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ui.R
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# library(shinydashboard)
library(shiny)
library(shinyjs)
library(tools)
library(ggplot2)
library(shinydashboard)
library(data.table)
library(DT)
library(zoo)
library(pander)
library(seqinr)
#library(Biostrings)
source("functions.R")
demomode <<- FALSE
########## startup settings ##########
if (file.exists("/home/eden/eden.sh")) {
# we are inside the docker container
# packrat::on()
csv.path <<- "/home/eden/data/csv" # folder where processed .tar files are located in csv format (one file for a sample)
tar.path <<- "/home/eden/data/tar" # folder where .tar files are located (eden output)
raw.path <<- "/home/eden/data/raw" # folder where unpacked .tar files are located
down.path <<- "/home/eden/data/eden_data" # folder where unpacked .tar files are located
annotation.path <<- "/home/eden/tigr_data" # folder werhere TIGR_ROLE_NAMES and TIGRFAMS_ROLE_LINK are located
dir.create(csv.path)
dir.create(raw.path)
dir.create(tar.path)
dir.create(down.path)
} else {
# we are online hosted
csv.path <<- "csv"
tar.path <<- "tar"
raw.path <<- "raw"
down.path <<- "eden_files"
dir.create(csv.path)
dir.create(raw.path)
dir.create(down.path)
annotation.path <<- "annotation"
}
# check if .csv files are located
# TODO(pmuench): if no_csv == TRUE dont show tabs
dirs <- list.dirs(csv.path,recursive=FALSE)
files.list <- list.files(dirs, ".*\\.csv", recursive=TRUE, full.names=TRUE)
if (length(files.list) > 0){
no_csv <<- FALSE
} else {
no_csv <<- TRUE
}
# check if .tar files are located
files.list <- list.files(tar.path, ".*\\.tar", recursive=TRUE, full.names=TRUE)
if (length(files.list) > 0){
no_tar <<- FALSE
} else {
no_tar <<- TRUE
}
# check if there are new tar files
tar.list <- basename(list.files(tar.path, ".*\\.tar", recursive=TRUE, full.names=TRUE))
csv.list <- basename(list.dirs(csv.path,recursive=FALSE))
if (any(is.na(match(tar.list, csv.list)))) { # true if the match is not complete (one tar file name dont match to csv file name)
new_files <<- TRUE
} else {
new_files <<- FALSE
}
# set path variable
if (file.exists("/home/eden/eden.sh")) {
# we are inside the docker
packrat::on()
# folders to store input faa and ffn files
faa.path <<- "/home/eden/data/faa"
ffn.path <<- "/home/eden/data/ffn"
sample.path <<- "/home/eden/data/samples.txt"
hmm.path <<- "/home/eden/data/model.hmm"
tar.path <<- "/home/eden/data/tar"
fasta.path <<- "/home/eden/data/fasta"
folder.path <<- "data"
log.path <<- "/home/eden/shinylog.txt"
lock.file <<- "/home/eden/lock.txt"
} else {
# we are online/local hosted
# folders to store input faa and ffn files
log.path <<- "log.txt"
faa.path <<- "faa"
ffn.path <<- "ffn"
fasta.path <<- "fasta"
tar.path <<- "tar"
folder.path <<- NULL
sample.path <<- "samples.txt"
hmm.path <<- "model.hmm"
log.path <<- "log.txt"
lock.file <<- "lock.txt"
}
jsResetCode <- "shinyjs.reset = function() {history.go(0)}"
if (!file.exists(fasta.path)) {
dir.create(fasta.path)
}
if (!file.exists(faa.path)) {
dir.create(faa.path)
}
if (!file.exists(ffn.path)) {
dir.create(ffn.path)
}
Sys.chmod(fasta.path, mode = "0777", use_umask = TRUE)
Sys.chmod(ffn.path, mode = "0777", use_umask = TRUE)
Sys.chmod(faa.path, mode = "0777", use_umask = TRUE)
########## dashboard header ##########
dbHeader <- dashboardHeader( titleWidth=200,
# Set height of dashboardHeader
tags$li(class = "dropdown",
tags$style(".main-header {max-height: 60px}"),
