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Merge branch 'master' into pr/72

# Conflicts:
#	README.md
#	misc/bsModal.R
#	misc/plot.shiny.km.R
#	platforms/geo-platform-update.sh
#	rsconnect/shinyapps.io/jasminedumas/shinyGEO.dcf
#	server.r
#	server/server-clinical.R
#	server/server-report.R
#	server/server-selection.R
#	server/server-survival.R
#	server/settings.R
#	ui/ui.dashboard.body.R
#	ui/ui.dashboard.header.R
#	ui/ui.dashboard.sidebar.R
#	ui/ui.tab.analyses.R
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jasdumas committed Apr 16, 2016
2 parents b9ae715 + b1e2939 commit 5b128137a692b2e669403a9bd40cff9842b8c24c
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@@ -2,3 +2,9 @@
.Rhistory
.RData
.Ruserdata
DESCRIPTION
LICENSE.txt
README.md
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0 RData/GSE13.RData 100644 → 100755
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0 RData/GSE19915.RData 100644 → 100755
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0 RData/getTestData.R 100644 → 100755
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@@ -0,0 +1,35 @@
### modify function from shinydashboard to use local adminLTE files
addDeps <- function(x) {
if (getOption("shiny.minified", TRUE)) {
adminLTE_js <- "app.min.js"
adminLTE_css <- c("AdminLTE.min.css", "_all-skins.min.css")
} else {
adminLTE_js <- "app.js"
adminLTE_css <- c("AdminLTE.css", "_all-skins.css")
}
dashboardDeps <- list(
htmlDependency("AdminLTE", "2.0.6",
"www/AdminLTE",
script = adminLTE_js,
stylesheet = adminLTE_css
),
htmlDependency("shinydashboard",
as.character(utils::packageVersion("shinydashboard")),
c(file = system.file(package = "shinydashboard")),
script = "shinydashboard.js",
stylesheet = "shinydashboard.css"
)
)
appendDependencies(x, dashboardDeps)
}
e=environment(getFromNamespace("addDeps", "shinydashboard"))
environment(addDeps) = e
assignInNamespace("addDeps", addDeps, "shinydashboard")
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0 platforms/platforms.RData 100644 → 100755
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0 platforms/process-platforms.R 100644 → 100755
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@@ -2,6 +2,12 @@ name: shinyGEO
account: jasminedumas
server: shinyapps.io
appId: 62916
<<<<<<< HEAD
bundleId: 421244
url: https://jasminedumas.shinyapps.io/shinyGEO/
when: 1460756572.05498
=======
bundleId: 416758
url: https://jasminedumas.shinyapps.io/shinyGEO/
when: 1460426920.7687
>>>>>>> master
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0 series/process-series.R 100644 → 100755
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0 server/formatDE.R 100644 → 100755
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4 server/server-clinical.R 100644 → 100755
@@ -25,7 +25,11 @@ clinicalDataProcessed <- reactive({
i = num.levels > 1 | 1:ncol(p) %in% g
# keep source_name_ch1 and description
<<<<<<< HEAD:server/server-clinical.R
keep = colnames(p) %in% c("source_name_ch1", "DESCRIPTION")
=======
keep = colnames(p) %in% c("source_name_ch1", "description")
>>>>>>> master:server/server-clinical.R
if (sum(keep) > 0) {
i[keep] = TRUE
}
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<<<<<<< HEAD:ui/ui.dashboard.body.R
#####################################
# dashboard body
#####################################
@@ -194,4 +195,27 @@ body = dashboardBody(
)
)
=======
library(shinyAce)
library(RCurl)
library(shinyBS)
library(shinydashboard)
source("misc/addDeps.R")
source("misc/html.R")
source("misc/bsModal.R")
source("ui/ui.dashboard.header.R")
source("ui/ui.dashboard.sidebar.R")
source("ui/ui.dashboard.body.R")
shinyUI(
dashboardPage(
header,
sidebar,
body
)
)
>>>>>>> master:ui.r
@@ -0,0 +1,197 @@
#####################################
# dashboard body
#####################################
source("ui/ui.tab.expression.R")
source("ui/ui.tab.analyses.R")
source("ui/ui.tab.reproducible.R")
source("ui/ui.tab.about.R")
source("misc/html.R")
## fileUploadBar without label
fileUploadBar = fileInput('fileUpload', 'select file',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv'))
fileUploadBar[[3]][1] = NULL
header = dashboardHeader(
title = uiOutput("shinyTitle"), titleWidth = 350, disable = FALSE
)
# add id to sidebar toggle link so that we can refresh when clicked
tmp = header$children[[3]]$children[[2]]
tmp = gsub("\"#\"", "\"#\" id = \"sidebarToggle\"", tmp)
header$children[[3]]$children[[2]] = tmp
gse.input = div(style = "display:inline-block; width: 75%",
selectizeInput('GSE', label = "Accession Number", choices = NULL, width = 275,
options = list(placeholder = "Please enter a GSE #",
maxOptions = 100)
)
)
gse.button = div(style = "display:inline-block; width: 11%",
actionButton("submitButton", "Go!")
