixed;
top: 80px;
left: 0px;
width: 100%;
padding: 5px 0px 5px 0px;
text-align: center;
font-weight: bold;
font-size: 100%;
color: #000000;
background-color: #DDDDDD;
z-index: 105;
}
.js-irs-3 .irs-grid-text{
display:none;
}
/* basic positioning */
.legend { list-style: none; }
.legend li { float: left; margin-right: 10px; }
.legend span { border: 1px solid #ccc; float: left; width: 12px; height: 12px; margin: 2px; }
")
,tags$script('window.onbeforeunload = function() { return "Please use the button on the webpage"; };')
,tags$link(rel = "icon", type = "image/ico", href = "images/grein_favicon.ico")
,tags$style(type="text/css",
".shiny-output-error { visibility: hidden; }",
".shiny-output-error:before { visibility: hidden; }")
,tags$link(href="css/chardinjs.css",rel="stylesheet")
,tags$link(href="css/ilincs.css",rel="stylesheet")
)
,useShinyjs()
,column(1
)
,column(10,
wellPanel(
includeMarkdown("www/description1.Rmd")
)
)
,column(1
)
,includeHTML("www/html/footer.html")
),
tabPanel(tags$b('GEO datasets'), value='datasets'
,includeMarkdown("www/title.Rmd")
,div(style="height:2px;border-width:0;color:gray;background-color:gray", hr())
,column(4, offset=0, style='padding:0px 20px 0px 0px;'
,tags$br()
,plotlyOutput("samplesize_den", width = "auto", height = "300px") %>% withSpinner(type=5), br()
)
,column(4, offset=0, style='padding:10px 0px 0px 10px;'
,br()
, plotlyOutput("study_stat", width = "auto", height = "300px") %>% withSpinner(type=5), br()
)
,column(4, offset=0, style='padding:10px 20px 0px 0px;'
,tags$br()
,plotlyOutput("sample_stat", width = "auto", height = "300px") %>% withSpinner(type=5), br()
)
,column(12, offset=0, style='padding:0px;'
,div(style="height:2px;border-width:0;color:gray;background-color:gray", hr())
,div(style="color:#337ab7;", titlePanel(""))
)
,column(4, offset=0, style='padding:0px;'
,tags$br()
,div(style="display: inline-block;vertical-align:right; ",h4('Search for GEO series (GSE) accession'))
,div(style="display: inline-block;vertical-align:right;", bsButton("user_geo_bs", label = "", icon = icon("info-circle"),style="", size = "medium"))
,bsPopover(id = "user_geo_bs", title = "",
content = paste0("Please type your GEO accession id (e.g., GSE46597) in this box to see if the dataset is already processed. If not, you can initialize the processing of the data. The dataset will be processed and uploaded soon."),
placement = "right", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#user_geo_bs {background-color: white; border:none;}')
,div(style="display: inline-block;vertical-align:right;line-height:0px;",textInput('user_geo', '', width='340px'))
,div(style="width:400px;", verbatimTextOutput("warn"))
,div(style="width:400px;",verbatimTextOutput("warn2"))
,div(style="width:400px;",verbatimTextOutput("warn3"))
,div(style="width:400px;",verbatimTextOutput("warn4"))
,div(style="width:400px;",verbatimTextOutput("warn5"))
,tags$style(type='text/css', '#warn {color: red; font-size:15px;}')
,tags$style(type='text/css', '#warn2 {color: red; font-size:15px;}')
,tags$style(type='text/css', '#warn3 {color: red; font-size:15px;}')
,tags$style(type='text/css', '#warn4 {color: red; font-size:15px;}')
,tags$style(type='text/css', '#warn5 {color: red; font-size:15px;}')
,div(style="display: ;vertical-align:bottom;", shinyjs::hidden(actionButton("start_process","Start processing", icon("refresh"),
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")))
,tags$style(type='text/css', "label {font-size: 18px;}")
)
,column(4, offset=0, style='padding:0px;'
,tags$br()
