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ui.R
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ui.R
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LIR_Info_Title <- paste("Click on an image to view the LIRs identified in a genome;",
"Number_of_LIR: number of LIRs identified by IRF;",
"Length: length of a LIR;",
"Left_start: start coordinate of the left arm of a LIR;",
"Left_end: end coordinate of the left arm of a LIR;",
"Left_len: length of the left arm of a LIR;",
"Right_start: start coordinate of the right arm of a LIR;",
"Right_end: end coordinate of the right arm of a LIR;",
"Right_len: length of the right arm of a LIR;",
"Loop_len: length of the loop between the left and the right arm;",
"Match_per: percentage of sequence matches between the left and the right arm;",
"Indel_per: percentage of indels between the left and the right arm;",
sep = "<br>")
search_help_Title <- paste("Click on a row to check the details of the LIR!",
"Left_start: start coordinate of the left arm of a LIR;",
"Left_end: end coordinate of the left arm of a LIR;",
"Left_len: length of the left arm of a LIR;",
"Right_start: start coordinate of the right arm of a LIR;",
"Right_end: end coordinate of the right arm of a LIR;",
"Right_len: length of the right arm of a LIR;",
"Loop_len: length of the loop between the left and the right arm;",
"Match_per: percentage of sequence matches between the left and the right arm;",
"Indel_per: percentage of indels between the left and the right arm;",
sep = "<br>")
Blast_Info_Title <- paste("qseqid: Query sequence ID;",
"qlen: Query sequence length;",
"sseqid: Subject sequence ID;",
"slen: Subject sequence length;",
"qstart: Start of alignment in query;",
"qend: End of alignment in query;",
"sstart: Start of alignment in subject;",
"send: End of alignment in subject;",
"bitscore: Bit score;",
"evalue: Expect value;",
"gaps: Number of gaps;",
"pident: Percentage of identical matches;",
"length: Alignment length;",
sep = "<br>")
Align_Info_Title <- paste("Click on a row to check the details of the LIR and the alignment!",
"Set the values of each column to identify candidate LIRs encoding hpRNA;",
"sRNA_number: number of sRNAs aligned to the LIR;",
"sRNA_21_22_percent: percentage of 21-nt and 22-nt sRNAs among all sRNAs aligned to the LIR;",
"sRNA_24_percent: percentage of 24-nt sRNAs among all sRNAs aligned to the LIR;",
"sRNA_in_arm_percent: percentage of sRNAs aligned to the arms of the LIR among all sRNAs aligned to the LIR;",
"sRNA_in_loop_percent: percentage of sRNAs aligned to the loop of the LIR among all sRNAs aligned to the LIR;",
"sRNA_in_flank_percent: percentage of sRNAs aligned to the flanking sequences of the LIR among all sRNAs aligned to the LIR;",
"sRNA_read_number: number of sRNA sequencing reads aligned to the LIR;",
sep = "<br>")
Target_Info_Title <- paste("Identify protein-coding genes targeted by the small RNAs derived from a LIR through detecting the complementary matches between small RNAs and the cDNA sequence of protein-coding genes.",
"sRNA_number: number of sRNAs complementary aligned to the cDNA;",
"sRNA_21_number: number of 21-nt sRNAs complementary aligned to the cDNA;",
"sRNA_22_number: number of 22-nt sRNAs complementary aligned to the cDNA;",
"sRNA_24_number: number of 24-nt sRNAs complementary aligned to the cDNA;",
sep = "<br>")
Bowtiedb.fl <- read.table("Bowtiedb.txt", head=T, as.is=T)
Bowtiedb.cDNA.fl <- read.table("Bowtiedb_cDNA.txt", head=T, as.is=T, sep="\t")
source("box_format.R")
shinyUI(
fluidPage(
titlePanel(title=div(
img(src="headerN.png"),
span("LIRBase:", style = "font-size:36px;color:white;"),
span("a comprehensive collection of long inverted repeats in eukaryotes", style = "font-size:28px;color:white;"),
style = "background-color:#0073B7;margin-left: -15px;margin-right: -15px;margin-top: -20px;margin-bottom: -10px;"
), windowTitle = "Welcome to LIRBase!"