tags$style(".main-header .logo {height: 60px;}"),
tags$style(".sidebar-toggle {height: 60px; padding-top: 1px !important;}"),
tags$style(".navbar {min-height:60px !important}")
)
)
dbHeader$children[[2]]$children <- tags$a(href='',
tags$img(src='logo.png',height='47',width='115'))
dashboardPage(skin = "black",
dbHeader,
########## dashboard sidebar ##########
dashboardSidebar(width = 200, tags$style(".left-side, .main-sidebar {padding-top: 60px}"), sidebarMenu(id = "sid",
menuItem(
"Dashboard",
tabName = "dashboard",
icon = icon("dashboard")
),
menuItem("Start new job", tabName = "newjob", icon = icon("road"), badgeLabel = textOutput("text3"), badgeColor = "green"),
menuItem("Visualize job", tabName = "showjob", icon = icon("pie-chart"), badgeLabel = textOutput("samplesnum"), badgeColor = "green"),
conditionalPanel(
condition = "input.sid == 'showjob'",
uiOutput("main_ui")
),
menuItem("View log", tabName = "log", icon = icon("binoculars", lib = "font-awesome" )),
menuItem("Get example files", icon = icon("file-archive-o", lib = "font-awesome"),
href = 'https://www.dropbox.com/s/pd7tj6ztua2s3ma/sample_files.zip?dl=1'),
menuItem("Developer", tabName = "developer", icon = icon("cogs", lib = "font-awesome")),
menuItem("Bug Reports", icon = icon("bug"),
href = "https://github.com/philippmuench/eden/issues"),
menuItem("Support", icon = icon("envelope", lib = "font-awesome"),
href = "mailto:philipp.muench@helmholtz-hzi.de"),
htmlOutput("log")
)
),
########## dashboard body ##########
dashboardBody( useShinyjs(),
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "edentheme.css")
),
tabItems(
tabItem(tabName = "dashboard",
# fluidRow(
# infoBoxOutput("lockfileBox")
# ),
fluidRow(column(width=12,
htmlOutput("welcome")),
htmlOutput("statusfinished"),
htmlOutput("statuscheck"),
htmlOutput("statusrunning")
)),
### body: newjob
tabItem(tabName = "newjob",
h2("Start a new job"),
fluidRow(
column(width=6,
box( title = htmlOutput("box1statustest"), #"File upload",
uiOutput("upload_ui_head"),
tableOutput("fasta_uploaded"),
tableOutput("faa_uploaded"),
tableOutput("ffn_uploaded"), status = "primary", solidHeader=T, width = NULL
),
box( title = htmlOutput("box2status"), uiOutput("upload_ui_mid"),status = "primary", solidHeader=T, width = NULL),
box( title = "Reset", uiOutput("reset_ui_buttons"),status = "primary", solidHeader=T, width = NULL),
uiOutput("startEDEN")),
column(width=6,
box( title = htmlOutput("box3status"), uiOutput("upload_ui_hmm"),tableOutput("hmm_uploaded"), width = NULL, status = "primary", solidHeader=T),
box( title = uiOutput("box4status"), uiOutput("upload_ui_bottom"), status = "primary", solidHeader=T, width = NULL)))),
# body: inspect job
tabItem(tabName = "showjob",
h2("inspect a job"),
fluidRow(
useShinyjs(),
box( id ="figurebox", title = "Figures and tables", status = "primary", solidHeader= T, width = 12,
tabsetPanel(id = "tabset",
tabPanel(
"Overview",
div(DT::dataTableOutput("table"), style = "font-size:80%"),
htmlOutput("overview_table"),
htmlOutput("summary2"),
value = "overview"
),
tabPanel(
"Annotation",
plotOutput("annotationplotglobal", width = "100%", height =
"auto"),
htmlOutput("annotation_figure"),
value = "annotation"
),
tabPanel(
"Alignment Plot",
htmlOutput("alignment_hint"),
plotOutput("alignmentplot", width = "100%", height =
"auto"),
htmlOutput("alignment_figure"),
value = "alignment"
),
tabPanel(
"Categories",
plotOutput("annotationplot", width = "100%", height =