,div(style="display: inline-block;vertical-align:right; ",h4('Search by ontologies', tags$a(href='http://metasra.biostat.wisc.edu/',target="_blank","(MetaSRA)", style="color: #337ab7")))
,bsPopover(id = "sample_ont_ser_bs", title = "",
content = paste0("Search by ontological annotations of samples and datasets provided by MetaSRA project."),
placement = "right", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#sample_ont_ser_bs {background-color: white; border:none;}')
,div(style="display: inline-block;vertical-align:right;", bsButton("sample_ont_ser_bs", label = "", icon = icon("info-circle"),style="", size = "medium"))
,div(style="display: inline-block;vertical-align:right;line-height:0px;",textInput('sample_ont_ser', '', width="325px"))
,div(style="width:320px;",verbatimTextOutput("warn_ont"))
,div(style="width:320px;",verbatimTextOutput("warn_ont2"))
,tags$style(type='text/css', '#warn_ont {color: red; font-size:15px;}')
,tags$style(type='text/css', '#warn_ont2 {color: red; font-size:15px;}')
)
,column(4, offset=0, style='padding:0px;'
,div(style="line-height:20px", br())
#User requested datasets in the processing queue
,div(style="display: inline-block;vertical-align:right; ",h4('User requested datasets'))
,div(style="display: inline-block;vertical-align:right;", bsButton("process_log_bs", label = "", icon = icon("info-circle"),style="", size = "medium"))
,bsPopover(id = "process_log_bs", title = "",
content = paste0("Click `Processing console` button to see status of the user requested datasets in the processing queue."),
placement = "right", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#process_log_bs {background-color: white; border:none;}')
,div(style="line-height:0px;", selectInput("geo_next_lp", " ", choices="", selected=""))
,div(style="margin:-10px;", br()), actionButton("process_log","Processing console", style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
,column(12, offset=0, style='padding:0px;'
,tags$hr()
,div(style="color:#337ab7; text-align:center;", titlePanel(h1("Select a dataset")))
)
,DT::dataTableOutput('datatable'), br()
,includeHTML("www/html/footer.html")
)
,tabPanel(tags$b('Explore dataset'), value='explore'
,column(3, offset=0
,wellPanel(
textInput('geo_acc', h3('Selected study'))
,conditionalPanel("input.geo_acc != ''"
,actionButton("analysisbtn", "Analyze", icon("th"), style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #337ab7; border-color: #2e6da4")
,conditionalPanel("input.tab2 == 'metadata'"
,br(),tags$div(class="metadata_column_class", uiOutput("metadata_column"))
,tags$head(tags$style(HTML(".metadata_column_class label{font-size: 16px;}")))
,tags$div(class="full_metacol_class", uiOutput("full_metacol"))
,tags$head(tags$style(HTML(".full_metacol_class label{font-size: 16px;}")))
,br(), shinyjs::hidden(downloadButton('downloadmeta', label = "Download metadata", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
)
,conditionalPanel("input.tab2 == 'countsTable'"
,br(),uiOutput("counts_sample_ui")
,actionButton(inputId = "load_counts", label = "Show counts table",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000"), br()
,conditionalPanel("input.load_counts != ''"
,br(),br(),downloadButton('downloadcounts', label = "Download data", style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
,tags$div(class="dl_counts_type_class", radioButtons('download_type_counts', label = "", choices = c("Gene level", "Transcript level"), inline=T))
,tags$head(tags$style(HTML(".dl_counts_type_class label{font-size: 16px;}")))
)
)