),
includeCSS("www/footer.css"),
shinydisconnect::disconnectMessage(
text = "Your session timed out, reload the application!",
refresh = "Reload now",
background = "#f89f43",
colour = "white",
overlayColour = "grey",
overlayOpacity = 0.75,
top = 250,
refreshColour = "brown"
),
htmlwidgets::getDependency('sparkline'),
navbarPage(id = "The_page",
# title = HTML("<strong style='font-size:18px'>LIRBase</strong>"),
title = "",
windowTitle = "Welcome to LIRBase!",
## Home
tabPanel(HTML("<strong style='font-size:18px'>Home</strong>"),
tags$head(
tags$style("
input[type='file'] {width:5em;}
.toggleButton {width:100%;}
.clearButton {float:right; font-size:12px;}
.fa-angle-down:before, .fa-angle-up:before {float:right;}
.popover{text-align:left;width:500px;background-color:#000000;}
.popover-title{color:#FFFFFF;font-size:16px;background-color:#000000;border-color:#000000;}
.jhr{display: inline; vertical-align: top; padding-left: 10px;}
#sidebarPanel_1 {width:25em;}
#mainPanel_1 {left:28em; position:absolute; min-width:27em;}
.popover{max-width: 60%;}
"),
tags$style(HTML(".shiny-output-error-validation {color: red;}")),
tags$style(HTML(
".checkbox {margin: 0}
.checkbox p {margin: 0;}
.shiny-input-container {margin-bottom: 0;}
.navbar-default .navbar-brand {color: black; font-size:150%;}
.navbar-default .navbar-nav > li > a {color:black; font-size:120%;}
.shiny-input-container:not(.shiny-input-container-inline) {width: 100%;}
")),
tags$script(HTML('Shiny.addCustomMessageHandler("jsCode",function(message) {eval(message.value);});'))
),
tags$head(tags$script(HTML('Shiny.addCustomMessageHandler("jsCode",function(message) {eval(message.value);});')),
tags$style(
HTML(
"
#inputs-table {
border-collapse: collapse;
}
#inputs-table td {
padding: 3px;
vertical-align: bottom;
}
.multicol .shiny-options-group{
-webkit-column-count: 2; /* Chrome, Safari, Opera */
-moz-column-count: 2; /* Firefox */
column-count: 2;
-moz-column-fill: balanced;
-column-fill: balanced;
}
.checkbox{
margin-top: 0px !important;
-webkit-margin-after: 1px !important;
}
"
) #/ HTML
) #/ style
), #/ head
icon = icon("home", class = NULL, lib = "font-awesome"),
source("Homepage.R", local = TRUE)$value
# htmlwidgets::getDependency('sparkline'),
# dataTableOutput("IRFsummary")
),
# Browse
navbarMenu(
HTML("<strong style='font-size:18px'>Browse</strong>"),
icon = icon("folder-open-o", class = NULL, lib = "font-awesome"),
tabPanel(HTML("<strong style='font-size:17px'>Invertebrate metazoa</strong>"), icon = icon("folder-open-o", class = NULL, lib = "font-awesome"),
column(12,
fixedRow(
column(12,
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Browse long inverted repeats identified in 77 Invertebrate metazoa genomes</b></font>'),
bsButton("qLIRInfoTitle_Metazoa", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qLIRInfoTitle_Metazoa", title = LIR_Info_Title, content = NULL, trigger = "focus", options = list(container = "body"))
)
),
tabsetPanel(id = "browser_Metazoa",
tabPanel(title = HTML("<strong style='font-size:18px'>Species</strong>"), id = "browser_Metazoa_Species",
DT::dataTableOutput('HTMLtable_Metazoa')
),
tabPanel(title = HTML("<strong style='font-size:18px'>LIRs of Invertebrate metazoa</strong>"), id = "browser_LIR_Metazoa",
shinycssloaders::withSpinner(DT::dataTableOutput("LIR_info_num_Metazoa")),
br(),
htmlOutput("IRFbrowse_title_Metazoa"),
tags$head(tags$style("#IRFbrowse_title_Metazoa{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(DT::dataTableOutput("IRFbrowse_Metazoa")),
br(),
conditionalPanel(condition = "typeof input.IRFbrowse_Metazoa_rows_selected !== 'undefined' && input.IRFbrowse_Metazoa_rows_selected.length > 0",
fixedRow(
column(4,
shinyWidgets::actionBttn("Browse_LIR_op_Metazoa", "Overlaps between the selected LIR and genes",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Browse_LIR_seq_Metazoa", "Sequence of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Browse_LIR_detail_Metazoa", "Structure of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
