R/scanMiRui.R
In ETHZ-INS/scanMiRApp: scanMiR shiny application
Defines functions
scanMiRui
Documented in
scanMiRui
#' scanMiRui
#'
#' UI for the scanMiR app.
#'
#' @import shiny shinydashboard
#' @importFrom plotly plotlyOutput ggplotly
#' @importFrom shinycssloaders withSpinner
#' @importFrom rintrojs introjsUI introBox
#' @importFrom shinyjqui jqui_resizable
#' @importFrom waiter use_waiter waiter_show_on_load spin_1
#' @return A shiny ui
#' @export
#' @examples
#' ui <- scanMiRui()
scanMiRui <- function(){
scanMiRlogo <- paste0("https://raw.git",
"hubusercontent.com/ETHZ-INS/scanMiR/",
"master/inst/docs/sticker.svg")
mer12scheme <- paste0("https://raw.git",
"hubusercontent.com/ETHZ-INS/scanMiR/",
"master/inst/docs/12mer.png")
dashboardPage( skin="black",
dashboardHeader(title = "scanMiRApp", titleWidth = "300px",
tags$li(class="dropdown",
actionLink("helpBtn", label="Quick start",
icon=icon("question")))),
## Sidebar content
dashboardSidebar( width = "200px",
sidebarMenu(id="main_tabs",
menuItem("About", tabName="tab_about"),
menuItemOutput("menuCollection"),
menuItem("Search in\ngene/sequence", id="menuSearch",
menuSubItem("subject", "tab_subject"),
menuItemOutput("menuMirnas"),
menuSubItem("options", "tab_options"),
menuSubItem("hits", "tab_hits"),
startExpanded=TRUE
),
menuItem(tags$span(id="menuMiRNA", "miRNA-based"), tabName="tab_mirna")
),
tags$a(
href=paste0("https://git","hub.com/ETHZ-INS/scanMiR"), target="_blank",
tags$img(src=scanMiRlogo),
style="display: block; position: fixed; bottom: 5px; left: 20px;")
),
## Body Content
dashboardBody(
introjsUI(),
use_waiter(),
waiter_show_on_load(html = tagList(
tags$img(src=scanMiRlogo), tags$br(), tags$br(),
tags$h3("Please wait while the application is initialized..."),
spin_1()
)),
tabItems(
tabItem( tabName = "tab_collection",
tags$h3("Select a miRNA collection"), tags$br(),
column(6,
tabBox(id="collection_type", width=12,
tabPanel( title="Pre-built", value="prebuilt",
actionButton(inputId="help_collections", label="",
style="float:right;", icon=icon("question-circle")),
selectInput("mirlist", "miRNA collection", choices=c()))
)),
column(6, valueBoxOutput("selected_collection", width=12)),
box(width=12, title="Extra collection information",
collapsible=TRUE, collapsed=TRUE,
withSpinner(verbatimTextOutput("collection_summary")))
),
tabItem(tabName="tab_subject",
tags$div(id="subjectsbox", style="min-height: 200px;",
tabBox(
title="Search bindings in", side="right",
id="subjet_type", width=12, selected = "transcript",
tabPanel(
title="Custom sequence", value="custom",
textAreaInput(
inputId="customseq", label="Sequence (RNA or DNA)",
placeholder=paste0("Paste in here a sequence in which you want",
" to search for binding sites"),
width = "100%", height = "250px"),
checkboxInput(inputId="circular", label="circularize"),
verbatimTextOutput("custom_info"),
actionButton("rndseq", "Generate random sequence")
),
tabPanel(
title="Transcript", value="transcript",
selectizeInput("annotation", "Genome & Annotation", choices=c()),
tags$div(id="txbox",
tags$div(selectizeInput("gene", "Gene", choices=c()),
style="float: left; padding-right: 10px;"),
tags$br(), tags$p(style="text-align: left;", "Type in the first ",
"few letters of a gene name to populate the list"),
htmlOutput("gene_link"),
tags$div(style="clear: left;"),
selectizeInput("transcript", "Transcript", choices=c()),
introBox(selectInput("seqFeature", "Part to scan",
choices=c("3' UTR only", "CDS+UTR", "whole transcript")),
data.hint="You can decide here whether you want to scan
just the 3' UTR or also include the coding sequence,
or scan the whole transcript."),
withSpinner(tableOutput("tx_overview")))
)
)
)),
tabItem(tabName="tab_mirnas",
box(id="mirnasbox", width=12,
column(12, selectizeInput("mirnas", choices=c(), multiple=TRUE,
label="Selected miRNAs: (type in to filter)")),
column(8, actionButton("mirnas_vert",
"Select miRNAs conserved across vertebrates"),
tags$br(), actionButton("mirnas_mammals",
"Select miRNAs conserved across mammals"),
tags$br(), actionButton("mirnas_confident",
"Select confidently annotated miRNAs")
),
column(4, "The conservation status of miRNAs is obtained from",
tags$a(href="http://www.targetscan.org/", target="_blank",
"TargetScan")),
column(8,