,conditionalPanel("input.preplots == 'corr' | input.preplots == 'dens'"
,br(),br(),uiOutput("cor_sample_ui")
,uiOutput("draw_cor_ui")
,uiOutput("draw_dens_ui")
)
,conditionalPanel("input.preplots == 'heatmap'"
,br(),tags$div(class="heat_prop_class", uiOutput("heat_prop"))
,tags$head(tags$style(HTML(".heat_prop_class label{font-size: 16px;}")))
,uiOutput("cluster_meth")
,uiOutput("cluster_genes")
,conditionalPanel("input.heatvis=='static' && input.fir_or_scr=='fitinscreen'"
,actionButton("draw_heat", "Draw heatmap",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
,conditionalPanel("input.draw_heat != ''"
,br(), div(style="display: inline-block;vertical-align:right;", downloadButton('download', label = "Download", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
,div(style="display: inline-block;vertical-align:right;", radioButtons('download_type_fit', label = "", choices = c("png", "csv"), inline = T))
)
)
,conditionalPanel("input.heatvis=='static' && input.fir_or_scr=='scrollable'"
,actionButton("draw_heatscr", "Draw heatmap",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
,conditionalPanel("input.draw_heatscr != ''"
,br(), div(style="display: inline-block;vertical-align:right;", downloadButton('downloadscr', label = "Download", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
,div(style="display: inline-block;vertical-align:right;", radioButtons('download_type_scr', label = "", choices = c("png", "csv"), inline = T))
)
)
,conditionalPanel("input.heatvis=='inter'"
,actionButton("draw_heatint", "Draw heatmap",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
)
)
,conditionalPanel("input.tab2 == 'plots' && input.preplots == 'pca'"
,br(),uiOutput("pca_prop")
,conditionalPanel("input.pcap == 'pca2'"
,actionButton("draw_pca", "Plot PCA",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000"), br()
,br(), plotOutput("legendplot", height='auto')
)
,conditionalPanel("input.pcap == 'pca3'"
,actionButton("draw_pca3", "Plot PCA",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000"), br()
,br(), plotOutput("legendplot3", height='auto')
)
,conditionalPanel("input.pcap == 'tsne2'"
,actionButton("draw_tsne2", "Plot t-SNE",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000"), br()
)
,conditionalPanel("input.pcap == 'tsne3'"
,actionButton("draw_tsne3", "Plot t-SNE",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000"), br()
)
)
)
)
)
,column(9, offset=0
,wellPanel(
conditionalPanel("input.geo_acc != ''"
,tabsetPanel( id="tab2"
,tabPanel("Description", value="summary", br()
,DT::dataTableOutput('geo_summary') %>% withSpinner(type=5)
)
,tabPanel("Metadata",value="metadata", br()
,DT::dataTableOutput('metadata') %>% withSpinner(type=5)
,DT::dataTableOutput('metadata_full', width = 900)
,DT::dataTableOutput('ontology', width = 900)
)
,tabPanel("Counts table",value="countsTable", br()
,verbatimTextOutput("counts_warn")
,tags$style(type='text/css', '#counts_warn {color: red; font-weight: bold; font-size:18px;}')
,DT::dataTableOutput('counts', width=900) %>% withSpinner(type=5)
)
,tabPanel("QC report",value="qc", br()
,downloadButton('downloadqc', label = "Download QC report", style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
,htmlOutput('multiqc') %>% withSpinner(type=5)
)
,tabPanel("Visualization",value="plots", br()
,tabsetPanel(id="preplots"
,tabPanel("Correlation plot",value="corr", br()
,verbatimTextOutput("corr_warn")
,tags$style(type='text/css', '#corr_warn {color: red; font-weight: bold; font-size:18px;}')
,plotlyOutput("corplot") %>% withSpinner(type=5)