)
)
)
)
),
bsModal("BrowseLIRop_Metazoa", "Overlaps between the selected LIR and genes", "Browse_LIR_op_Metazoa", size = "large",
htmlOutput("LIR_gene_op_title_Metazoa"),
tags$head(tags$style("#LIR_gene_op_title_Metazoa{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(DT::dataTableOutput("LIR_gene_op_Metazoa"))
),
bsModal("BrowseLIRseq_Metazoa", "Sequence of the selected LIR", "Browse_LIR_seq_Metazoa", size = "large",
htmlOutput("LIR_sequence_title_Metazoa"),
tags$head(tags$style("#LIR_sequence_title_Metazoa{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(htmlOutput("LIR_sequence_Metazoa", placeholder = FALSE)),
tags$head(tags$style("#LIR_sequence_Metazoa {
width: 100%;
padding: 6px 12px;
height: 400px;
white-space: pre-wrap;
background: white;
overflow: auto;
}"
))
),
bsModal("BrowseLIRdetail_Metazoa", "Structure of the selected LIR", "Browse_LIR_detail_Metazoa", size = "large",
htmlOutput("LIR_detail_title_Metazoa"),
tags$head(tags$style("#LIR_detail_title_Metazoa{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(verbatimTextOutput("LIR_detail_Metazoa")),
tags$head(tags$style("#LIR_detail_Metazoa {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
}"
))
),
br(),br()
)
),
tabPanel(HTML("<strong style='font-size:17px'>Plant</strong>"), icon = icon("folder-open-o", class = NULL, lib = "font-awesome"),
column(12,
fixedRow(
column(12,
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Browse long inverted repeats identified in 142 Plant genomes</b></font>'),
bsButton("qLIRInfoTitle_Plant", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qLIRInfoTitle_Plant", title = LIR_Info_Title, content = NULL, trigger = "focus", options = list(container = "body"))
)
),
tabsetPanel(id = "browser_Plant",
tabPanel(title = HTML("<strong style='font-size:18px'>Species</strong>"), id = "browser_Plant_Species",
DT::dataTableOutput('HTMLtable_Plant')
),
tabPanel(title = HTML("<strong style='font-size:18px'>LIRs of Plant</strong>"), id = "browser_LIR_Plant",
shinycssloaders::withSpinner(DT::dataTableOutput("LIR_info_num_Plant")),
br(),
htmlOutput("IRFbrowse_title_Plant"),
tags$head(tags$style("#IRFbrowse_title_Plant{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(DT::dataTableOutput("IRFbrowse_Plant")),
br(),
conditionalPanel(condition = "typeof input.IRFbrowse_Plant_rows_selected !== 'undefined' && input.IRFbrowse_Plant_rows_selected.length > 0",
fixedRow(
column(4,
shinyWidgets::actionBttn("Browse_LIR_op_Plant", "Overlaps between the selected LIR and genes",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Browse_LIR_seq_Plant", "Sequence of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Browse_LIR_detail_Plant", "Structure of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
)
)
)
)
),
bsModal("BrowseLIRop_Plant", "Overlaps between the selected LIR and genes", "Browse_LIR_op_Plant", size = "large",
htmlOutput("LIR_gene_op_title_Plant"),
tags$head(tags$style("#LIR_gene_op_title_Plant{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(DT::dataTableOutput("LIR_gene_op_Plant"))
),
bsModal("BrowseLIRseq_Plant", "Sequence of the selected LIR", "Browse_LIR_seq_Plant", size = "large",
htmlOutput("LIR_sequence_title_Plant"),
tags$head(tags$style("#LIR_sequence_title_Plant{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(htmlOutput("LIR_sequence_Plant", placeholder = FALSE)),
tags$head(tags$style("#LIR_sequence_Plant {
width: 100%;
padding: 6px 12px;
height: 400px;
white-space: pre-wrap;
background: white;
overflow: auto;
}"
))
),
bsModal("BrowseLIRdetail_Plant", "Structure of the selected LIR", "Browse_LIR_detail_Plant", size = "large",
htmlOutput("LIR_detail_title_Plant"),
tags$head(tags$style("#LIR_detail_title_Plant{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(verbatimTextOutput("LIR_detail_Plant")),
tags$head(tags$style("#LIR_detail_Plant {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
}"
))
),
br(),br()
)
),