checkboxInput("mirnas_all", "Search for all miRNAs")
),
column(4, actionButton("mirnas_clear",
"Clear all selected miRNAs"))
)
),
tabItem(tabName="tab_options",
box( width=6,
sliderInput("minDist",
label=paste("Minimum distance in NT between two binding sites",
"of the same miRNA"),
min = 0, max = 20, value = 7, step = 1),
sliderInput(inputId="shadow",
label=paste("Ribosomal shadow at the beginning of the 3'UTR,",
"recommended is 15 NT"),
min = 0, max = 20, value = 15, step = 1),
sliderInput(inputId="maxLogKd", label = "Maximum log_kd to report",
min = -4, max = 0, value = -1, step = 0.25)
),
box(width=6, checkboxInput("keepmatchseq", "Keep matched sequence"),
checkboxInput("scanNonCanonical",
"Search also for non-canonical sites", value=TRUE))
),
tabItem(tabName="tab_hits",
fluidRow(
column(2, tags$div(id="scanBtnBox",
style="display: inline-block; min-height: 30px; min-width: 100px;",
uiOutput("scanBtn"), HTML(" "))),
column(10, tags$h5(textOutput("scan_target")))
),
tags$div(id="hitsbox", style="min-height: 300px;",
box(width=12, collapsible=TRUE, collapsed=TRUE,
title="Display sites along transcript",
actionButton("manhattanHelp", label="", style="float: right;",
icon=icon("question-circle")),
tags$p("Hover on points to view details, and click to ",
"visualize the alignment on the target sequence. You may
also select miRNAs to show/hide by clicking on the legend."),
withSpinner(plotlyOutput("manhattan")),
column(6, numericInput("manhattan_n", "Number of top miRNAs displayed",
value=10, min=1, max=50)),
column(6, checkboxInput("manhattan_ordinal", "Ordinal position",
value=FALSE))
),
box(width=12, title="Aggregated per miRNA", collapsible=TRUE, collapsed=TRUE,
withSpinner(DTOutput("agghits_table")),
column(6,tags$p(downloadLink('dl_agghits', label = "Download all"))),
column(6, actionButton("help_aggregatedHits","About aggregation...",
icon=icon("question-circle")))
),
box(width=12, title="Table", collapsible=TRUE,
fluidRow(
column(6,
tags$p("Double click on a row to visualize the alignment",
" on the target sequence.")),
column(6, style="text-align: right;",
actionButton("colHelp","What are those columns?",
icon=icon("question-circle")),
actionButton("stypeHelp","Site types",
icon=icon("question-circle"))
)
),
withSpinner(DTOutput("hits_table")),
tags$p(downloadLink('dl_hits', label = "Download all"))
)),
box(width=12, title="Cached hits", collapsible=TRUE, collapsed=TRUE,
textOutput("cache.info"),
uiOutput("cached.results"),
actionButton("loadCache", "Load"),
actionButton("deleteCache", "Delete")
)
),
# miRNA-based
tabItem(tabName="tab_mirna",
fluidRow(
column(5, tags$div(id="mirnainput",
selectizeInput("mirna", "miRNA", choices=c()))),
column(4, tags$strong("TargetScan conservation status"),
textOutput("modconservation")),
column(3, htmlOutput("mirbase_link"))
),
tags$div(id="affinitybox", style="min-height: 40px;",
box(width=12, title="Affinity plot", collapsible=TRUE,
collapsed=TRUE,
withSpinner(jqui_resizable(plotOutput("modplot")))
)
),
tags$div(id="targetsbox", style="min-height: 100px;",
box(width=12, title="Targets", collapsible=TRUE,
uiOutput("targets_ui"))
)
),
tabItem(tabName = "tab_about",
## TAB ABOUT
box(width=12, title="miRNA binding prediction",
tags$div(style="font-size: 110%;",
tags$img(src=mer12scheme, style="float: right; margin: 20px; width: 25%;"),
tags$p("micro-RNAs (miRNAs) regulate transcripts stability and
translation by targeting the Argonaute complex to RNAs exhibiting a
partial complementarity with, in particular, the miRNA's seed
sequence. For a general review on miRNA biology and targeting, see
", tags$a(href="https://doi.org/10.1016/j.cell.2018.03.006",
"Bartel (2018)",.noWS = "outside"),".",
tags$a(href="https://dx.doi.org/10.1126/science.aav1741",
"McGeary, Lin et al. (2019)"), " have additionally shown the
relevance of flanking nucleotides by empirically measuring the affinity
(specifically the dissociation rate constant, KD) of a set of miRNAs to
random 12-mer sequences, and then computationally extrapolating to other
miRNAs). The ",
tags$a( href=paste0("https://git","hub.com/ETHZ-INS/scanMiR"),
target="_blank", "scanMiR package",.noWS = "outside"), ", to which this app is an
interface, builds on this work to offer a powerful and flexible binding
and repression prediction framework."))