)
,tabPanel("Density plot",value="dens", br()
,verbatimTextOutput("dens_warn")
,tags$style(type='text/css', '#dens_warn {color: red; font-weight: bold; font-size:18px;}')
,plotlyOutput("densityp", width = "auto", height = "auto") %>% withSpinner(type=5)
)
,tabPanel("Heatmap",value="heatmap"
,br()
,verbatimTextOutput("heat_warn")
,tags$style(type='text/css', '#heat_warn {color: red; font-weight: bold; font-size:18px;}')
,tabsetPanel(id="heatvis"
,tabPanel(div(style="display: inline-block;vertical-align:right;","Static heatmap", bsButton("heat_stat_bs", label = "", icon = icon("info-circle"),style="", size = "small")), value="static"
,bsPopover(id = "heat_stat_bs", title = "",
content = paste0("Highly variable genes are selected based on median absolute deviation (MAD) values of the genes."),
placement = "bottom", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#heat_stat_bs {background-color: transparent; border:none;}')
,br()
,tabsetPanel(id="fir_or_scr"
,tabPanel("Fit in screen",value="fitinscreen", br()
,plotOutput("HeatStatic", height= "auto") %>% withSpinner(type=5)
)
,tabPanel("Scrollable",value="scrollable", br()
,plotOutput("HeatStaticscr", height= "auto") %>% withSpinner(type=5)
)
)
)
,tabPanel(div(style="display: inline-block;vertical-align:right;","Interactive heatmap", bsButton("heat_int_bs", label = "", icon = icon("info-circle"),style="", size = "small")), value="inter"
,bsPopover(id = "heat_int_bs", title = "",
content = paste0("You can select any area in the following heatmap to zoom in and double-click to zoom out."),
placement = "bottom", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#heat_int_bs {background-color: transparent; border:none;}')
,br()
,uiOutput("iheatmapui", width = "auto", height = "auto"), br(), br()
)
)
),
tabPanel("PCA & t-SNE",value="pca", br()
,tabsetPanel(id="pcap"
,tabPanel("2D PCA plot",value="pca2"
,br()
,conditionalPanel("input.draw_pca != ''"
,downloadButton('downloadPCA2D', label = "Download image", style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
,br(),uiOutput("p2D_ui")
,br()
)
,tabPanel("3D PCA plot",value="pca3"
,br()
,conditionalPanel("input.draw_pca3 != ''"
,downloadButton('downloadPCA3D', label = "Download image", style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
,br(), uiOutput("pca3Dplot_ui")
,br()
)
,tabPanel("2D t-SNE plot",value="tsne2"
,br()
,uiOutput("t2Dplot_ui")
)
,tabPanel("3D t-SNE plot",value="tsne3"
,br()
,uiOutput("tsne3Dplot_ui")
)
)
)
)
)
)
)
)
)
,includeHTML("www/html/footer.html")
)
,tabPanel(tags$b('Analyze dataset'), value='analyze'
,column(3, offset=0.5,
wellPanel(
textInput('geo_acc2', h3('Selected study'))
,conditionalPanel("input.geo_acc != ''"
,conditionalPanel("input.signature == 'power'"
,uiOutput("power_ui")
,uiOutput("samples")
,uiOutput("alpha")
,uiOutput("effect")
,conditionalPanel("input.sigtab== 'power_curve'"
,uiOutput("depth_ui")
)
,br(), uiOutput("gen_pow_btn_ui")
,uiOutput("gen_detect_btn_ui")
)
,conditionalPanel("input.signature == 'sig_data'"
,conditionalPanel("input.cr_reg_sig == 'meta_reg'"
,uiOutput("metadata_analysis")
,uiOutput("ana_type")
,uiOutput("group1")
,uiOutput("group2")
,uiOutput("cov")
,br(), uiOutput("gen_reg_sig_ui")
)
,conditionalPanel("input.signature == 'sig_data' && input.cr_reg_sig == 'sig_reg'"
,br(),actionButton("heatmap_mod_regsig", "Show visualization", style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
,bsModal("modalheatmap_regsig", "", "heatmap_mod_regsig", size = "large"
,column(4, offset=-0.5
,wellPanel(