tabPanel(HTML("<strong style='font-size:17px'>Vertebrate</strong>"), icon = icon("folder-open-o", class = NULL, lib = "font-awesome"),
column(12,
fixedRow(
column(12,
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Browse long inverted repeats identified in 208 Vertebrate genomes</b></font>'),
bsButton("qLIRInfoTitle_Vertebrate", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qLIRInfoTitle_Vertebrate", title = LIR_Info_Title, content = NULL, trigger = "focus", options = list(container = "body"))
)
),
tabsetPanel(id = "browser_Vertebrate",
tabPanel(title = HTML("<strong style='font-size:18px'>Species</strong>"), id = "browser_Vertebrate_Species",
DT::dataTableOutput('HTMLtable_Vertebrate')
),
tabPanel(title = HTML("<strong style='font-size:18px'>LIRs of Vertebrate</strong>"), id = "browser_LIR_Vertebrate",
shinycssloaders::withSpinner(DT::dataTableOutput("LIR_info_num_Vertebrate")),
br(),
htmlOutput("IRFbrowse_title_Vertebrate"),
tags$head(tags$style("#IRFbrowse_title_Vertebrate{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(DT::dataTableOutput("IRFbrowse_Vertebrate")),
br(),
conditionalPanel(condition = "typeof input.IRFbrowse_Vertebrate_rows_selected !== 'undefined' && input.IRFbrowse_Vertebrate_rows_selected.length > 0",
fixedRow(
column(4,
shinyWidgets::actionBttn("Browse_LIR_op_Vertebrate", "Overlaps between the selected LIR and genes",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Browse_LIR_seq_Vertebrate", "Sequence of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Browse_LIR_detail_Vertebrate", "Structure of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
)
)
)
)
),
bsModal("BrowseLIRop_Vertebrate", "Overlaps between the selected LIR and genes", "Browse_LIR_op_Vertebrate", size = "large",
htmlOutput("LIR_gene_op_title_Vertebrate"),
tags$head(tags$style("#LIR_gene_op_title_Vertebrate{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(DT::dataTableOutput("LIR_gene_op_Vertebrate"))
),
bsModal("BrowseLIRseq_Vertebrate", "Sequence of the selected LIR", "Browse_LIR_seq_Vertebrate", size = "large",
htmlOutput("LIR_sequence_title_Vertebrate"),
tags$head(tags$style("#LIR_sequence_title_Vertebrate{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(htmlOutput("LIR_sequence_Vertebrate", placeholder = FALSE)),
tags$head(tags$style("#LIR_sequence_Vertebrate {
width: 100%;
padding: 6px 12px;
height: 400px;
white-space: pre-wrap;
background: white;
overflow: auto;
}"
))
),
bsModal("BrowseLIRdetail_Vertebrate", "Structure of the selected LIR", "Browse_LIR_detail_Vertebrate", size = "large",
htmlOutput("LIR_detail_title_Vertebrate"),
tags$head(tags$style("#LIR_detail_title_Vertebrate{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(verbatimTextOutput("LIR_detail_Vertebrate")),
tags$head(tags$style("#LIR_detail_Vertebrate {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
}"
))
),
br(),br()
)
)
),
# Search
navbarMenu(
HTML("<strong style='font-size:18px'>Search</strong>"),
icon = icon("search", class = NULL, lib = "font-awesome"),
tabPanel(HTML("<strong style='font-size:17px'>Search by genomic location</strong>"), icon = icon("search-location"),
column(12,
fixedRow(
column(12,
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Search by genomic location</b></font>'),
bsButton("qSearchRegTitle", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qSearchRegTitle", "Search for the information of long inverted repeats identified in any of the 427 genomes by genomic locations!", trigger = "focus")
)
),
fixedRow(
column(6,
shinyWidgets::multiInput(
inputId = "chooseGenomeReg",
label = tags$div(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red">Choose genome</font>')),
choices = NULL, width = '100%',
choiceNames = BLASTdb.fl$Accession,
choiceValues = BLASTdb.fl$Accession,
options = list(
enable_search = TRUE, limit = 1,
non_selected_header = "Choose from:",
selected_header = "You have selected:"
)
)
),
column(6,
shinyWidgets::pickerInput(inputId = "chooseChromosomeReg",