),
box(width=12, title="Getting started",
tags$div( style="font-size: 110%;",
tags$p("For a quick tour of the app, ", actionLink("helpLink", "click here",.noWS = "outside"),"."),
tags$p("There are two main ways to use scanMiRApp:"),
tags$br(), tags$h4("Transcript-centered:"),
tags$p("In the 'Search in gene/sequence' menu, you'll be able to ",
"scan the sequence of a given transcript for binding sites ",
"of (sets of) miRNA(s)."),
tags$br(), tags$h4("miRNA-centered:"),
tags$p("In the 'miRNA-based' tab on the left, you'll be able to ",
"visualize information relative to a selected miRNA, ",
"including for instance its general binding profile and its",
"top targets.")
)
),
tags$div(style="text-align: right; font-weight: normal;",
tags$p("The shiny app was developed by Pierre-Luc Germain and ",
"Michael Soutschek in the context of broader research in the ",
tags$a( href="http://schrattlab.ethz.ch", "Schratt lab",
target="_blank",.noWS = "outside"), ".",
tags$br(), "Bugs reports and feature requests are welcome on the ",
tags$a( href=paste0("https://git","hub.com/ETHZ-INS/scanMiRApp/issues"),
target="_blank", "github repository",.noWS = "outside"), "."),
textOutput("pkgVersions")
)
## END TAB ABOUT
)
),
tags$head(tags$style(HTML('.content-wrapper { overflow: auto; }')))
)
)
}
ETHZ-INS/scanMiRApp documentation built on March 16, 2024, 5:30 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.
Defines functions scanMiRui
Documented in scanMiRui
#' scanMiRui
#'
#' UI for the scanMiR app.
#'
#' @import shiny shinydashboard
#' @importFrom plotly plotlyOutput ggplotly
#' @importFrom shinycssloaders withSpinner
#' @importFrom rintrojs introjsUI introBox
#' @importFrom shinyjqui jqui_resizable
#' @importFrom waiter use_waiter waiter_show_on_load spin_1
#' @return A shiny ui
#' @export
#' @examples
#' ui <- scanMiRui()
scanMiRui <- function(){
scanMiRlogo <- paste0("https://raw.git",
"hubusercontent.com/ETHZ-INS/scanMiR/",
"master/inst/docs/sticker.svg")
mer12scheme <- paste0("https://raw.git",
"hubusercontent.com/ETHZ-INS/scanMiR/",
"master/inst/docs/12mer.png")
dashboardPage( skin="black",
dashboardHeader(title = "scanMiRApp", titleWidth = "300px",
tags$li(class="dropdown",
actionLink("helpBtn", label="Quick start",
icon=icon("question")))),
## Sidebar content
dashboardSidebar( width = "200px",
sidebarMenu(id="main_tabs",
menuItem("About", tabName="tab_about"),
menuItemOutput("menuCollection"),
menuItem("Search in\ngene/sequence", id="menuSearch",
menuSubItem("subject", "tab_subject"),
menuItemOutput("menuMirnas"),
menuSubItem("options", "tab_options"),
menuSubItem("hits", "tab_hits"),
startExpanded=TRUE
),
menuItem(tags$span(id="menuMiRNA", "miRNA-based"), tabName="tab_mirna")
),
tags$a(
href=paste0("https://git","hub.com/ETHZ-INS/scanMiR"), target="_blank",
tags$img(src=scanMiRlogo),
style="display: block; position: fixed; bottom: 5px; left: 20px;")
),
## Body Content
dashboardBody(
introjsUI(),
use_waiter(),
waiter_show_on_load(html = tagList(
tags$img(src=scanMiRlogo), tags$br(), tags$br(),
tags$h3("Please wait while the application is initialized..."),
spin_1()
)),
tabItems(
tabItem( tabName = "tab_collection",
tags$h3("Select a miRNA collection"), tags$br(),
column(6,
tabBox(id="collection_type", width=12,
tabPanel( title="Pre-built", value="prebuilt",
actionButton(inputId="help_collections", label="",
style="float:right;", icon=icon("question-circle")),
selectInput("mirlist", "miRNA collection", choices=c()))
)),
column(6, valueBoxOutput("selected_collection", width=12)),
box(width=12, title="Extra collection information",
collapsible=TRUE, collapsed=TRUE,
withSpinner(verbatimTextOutput("collection_summary")))
),
tabItem(tabName="tab_subject",
tags$div(id="subjectsbox", style="min-height: 200px;",