conditionalPanel("input.heatmodal_regsig=='static_mod_regsig' || input.heatmodal_regsig=='inter_mod_regsig'"
,tags$div(class="heat_typeui_mod_regsig_class",uiOutput("heat_typeui_mod_regsig"))
,tags$head(tags$style(HTML(".heat_typeui_mod_regsig_class label{font-size: 15px;}")))
,tags$div(class="heat_prop_mod_regsig_class",uiOutput("heat_prop_mod_regsig"))
,tags$head(tags$style(HTML(".heat_prop_mod_regsig_class label{font-size: 15px;}")))
,uiOutput("cluster_meth_mod_regsig")
,uiOutput("cluster_genes_mod_regsig"), br()
,conditionalPanel("input.heatmodal_regsig=='static_mod_regsig' && input.fit_or_scr_mod_regsig=='fitinscreen_mod_regsig'"
,actionButton("draw_heatfit_regsig", "Draw heatmap",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
,conditionalPanel("input.draw_heatfit_regsig != ''"
,br(), div(style="display: inline-block;vertical-align:right;", downloadButton('downloadfit_mod_regsig', label = "Download", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
,div(style="display: inline-block;vertical-align:right;", radioButtons('download_type_fit_mod_regsig', label = "", choices = c("png", "csv"), inline = T))
)
)
,conditionalPanel("input.heatmodal_regsig=='static_mod_regsig' && input.fit_or_scr_mod_regsig=='scrollable_mod_regsig'"
,actionButton("draw_heatscr_regsig", "Draw heatmap",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
,conditionalPanel("input.draw_heatscr_regsig != ''"
,br(), div(style="display: inline-block;vertical-align:right;", downloadButton('downloadscr_mod_regsig', label = "Download", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
,div(style="display: inline-block;vertical-align:right;", radioButtons('download_type_scr_mod_regsig', label = "", choices = c("png", "csv"), inline = T))
)
)
,conditionalPanel("input.heatmodal_regsig=='inter_mod_regsig'"
,actionButton("draw_heatint_regsig", "Draw heatmap",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
)
)
,conditionalPanel("input.heatmodal_regsig=='ma_mod_regsig'"
,uiOutput("fdrui_mod_regsig"), br()
,actionButton("draw_ma_regsig", "Draw MA plot",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000"), br()
)
)
)
,column(8, offset=-0.5
,wellPanel(
tabsetPanel(id="heatmodal_regsig",
tabPanel("Static heatmap",value="static_mod_regsig", br()
,conditionalPanel("input.heatmodal_regsig == 'static_mod_regsig'"
,div(style="margin-top: -20px;margin-bottom: 20px; color:#337ab7;", titlePanel(h4("Heatmap of top DE genes (ranked by adjusted p-values)")))
)
,tabsetPanel(id="fit_or_scr_mod_regsig"
,tabPanel("Fit in screen",value="fitinscreen_mod_regsig", br()
,plotOutput("fitscreen_mod_regsig", height="auto") %>% withSpinner(type=5)
)
,tabPanel("Scrollable",value="scrollable_mod_regsig", br()
,plotOutput("scroll_mod_regsig", height="auto") %>% withSpinner(type=5)
)
)
),
tabPanel("Interactive heatmap",value="inter_mod_regsig", br()
,conditionalPanel("input.heatmodal_regsig == 'inter_mod_regsig'"
,div(style="margin-top: -20px;margin-bottom: 20px; color:#337ab7;", titlePanel(h4("Heatmap of top DE genes (ranked by adjusted p-values)")))
)
,conditionalPanel("input.draw_heatint_regsig != ''"
,uiOutput("iheatmapui_mod_regsig", width = "auto", height = "auto")
)
),
tabPanel("MA plot",value="ma_mod_regsig", br()
,conditionalPanel("input.heatmodal_regsig == 'ma_mod_regsig'"
,div(style="margin-top: -20px;margin-bottom: 20px; color:#337ab7;", titlePanel(h4("log-fold change (M) vs. log-average expression (A) plot")))
)
,downloadButton('downloadMA', label = "Download image", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"), br()