label = tags$div(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red">Choose chromosome</font>')),
choices = NULL, width = '100%', selected = NULL, options = list(
`live-search` = TRUE
)),
uiOutput("searchRegion"),
br(),
shinysky::actionButton("submitSearchReg", strong("Search!",
bsButton("qpSearchReg", label="", icon=icon("question"), style="info", size="small")
), styleclass = "success"),
conditionalPanel(condition="input.submitSearchReg != '0'", shinysky::busyIndicator(HTML("<p style='color:red;font-size:30px;'>Calculation In progress...</p>"), wait = 0)),
bsPopover("qpSearchReg", "Click this button to start the search!", trigger = "focus")
)
),
br(),
fluidRow(
column(6,
downloadButton("searchRegDownIRFresult.txt", "Structure of LIRs in the search result", style = "width:95%;", class = "buttDown"),
tags$head(tags$style(".buttDown{background-color:black; color: white; font-size: 16px;}"))
),
column(6,
downloadButton("searchRegDownIRFfasta.txt", "Sequence of LIRs in the search result", style = "width:95%;", class = "buttDown")
)
),
br(),
conditionalPanel(condition="input.submitSearchReg > 0",
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Search result</b></font>'),
bsButton("qSearchRegHelp", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qSearchRegHelp", title = search_help_Title, trigger = "focus", content = NULL)
),
DT::dataTableOutput("LIRsearchRegResult"),
conditionalPanel(condition = "typeof input.LIRsearchRegResult_rows_selected !== 'undefined' && input.LIRsearchRegResult_rows_selected.length > 0",
fixedRow(
column(4,
shinyWidgets::actionBttn("Search_Reg_LIR_op", "Overlaps between the selected LIR and genes",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Search_Reg_LIR_seq", "Sequence of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Search_Reg_LIR_detail", "Structure of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
)
)
),
br(),
bsModal("SearchRegLIRop", "Overlaps between the selected LIR and genes", "Search_Reg_LIR_op", size = "large",
htmlOutput("Search_reg_LIR_gene_op_title"),
tags$head(tags$style("#Search_reg_LIR_gene_op_title{color: red;
font-size: 22px;
font-style: bold;
}"
)),
DT::dataTableOutput("Search_reg_LIR_gene_op")
),
bsModal("SearchRegLIRseq", "Sequence of the selected LIR", "Search_Reg_LIR_seq", size = "large",
htmlOutput("LIR_detail_search_reg_fasta_title"),
tags$head(tags$style("#LIR_detail_search_reg_fasta_title{color: red;
font-size: 22px;
font-style: bold;
}"
)),
htmlOutput("LIR_detail_search_reg_fasta"),
tags$head(tags$style("#LIR_detail_search_reg_fasta {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
overflow: auto;
}"
))
),
bsModal("SearchRegLIRdetail", "Structure of the selected LIR", "Search_Reg_LIR_detail", size = "large",
htmlOutput("LIR_detail_search_reg_title"),
tags$head(tags$style("#LIR_detail_search_reg_title{color: red;
font-size: 22px;
font-style: bold;
}"
)),
verbatimTextOutput("LIR_detail_search_reg"),
tags$head(tags$style("#LIR_detail_search_reg {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
}"
))
),
br(),br()
)
),
tabPanel(HTML("<strong style='font-size:17px'>Search by LIR identifier</strong>"), icon = icon("id-card"),
column(12,
fixedRow(
column(6,
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Search by LIR identifier</b></font>'),
bsButton("qSearchIDTitle", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qSearchIDTitle", "Search for the information of long inverted repeats identified in any of the 427 genomes by the identifier of LIRs!", trigger = "focus")
)
),
tabsetPanel(id = "search_ID",
tabPanel(HTML("<strong style='font-size:18px'>Input</strong>"),
fluidRow(
column(6,
textAreaInput("LIRID", label = tags$div(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red">Input LIR identifiers</font>')),
value = "", resize = "vertical", height='400px', width = '100%',
placeholder = "One item in one row")
),
column(6,
shinyWidgets::pickerInput(
inputId = "chooseGenomeID",
label = tags$div(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red">Choose genome</font>')),