tabBox(
title="Search bindings in", side="right",
id="subjet_type", width=12, selected = "transcript",
tabPanel(
title="Custom sequence", value="custom",
textAreaInput(
inputId="customseq", label="Sequence (RNA or DNA)",
placeholder=paste0("Paste in here a sequence in which you want",
" to search for binding sites"),
width = "100%", height = "250px"),
checkboxInput(inputId="circular", label="circularize"),
verbatimTextOutput("custom_info"),
actionButton("rndseq", "Generate random sequence")
),
tabPanel(
title="Transcript", value="transcript",
selectizeInput("annotation", "Genome & Annotation", choices=c()),
tags$div(id="txbox",
tags$div(selectizeInput("gene", "Gene", choices=c()),
style="float: left; padding-right: 10px;"),
tags$br(), tags$p(style="text-align: left;", "Type in the first ",
"few letters of a gene name to populate the list"),
htmlOutput("gene_link"),
tags$div(style="clear: left;"),
selectizeInput("transcript", "Transcript", choices=c()),
introBox(selectInput("seqFeature", "Part to scan",
choices=c("3' UTR only", "CDS+UTR", "whole transcript")),
data.hint="You can decide here whether you want to scan
just the 3' UTR or also include the coding sequence,
or scan the whole transcript."),
withSpinner(tableOutput("tx_overview")))
)
)
)),
tabItem(tabName="tab_mirnas",
box(id="mirnasbox", width=12,
column(12, selectizeInput("mirnas", choices=c(), multiple=TRUE,
label="Selected miRNAs: (type in to filter)")),
column(8, actionButton("mirnas_vert",
"Select miRNAs conserved across vertebrates"),
tags$br(), actionButton("mirnas_mammals",
"Select miRNAs conserved across mammals"),
tags$br(), actionButton("mirnas_confident",
"Select confidently annotated miRNAs")
),
column(4, "The conservation status of miRNAs is obtained from",
tags$a(href="http://www.targetscan.org/", target="_blank",
"TargetScan")),
column(8,
checkboxInput("mirnas_all", "Search for all miRNAs")
),
column(4, actionButton("mirnas_clear",
"Clear all selected miRNAs"))
)
),
tabItem(tabName="tab_options",
box( width=6,
sliderInput("minDist",
label=paste("Minimum distance in NT between two binding sites",
"of the same miRNA"),
min = 0, max = 20, value = 7, step = 1),
sliderInput(inputId="shadow",
label=paste("Ribosomal shadow at the beginning of the 3'UTR,",
"recommended is 15 NT"),
min = 0, max = 20, value = 15, step = 1),
sliderInput(inputId="maxLogKd", label = "Maximum log_kd to report",
min = -4, max = 0, value = -1, step = 0.25)
),
box(width=6, checkboxInput("keepmatchseq", "Keep matched sequence"),
checkboxInput("scanNonCanonical",
"Search also for non-canonical sites", value=TRUE))
),
tabItem(tabName="tab_hits",
fluidRow(
column(2, tags$div(id="scanBtnBox",
style="display: inline-block; min-height: 30px; min-width: 100px;",
uiOutput("scanBtn"), HTML(" "))),
column(10, tags$h5(textOutput("scan_target")))
),
tags$div(id="hitsbox", style="min-height: 300px;",
box(width=12, collapsible=TRUE, collapsed=TRUE,
title="Display sites along transcript",
actionButton("manhattanHelp", label="", style="float: right;",
icon=icon("question-circle")),
tags$p("Hover on points to view details, and click to ",
"visualize the alignment on the target sequence. You may
also select miRNAs to show/hide by clicking on the legend."),
withSpinner(plotlyOutput("manhattan")),
column(6, numericInput("manhattan_n", "Number of top miRNAs displayed",
value=10, min=1, max=50)),
column(6, checkboxInput("manhattan_ordinal", "Ordinal position",
value=FALSE))
),
box(width=12, title="Aggregated per miRNA", collapsible=TRUE, collapsed=TRUE,
withSpinner(DTOutput("agghits_table")),
column(6,tags$p(downloadLink('dl_agghits', label = "Download all"))),
column(6, actionButton("help_aggregatedHits","About aggregation...",
icon=icon("question-circle")))