,br(), uiOutput("maplotui_mod_regsig", width = "auto", height = "auto"), br()
,br(), DT::dataTableOutput("maplot_clickedpoints", width=500)
)
)
)
)
)
,br(), br(), downloadButton('downloadsigdata', label = "Download signature", style="color: #fff; background-color: #337ab7; border-color: #2e6da4;")
,br(), br(),uiOutput("dynamiclink")
)
)
,conditionalPanel("input.signature == 'exp_desg' && input.expr_design=='sig_meta'"
,uiOutput("user_meta_prop")
,uiOutput("user_ana_type")
,uiOutput("user_cov_ui")
,br(), uiOutput("gen_sig_btn_ui"), br()
)
,conditionalPanel("input.signature == 'exp_desg' && input.expr_design=='user_exp_sig'"
,br(), actionButton("heatmap_mod", "Show visualization", style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
,bsModal("modalheatmap", "", "heatmap_mod", size = "large"
,column(4, offset=-0.5
,wellPanel(
conditionalPanel("input.heatmodal=='static_mod' || input.heatmodal=='inter_mod'"
,tags$div(class="heat_type_mod_class", uiOutput("heat_typeui_mod"))
,tags$head(tags$style(HTML(".heat_type_mod_class label{font-size: 15px;}")))
,tags$div(class="heat_prop_mod_class",uiOutput("heat_prop_mod"))
,tags$head(tags$style(HTML(".heat_prop_mod_class label{font-size: 15px;}")))
,uiOutput("cluster_meth_mod")
,uiOutput("cluster_genes_mod"), br()
,conditionalPanel("input.heatmodal=='static_mod' && input.fit_or_scr_mod=='fitinscreen_mod'"
,actionButton("draw_heatfit", "Draw heatmap",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
,conditionalPanel("input.draw_heatfit != ''"
,br(),div(style="display: inline-block;vertical-align:right;", downloadButton('downloadfit_mod', label = "Download", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
,div(style="display: inline-block;vertical-align:right;", radioButtons('download_type_fit_mod', label = "", choices = c("png", "csv"), inline = T))
)
)
,conditionalPanel("input.heatmodal=='static_mod' && input.fit_or_scr_mod=='scrollable_mod'"
,actionButton("draw_heatscr_mod", "Draw heatmap",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
,conditionalPanel("input.draw_heatscr_mod != ''"
,br(), div(style="display: inline-block;vertical-align:right;", downloadButton('downloadscr_mod', label = "Download", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
,div(style="display: inline-block;vertical-align:right;", radioButtons('download_type_scr_mod', label = "", choices = c("png", "csv"), inline = T))
)
)
,conditionalPanel("input.heatmodal=='inter_mod'"
,actionButton("draw_heatint_mod", "Draw heatmap",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000")
)
)
,conditionalPanel("input.heatmodal=='ma_mod'"
,uiOutput("fdrui_mod"), br()
,actionButton("draw_ma", "Draw MA plot",style="color: #fff; box-shadow: 1px 1px 1px 1px #888; background-color: #800000; border-color: #800000"), br()
)
)
)
,column(8, offset=-0.5
,wellPanel(
tabsetPanel(id="heatmodal",
tabPanel("Static heatmap",value="static_mod", br()
,conditionalPanel("input.heatmodal == 'static_mod'"
,div(style="margin-top: -20px;margin-bottom: 20px; color:#337ab7;", titlePanel(h4("Heatmap of top DE genes (ranked by adjusted p-values)")))
)
,tabsetPanel(id="fit_or_scr_mod"
,tabPanel("Fit in screen",value="fitinscreen_mod", br()
,plotOutput("fitscreen_mod", height="auto") %>% withSpinner(type=5)
)
,tabPanel("Scrollable",value="scrollable_mod", br()
,plotOutput("scroll_mod", height="auto") %>% withSpinner(type=5)
)
)
),
tabPanel("Interactive heatmap",value="inter_mod", br()
,conditionalPanel("input.heatmodal == 'inter_mod'"