width = '100%', selected = NULL,
choices = list(
`Invertebrate metazoa` = BLASTdb.fl$Accession[BLASTdb.fl$Division == "Metazoa"],
Plant = BLASTdb.fl$Accession[BLASTdb.fl$Division == "Plant"],
Vertebrate = BLASTdb.fl$Accession[BLASTdb.fl$Division == "Vertebrate"]
),
options = list(
`live-search` = TRUE
)
),
br(),
shinysky::actionButton("submitSearchID", strong("Search!",
bsButton("qpSearchID", label="", icon=icon("question"), style="info", size="small")
), styleclass = "success"),
shinysky::actionButton("clear2", strong("Reset"), styleclass = "warning"),
shinysky::actionButton("searchIDExam", strong("Load example"), styleclass = "info"),
conditionalPanel(condition="input.submitSearchID != '0'", shinysky::busyIndicator(HTML("<p style='color:red;font-size:30px;'>Calculation In progress...</p>"), wait = 0)),
bsPopover("qpSearchID", "Click this button to start the search!", trigger = "focus")
)
)
),
tabPanel(HTML("<strong style='font-size:18px'>Output</strong>"),
fluidRow(
column(6,
downloadButton("searchIDDownIRFresult.txt", "Structure of LIRs in the search result", style = "width:100%;", class = "buttDown"),
),
column(6,
downloadButton("searchIDDownIRFfasta.txt", "Sequence of LIRs in the search result", style = "width:100%;", class = "buttDown")
)
),
br(),
conditionalPanel(condition="input.submitSearchID > 0",
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Search result</b></font>'),
bsButton("qSearchIDHelp", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qSearchIDHelp", title = search_help_Title, trigger = "focus", content = NULL)
),
DT::dataTableOutput("LIRsearchIDResult"),
conditionalPanel(condition = "typeof input.LIRsearchIDResult_rows_selected !== 'undefined' && input.LIRsearchIDResult_rows_selected.length > 0",
fixedRow(
column(4,
shinyWidgets::actionBttn("Search_ID_LIR_op", "Overlaps between the selected LIR and genes",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Search_ID_LIR_seq", "Sequence of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Search_ID_LIR_detail", "Structure of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
)
)
),
br()
)
),
bsModal("SearchIDLIRop", "Overlaps between the selected LIR and genes", "Search_ID_LIR_op", size = "large",
htmlOutput("Search_ID_LIR_gene_op_title"),
tags$head(tags$style("#Search_ID_LIR_gene_op_title{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(DT::dataTableOutput("Search_ID_LIR_gene_op"))
),
bsModal("SearchIDLIRseq", "Sequence of the selected LIR", "Search_ID_LIR_seq", size = "large",
htmlOutput("LIR_detail_search_ID_fasta_title"),
tags$head(tags$style("#LIR_detail_search_ID_fasta_title{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(htmlOutput("LIR_detail_search_ID_fasta")),
tags$head(tags$style("#LIR_detail_search_ID_fasta {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
overflow: auto;
}"
))
),
bsModal("SearchIDLIRdetail", "Structure of the selected LIR", "Search_ID_LIR_detail", size = "large",
htmlOutput("LIR_detail_search_ID_title"),
tags$head(tags$style("#LIR_detail_search_ID_title{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(verbatimTextOutput("LIR_detail_search_ID")),
tags$head(tags$style("#LIR_detail_search_ID {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
}"
))
),
br(),br()
)
),
# Blast
tabPanel(
HTML("<strong style='font-size:17px'>BLAST</strong>"),
icon = icon("rocket", class = NULL, lib = "font-awesome"),
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Search LIRBase by sequence similarity using BLAST</b></font>'),
bsButton("qBlastTitle", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qBlastTitle", title = Blast_Info_Title, content = NULL, trigger = "focus"),
column(12,
tabsetPanel(id = "BLAST_tab",
tabPanel(HTML("<strong style='font-size:18px'>Input</strong>"),
fixedRow(
column(5,
selectInput("In_blast", label = tags$div(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red">Paste or upload input data?</font>'),