)
gse.platform= conditionalPanel(condition = "output.sidebarDisplay=='PLATFORM'|output.sidebarDisplay=='ALL'",
div(style = "display:inline-block; width: 75%",
selectizeInput('platform', label = "Platform", choices = NULL, width = 275,
options = list(placeholder = "Please select a platform",
maxOptions = 10)
)
)
# Button was needed to trigger server-busy for please wait message based on server-busy
# div(style = "display:inline-block; width: 11%",
# actionButton("submitPlatform", "Go!")
# )
)
sidebar = dashboardSidebar(width = 350,
includeCSS('www/ecsu.css'),
includeScript('www/ecsu.js'),
gse.input, gse.button, gse.platform,
conditionalPanel(condition = "output.sidebarDisplay=='ALL'",
sidebarMenu(id = "tabs",
hr(),
menuItem("New Analysis", tabName = "NewAnalysis", icon = icon("refresh")),
hr(),
menuItem("Home", tabName = "Home", icon = icon("home"), selected = TRUE),
menuItem("Differential Expression Analysis",
tabName = "DifferentialExpressionAnalysis", icon = icon("flask")),
menuItem("Survival Analysis", tabName = "SurvivalAnalysis", icon = icon("life-ring")),
menuItem("View Sample Data Table", tabName = "FullDataTable", icon = icon("table")),
menuItem("Code", tabName = "Code", icon = icon("code")),
menuItem("About", tabName = "About", icon = icon("info-circle"))
)
)
)
####################################
# DE and survival analyses
####################################
analyses.common = conditionalPanel(condition = "input.tabs == 'DifferentialExpressionAnalysis' | input.tabs == 'SurvivalAnalysis'",
bsAlert("alert2"),
div(style = "display:inline-block; width: 40%",
selectizeInput('selectGenes', "Select Gene/Probe", choices = NULL)
),
div(style = "display:inline-block; width: 25%",
a(id = "platLink", "Change Search Feature",
#style="cursor:pointer; display:block; margin-bottom:5px;")
style="cursor:pointer; display:block; position:relative; bottom:20px;")
),
bsModal("platformModal", "Platform annotation",
"platLink", size = "large",
selectizeInput('geneColumn', 'Selected Feature', choices = NULL),
DT::dataTableOutput("platformData")
),
div(style = "display:inline-block; width: 35%",
conditionalPanel(condition = "input.tabs =='SurvivalAnalysis'",
genBSModal("autogenModal","Survival Analyses","",size="large")
)
)
)
body = dashboardBody(
conditionalPanel(condition = "input.tabs != 'About' & input.tabs != 'Code'",
bsAlert("alert1"),
uiOutput("busy")
),
shinyjs::useShinyjs(),
summaryBSModal("summaryBSModal","Clinical Data","ClinicalDataBtn", size = "large",
tabsetPanel(id = "tabClinicalData",
tabPanel("Summary View", DT::dataTableOutput("summaryModalTable")),
tabPanel("Standard View",
DT::dataTableOutput("clinicalData")
),
# sample selection
tabPanel("Sample Selection",
fluidRow(
column(12, bsAlert("selectionAlert1"))
),
fluidRow(
column(4, uiOutput("SampleSelectionCol1")),
column(4, uiOutput("SampleSelection1")),
column(4, HTML("<br><button id='btnSelection' type='button' class='btn btn-info action-button'>Apply Selection Criteria</button>"))
),
fluidRow(
column(4, uiOutput("SampleSelectionCol2")),
column(4, uiOutput("SampleSelection2"))
),
fluidRow(
column(12, bsAlert("selectionAlert2"))
)
),
tabPanel("Data Export",
fluidRow(
column(12,
bsAlert("ioAlert1"),
bsAlert("ioAlert2")
)
),
fluidRow(
column(4,
tags$h4(class="ioTitle","Download Dataset"),
hr(),
downloadButton("downloadSet","Download")
),
column(4,
tags$h4(class="ioTitle","Upload Dataset"),
hr(),
fileUploadBar
),
column(4,
tags$h4(class="ioTitle","Reset Clinical Data to Original"),
hr(),
HTML("<button id='ClinicalReset' type='button' class='btn btn-danger action-button'>Reset Clinical Data</button>")
)
)
)
)
),
# please wait conditional panel
## originally shiny-busy
conditionalPanel(
condition="$('html').hasClass('shiny-busy') & input.tabs == 'Home'",
# div(style = "position:center; width:100%; height:100; text-align:center",
# img(src="PleaseWait.gif", style = "width:50%")
# "Please wait..."
# )
HTML("<div class=\"progress\" style=\"height:25px !important\"><div class=\"progress-bar progress-bar-striped active\" role=\"progressbar\" aria-valuenow=\"40\" aria-valuemin=\"0\" aria-valuemax=\"100\" style=\"width:100%\">
<span id=\"bar-text\">Loading...</span></div></div>") ),
HTML("<link href='https://fonts.googleapis.com/css?family=Courgette' rel='stylesheet' type='text/css'>"),
analyses.common,
tabItems(
# First tab content
tab.expression,
tab.DE.analysis,
tab.survival.analysis,
tab.code,
tab.about
)
)
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0 ui/ui.tab.reproducible.R 100644 → 100755
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