),
box(width=12, title="Table", collapsible=TRUE,
fluidRow(
column(6,
tags$p("Double click on a row to visualize the alignment",
" on the target sequence.")),
column(6, style="text-align: right;",
actionButton("colHelp","What are those columns?",
icon=icon("question-circle")),
actionButton("stypeHelp","Site types",
icon=icon("question-circle"))
)
),
withSpinner(DTOutput("hits_table")),
tags$p(downloadLink('dl_hits', label = "Download all"))
)),
box(width=12, title="Cached hits", collapsible=TRUE, collapsed=TRUE,
textOutput("cache.info"),
uiOutput("cached.results"),
actionButton("loadCache", "Load"),
actionButton("deleteCache", "Delete")
)
),
# miRNA-based
tabItem(tabName="tab_mirna",
fluidRow(
column(5, tags$div(id="mirnainput",
selectizeInput("mirna", "miRNA", choices=c()))),
column(4, tags$strong("TargetScan conservation status"),
textOutput("modconservation")),
column(3, htmlOutput("mirbase_link"))
),
tags$div(id="affinitybox", style="min-height: 40px;",
box(width=12, title="Affinity plot", collapsible=TRUE,
collapsed=TRUE,
withSpinner(jqui_resizable(plotOutput("modplot")))
)
),
tags$div(id="targetsbox", style="min-height: 100px;",
box(width=12, title="Targets", collapsible=TRUE,
uiOutput("targets_ui"))
)
),
tabItem(tabName = "tab_about",
## TAB ABOUT
box(width=12, title="miRNA binding prediction",
tags$div(style="font-size: 110%;",
tags$img(src=mer12scheme, style="float: right; margin: 20px; width: 25%;"),
tags$p("micro-RNAs (miRNAs) regulate transcripts stability and
translation by targeting the Argonaute complex to RNAs exhibiting a
partial complementarity with, in particular, the miRNA's seed
sequence. For a general review on miRNA biology and targeting, see
", tags$a(href="https://doi.org/10.1016/j.cell.2018.03.006",
"Bartel (2018)",.noWS = "outside"),".",
tags$a(href="https://dx.doi.org/10.1126/science.aav1741",
"McGeary, Lin et al. (2019)"), " have additionally shown the
relevance of flanking nucleotides by empirically measuring the affinity
(specifically the dissociation rate constant, KD) of a set of miRNAs to
random 12-mer sequences, and then computationally extrapolating to other
miRNAs). The ",
tags$a( href=paste0("https://git","hub.com/ETHZ-INS/scanMiR"),
target="_blank", "scanMiR package",.noWS = "outside"), ", to which this app is an
interface, builds on this work to offer a powerful and flexible binding
and repression prediction framework."))
),
box(width=12, title="Getting started",
tags$div( style="font-size: 110%;",
tags$p("For a quick tour of the app, ", actionLink("helpLink", "click here",.noWS = "outside"),"."),
tags$p("There are two main ways to use scanMiRApp:"),
tags$br(), tags$h4("Transcript-centered:"),
tags$p("In the 'Search in gene/sequence' menu, you'll be able to ",
"scan the sequence of a given transcript for binding sites ",
"of (sets of) miRNA(s)."),
tags$br(), tags$h4("miRNA-centered:"),
tags$p("In the 'miRNA-based' tab on the left, you'll be able to ",
"visualize information relative to a selected miRNA, ",
"including for instance its general binding profile and its",
"top targets.")
)
),
tags$div(style="text-align: right; font-weight: normal;",
tags$p("The shiny app was developed by Pierre-Luc Germain and ",
"Michael Soutschek in the context of broader research in the ",
tags$a( href="http://schrattlab.ethz.ch", "Schratt lab",
target="_blank",.noWS = "outside"), ".",
tags$br(), "Bugs reports and feature requests are welcome on the ",
tags$a( href=paste0("https://git","hub.com/ETHZ-INS/scanMiRApp/issues"),
target="_blank", "github repository",.noWS = "outside"), "."),
textOutput("pkgVersions")
)
## END TAB ABOUT
)
),
tags$head(tags$style(HTML('.content-wrapper { overflow: auto; }')))
)
)
}
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