"auto"),
div(DT::dataTableOutput("table_annotaion"), style = "font-size:80%"),
value = "categories"
),
tabPanel(
"Histogram",
h4(""),
plotOutput("plot1", width = "100%", height = "auto"),
value = "histogram"
),
tabPanel(
"Boxplot",
h4(""),
plotOutput("plot4", width = "100%", height = "auto"),
div(DT::dataTableOutput("table_sample"), style = "font-size:80%"),
value = "box"
)
)
),
box( title = "Plot settings", status = "primary", solidHeader=T, width = 12,
# barplot download
conditionalPanel(
condition = "input.tabset=='overview'",
downloadButton("dlRaw", "Download raw data of selected families"),
downloadButton("dlTable", "Download filtered table")
),
# barplot download
conditionalPanel(
condition = "input.tabset=='annotation'",
downloadButton("dlAnnotationPlot", "Download barplot")
),
# sequenceplot options
conditionalPanel(
condition = "input.tabset=='alignment'",
checkboxInput('points', 'show points', value =
TRUE),
uiOutput('colorpoints'),
downloadButton("dlCurSequenceplot", "Download sequenceplot")
),
# histogram options
conditionalPanel(
condition = "input.tabset=='histogram'",
sliderInput(
'binSize',
'Number of bins',
min = 10,
max = 500,
value = min(10, 500),
step = 10,
round = 0
),
checkboxInput('facet', 'Facet by sample'),
downloadButton("dlCurPlot", "Download histogram")
),
# categorie options
conditionalPanel(
condition = "input.tabset=='categories'",
checkboxInput('navalues', 'remove NA', value =
TRUE),
checkboxInput('showmean', 'plot mean value', value =
TRUE),
checkboxInput('bysamplefacet', 'facet by sample'),
checkboxInput('bysamplecolor', 'color by sample'),
checkboxInput('showmeanselected', 'plot mean of selected families'),
selectInput(
"sortannotation",
label = "Order by",
choices = list("ratio" = "ratio", "p-value (not implemented)" = "pvalue"),
selected = "ratio"
),
downloadButton("dlCurAnnotationplot", "Download boxplot")
),
conditionalPanel(
condition = "input.tabset=='box'",
selectInput(
"oderchoice",
label = "Order by",
choices = list("Dataset name" = "default", "Mean ratio" = "mean"),
selected = "default"
),
checkboxInput('highlightbox', 'Highlight mean of selected elements'),
downloadButton("dlCurBoxPlot", "Download boxplot")
)
),
box( title = "Export & configure", status = "primary", solidHeader=T, width = 12,
condition = "input.tabset=='overview'",
actionButton('resetSelection', label = "Reset row selection"),
actionButton('reloadButton', label = "Reload/Import files")
#textOutput("reloadmsg")
)
)
),
# body: logtable
tabItem(tabName = "log",
h2("Log"),
fluidRow(column(width=12,htmlOutput("logtable")))),
# body: developer
tabItem(tabName = "developer",
h2("Developer informations"),
fluidRow(
column(width=6,
box( title ="URL components",
verbatimTextOutput("urlText"), width = NULL),
box( title ="Parsed query string",
verbatimTextOutput("queryText"), width = NULL),
box( title ="statusinformation",
verbatimTextOutput("sessioninfo"), width = NULL),
box( title ="command on button",
verbatimTextOutput("cmdinfo"), width = NULL),
box( title ="system state",
verbatimTextOutput("stateinfo"), width = NULL)
),
column(width=6,
box( title ="clientData values",
verbatimTextOutput("clientdataText"), width = NULL),
box( title ="session information",
verbatimTextOutput("statusinfo"), width = NULL),
box( title ="file information",
verbatimTextOutput("fileinfo"), width = NULL),
box( title ="viz information",
verbatimTextOutput("vizinfo"), width = NULL)
)
)
)
)
)
)