bsButton("qBlastIn", label="", icon=icon("question"), style="info", size="small")
), choices = list("Paste input data" = "paste",
"Upload input data" = "upload"),
selected = "paste"),
bsPopover("qBlastIn", "The input data must be DNA sequence in fasta format.", trigger = "focus"),
conditionalPanel(condition="input.In_blast == 'paste'",
textAreaInput("BlastSeqPaste", label = h4("Input sequence"),
value = "", resize = "vertical", height='400px', width = '100%',
placeholder = "The sequence must be in fasta format")
),
conditionalPanel(condition="input.In_blast == 'upload'",
fileInput("BlastSeqUpload",
label = h4("Upload file"), multiple = FALSE, width = "100%"),
downloadButton("BLAST_Input.txt", "Example BLAST input data", style = "width:100%;", class = "buttDown")
)
),
column(4,
shinyWidgets::multiInput(
inputId = "BLASTdb",
label = tags$div(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red">Choose BLAST databases</font>'),
bsButton("qblastDB", label="", icon=icon("question"), style="info", size="small")
),
choices = NULL, width = '100%',
choiceNames = BLASTdb.fl$Accession,
choiceValues = BLASTdb.fl$Accession,
options = list(
enable_search = TRUE,
non_selected_header = "Choose from:",
selected_header = "You have selected:"
)
),
bsPopover("qblastDB", "Choose one or multiple BLAST database to search against.",
trigger = "focus")
),
column(3,
textInput("BLASTev", label = tags$div(HTML('<i class="fa fa-play"></i> <font size="3" color="red">E-value cutoff</font>'),
bsButton("qBLASTev", label="", icon=icon("question"), style="info", size="small")),
value = "10", width = NULL, placeholder = NULL),
bsPopover("qBLASTev", "Set E-value threshold to filter the BLAST output.",
trigger = "focus"),
textInput("BLASTht", label = tags$div(HTML('<i class="fa fa-play"></i> <font size="3" color="red">Maximum no. of hits</font>'),
bsButton("qBLASTht", label="", icon=icon("question"), style="info", size="small")),
value = "10", width = NULL, placeholder = NULL),
bsPopover("qBLASTht", "Maximum number of BLAST hits to report for each subject.",
trigger = "focus"),
br(),
shinysky::actionButton("submitBLAST", strong("BLAST!",
bsButton("qBLASTGO", label="", icon=icon("question"), style="info", size="small")
), styleclass = "success"),
shinysky::actionButton("clear3", strong("Reset"), styleclass = "warning"),
shinysky::actionButton("blastExam", strong("Load example"), styleclass = "info"),
conditionalPanel(condition="input.submitBLAST != '0'", shinysky::busyIndicator(HTML("<p style='color:red;font-size:30px;'>Calculation In progress...</p>"), wait = 0)),
bsPopover("qBLASTGO", "Click this button to start the BLAST alignment!",
trigger = "focus"),
)
)
),
tabPanel(HTML("<strong style='font-size:18px'>Output</strong>"),
fixedRow(
column(4,
downloadButton("BLASTresult.txt", "BLAST result", style = "width:100%;", class = "buttDown")
),
column(4,
downloadButton("blastDownIRFresult.txt", "Structure of LIRs in the BLAST result", style = "width:100%;", class = "buttDown")
),
column(4,
downloadButton("blastDownIRFfasta.txt", "Sequence of LIRs in the BLAST result", style = "width:100%;", class = "buttDown")
)
),
br(),
conditionalPanel(condition="input.submitBLAST > 0",
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>BLAST output</b></font>'),
bsButton("qBLASTresultHelp", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qBLASTresultHelp", title = "Click on a row to check the details of the LIR and the BLAST alignment!", trigger = "focus", content = NULL)
),
DT::dataTableOutput("BLASTresult"),
br(),
conditionalPanel(condition = "typeof input.BLASTresult_rows_selected !== 'undefined' && input.BLASTresult_rows_selected.length > 0",
fixedRow(
column(4,
shinyWidgets::actionBttn("Blast_LIR_op", "Overlaps between the selected LIR and genes",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Blast_LIR_seq", "Sequence of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
),
column(4,
shinyWidgets::actionBttn("Blast_LIR_detail", "Structure of the selected LIR",