,div(style="margin-top: -20px;margin-bottom: 20px; color:#337ab7;", titlePanel(h4("Heatmap of top DE genes (ranked by adjusted p-values)")))
)
,conditionalPanel("input.draw_heatint_mod != ''"
,uiOutput("iheatmapui_mod", width = "auto", height = "auto")
)
),
tabPanel("MA plot",value="ma_mod", br()
,conditionalPanel("input.heatmodal == 'ma_mod'"
,div(style="margin-top: -20px;margin-bottom: 20px; color:#337ab7;", titlePanel(h4("log-fold change (M) vs. log-average expression (A) plot")))
)
,downloadButton('downloadMA_mod', label = "Download image", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"), br()
,br(), uiOutput("maplotui_mod", width = "auto", height = "auto"), br()
,br(), DT::dataTableOutput("maplot_clickedpoints_mod", width=500)
)
)
)
)
)
)
,conditionalPanel("input.signature == 'exp_desg' && input.expr_design=='user_exp_sig'"
,br(), shinyjs::hidden(downloadButton('download_user_sigdata', label = "Download signature", style="color: #fff; background-color: #337ab7; border-color: #2e6da4;")), br()
,br(), uiOutput("user_dynamiclink")
)
)
)
)
,column(9, offset=0.5,
wellPanel(
conditionalPanel("input.geo_acc !='' && input.geo_acc2 !=''"
,tabsetPanel( id="signature"
,tabPanel("Power analysis",value="power", br()
,tabsetPanel( id="sigtab"
,tabPanel(div(style="display: inline-block;vertical-align:right;","Power curve", bsButton("power_bs", label = "", icon = icon("info-circle"),style="", size = "small")),value="power_curve", br()
,bsPopover(id = "power_bs", title = "",
content = paste0("We use Bioconductor package <strong>RNASeqPower</strong> to estimate power."),
placement = "bottom", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#power_bs {background-color: transparent; border:none;}')
,plotlyOutput("powerplot", width = "auto", height = "auto") %>% withSpinner(type=5)
)
,tabPanel(div(style="display: inline-block;vertical-align:right;","Detectability of genes", bsButton("detect_bs", label = "", icon = icon("info-circle"),style="", size = "small")),value="detec_gene", br()
,bsPopover(id = "detect_bs", title = "",
content = paste0("The line of detectability is the estimated biological coefficient of variation values for different sequencing depths. Genes below this line have higher power to be detected as differentially expressed."),
placement = "bottom", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#detect_bs {background-color: transparent; border:none;}')
,div(style="display: inline-block;vertical-align:right; ",h4('Search for genes of interest'))
,div(style="display: inline-block;vertical-align:right;", bsButton("search_gene_bs", label = "", icon = icon("info-circle"),style="", size = "small"))
,bsPopover(id = "search_gene_bs", title = "",
content = paste0("You can type one or more gene symbols seperated by commas (e.g., TNMD,FGR) and click `Generate plot` button."),
placement = "right", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#search_gene_bs {background-color: transparent; border:none;}')
,div(style="line-height:0px;",textInput('search_gene', '',width='300px' ))
,verbatimTextOutput("gene_warn")
,tags$style(type='text/css', '#gene_warn {color: red; font-weight: bold; font-size:18px;}')
,verbatimTextOutput("gene_sym_warn")
,tags$style(type='text/css', '#gene_sym_warn {color: red; font-weight: bold; font-size:18px;}')
,verbatimTextOutput("gene_sym_green")
,tags$style(type='text/css', '#gene_sym_green {color: green; font-weight: bold; font-size:18px;}')
,plotlyOutput("detect_gene", width = "auto", height = "auto") %>% withSpinner(type=5)
)
)
)
,tabPanel(div(style="display: inline-block;vertical-align:right;","Create a signature",bsButton("reg_sig_bs", label = "", icon = icon("info-circle"),style="", size = "small")),value="sig_data", br()
,conditionalPanel("input.signature == 'sig_data'"
,bsPopover(id = "reg_sig_bs", title = "",
content = paste0("We use Bioconductor package <B>edgeR</B> to find differentially expressed genes between groups. Control group is considered as reference in computing log of fold change and p-values are adjusted for multiple comparison."),
placement = "bottom", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#reg_sig_bs {background-color: transparent; border:none;}')
), br()
,shinyjs::hidden(verbatimTextOutput("sig1_warn"))
,tags$style(type='text/css', '#sig1_warn {color: red; font-weight: bold; font-size:18px;}')
,tabsetPanel(id="cr_reg_sig"
,tabPanel("Metadata",value="meta_reg", br()
,verbatimTextOutput("rank_warn")
,tags$style(type='text/css', '#rank_warn {color: red; font-weight: bold; font-size:18px;}')
,verbatimTextOutput("level_warn")
,tags$style(type='text/css', '#level_warn {color: red; font-weight: bold; font-size:18px;}')
,DT::dataTableOutput('sig_meta', width = 900)
)
,tabPanel("Signature",value="sig_reg", br()
,DT::dataTableOutput('sig_data', width = 900) %>% withSpinner(type=5)
)
)
)
,tabPanel(div(style="display: inline-block;vertical-align:right;","User specific design", bsButton("user_sig_bs", label = "", icon = icon("info-circle"),style="", size = "small")),value="exp_desg", br()
,conditionalPanel("input.signature == 'exp_desg'"
,bsPopover(id = "user_sig_bs", title = "",
content = paste0("You can modify the experimental design by placing samples to your group of interest."),
placement = "bottom", trigger = "hover", options = list(container = "body")
)
,tags$style(type='text/css', '#user_sig_bs {background-color: transparent; border:none;}')
), br()
,shinyjs::hidden(verbatimTextOutput("sig2_warn"))
,tags$style(type='text/css', '#sig2_warn {color: red; font-weight: bold; font-size:18px;}')
,tabsetPanel(id="expr_design"
,tabPanel("Metadata",value="sig_meta", br()
,verbatimTextOutput("user_design_title")
,tags$style(type='text/css', '#user_design_title {color: navyblue; font-size:18px; font-weight: bold;}')
,conditionalPanel("input.signature == 'exp_desg' && input.expr_design=='sig_meta'"
,tags$style(".container { border:1px solid steelblue; margin: 0 auto; font-size:7px; width: 100%; height: 270px; overflow-y: scroll; }")
,column(6
,wellPanel(
uiOutput("user_g1_ui")
)
)
,column(6
,wellPanel(
uiOutput("user_g2_ui")
)
)
), tags$hr()
,verbatimTextOutput("user_rank_warn")
,tags$style(type='text/css', '#user_rank_warn {color: red; font-weight: bold; font-size:18px;}')
,verbatimTextOutput("user_level_warn")
,tags$style(type='text/css', '#user_level_warn {color: red; font-weight: bold; font-size:18px;}')
,DT::dataTableOutput('designtable', width = 900)
)
,tabPanel("Signature",value="user_exp_sig", br()
,DT::dataTableOutput('sigtable', width = 900) %>% withSpinner(type=5)
)
)
)
)
)
)
)
,includeHTML("www/html/footer.html")
)
,tabPanel(tags$b('Processing console'), value='out_cons'
,column(3, offset=0.5,
textInput('geo_current', h4('Currently processing')), br(),
selectInput("geo_next", "Waiting to process",choices="", selected="")
)
,column(9, offset=0.5,
tabsetPanel( id="process",
tabPanel("Processing log",value="log", br()
,verbatimTextOutput("steps")
,actionButton("show_log","Show log file", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"), br()
,br(), verbatimTextOutput('process_log_text')
)
)
)
,includeHTML("www/html/footer.html")
)
)
)