icon = icon("eye", class = NULL, lib = "font-awesome"),
block = TRUE, size = "sm", style="unite", color="default")
)
)
),
br(),
fixedRow(
htmlOutput("BLAST_hit_detail_title"),
tags$head(tags$style("#BLAST_hit_detail_title {
color: red;
font-size: 22px;
font-style: bold;
}"
))
),
fluidRow(
column(5,
tableOutput("BLAST_hit_summary"),
tags$head(tags$style("#BLAST_hit_summary {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
}"
))
),
column(7,
shinycssloaders::withSpinner(verbatimTextOutput("BLAST_hit_detail")),
tags$head(tags$style("#BLAST_hit_detail {
width: 800px;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
}"
))
)
),
br()
)
),
bsModal("BlastLIRop", "Overlaps between the selected LIR and genes", "Blast_LIR_op", size = "large",
htmlOutput("Blast_LIR_gene_op_title"),
tags$head(tags$style("#Blast_LIR_gene_op_title{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(DT::dataTableOutput("Blast_LIR_gene_op"))
),
bsModal("BlastLIRseq", "Sequence of the selected LIR", "Blast_LIR_seq", size = "large",
htmlOutput("LIR_detail_blast_fasta_title"),
tags$head(tags$style("#LIR_detail_blast_fasta_title{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(htmlOutput("LIR_detail_blast_fasta")),
tags$head(tags$style("#LIR_detail_blast_fasta {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
overflow: auto;
}"
))
),
bsModal("BlastLIRdetail", "Structure of the selected LIR", "Blast_LIR_detail", size = "large",
htmlOutput("LIR_detail_blast_title"),
tags$head(tags$style("#LIR_detail_blast_title{color: red;
font-size: 22px;
font-style: bold;
}"
)),
shinycssloaders::withSpinner(verbatimTextOutput("LIR_detail_blast")),
tags$head(tags$style("#LIR_detail_blast {
width: 100%;
padding: 6px 12px;
white-space: pre-wrap;
height: 400px;
background: white;
}"
))
),
br(),br()
)
)
),
# Annotate
tabPanel(
HTML("<strong style='font-size:18px'>Annotate</strong>"),
icon = icon("cogs", class = NULL, lib = "font-awesome"),
column(12,
sidebarPanel(width=4,
tags$div(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Annotate LIRs in user-uploaded DNA sequences</b></font>'),
bsButton("qAnnotateTitle", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qAnnotateTitle", "Detect long inverted repeats using IRF <br/> (https://tandem.bu.edu/irf/irf.download.html)!", trigger = "focus"),
selectInput("In_predict", label = tags$div(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red">Paste or upload input data?</font>'),
bsButton("qPredictIn", label="", icon=icon("question"), style="info", size="small")
), choices = list("Paste input data" = "paste",
"Upload input data" = "upload"),
selected = "paste"),
bsPopover("qPredictIn", "The input data must be DNA sequence in fasta format. Each sequence should have a unique ID start with >.", trigger = "focus"),
conditionalPanel(condition="input.In_predict == 'paste'",
textAreaInput("PreSeqPaste", label = h4("Input sequence"),
value = "", resize = "vertical", height='220px', width = '100%',
placeholder = "The sequence must be in fasta format")
),
conditionalPanel(condition="input.In_predict == 'upload'",
fileInput("PreSeqUpload",
label = h4("Upload file"), multiple = FALSE, width = "100%"),
downloadButton("Annotate_Input.txt", "Example input data", style = "width:100%;", class = "buttDown")
),
br(),
shinysky::actionButton("submitP", strong("Submit!",
bsButton("qp10", label="", icon=icon("question"), style="info", size="small")
), styleclass = "success"),
shinysky::actionButton("clear1", strong("Reset"), styleclass = "warning"),
shinysky::actionButton("predictExam", strong("Load example"), styleclass = "info"),
conditionalPanel(condition="input.submitP != '0'", shinysky::busyIndicator(HTML("<p style='color:red;font-size:30px;'>Calculation In progress...</p>"), wait = 0)),
bsPopover("qp10", "Click this button to start the annotation!",
trigger = "focus"),
br(),br(),
sliderInput("Match", label = tags$div(HTML('<i class="fa fa-play"></i> <font size="3" color="red">Matching weight</font>'),