R/shinyFuse.R
In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
Defines functions
doublegeneinfo_2_html
geneinfo_2_html
.multilink
.link2cosmic
.link2hpa
.link2uniprot
.link2gtex
.link2ncbi
shinyFuse
Documented in
shinyFuse
#' shinyFuse
#'
#' Exploring interactively the results of the annoFuse pipeline
#'
#' The application can also be started without specifying the location of the data,
#' which can be provided (via upload) at runtime.
#'
#' @param out_annofuse The character string specifying the location of the file
#' output by the annoFuse pipeline. This file needs to be structured with the set
#' of columns required for the later exploration steps in the interactive app.
#'
#' @return A Shiny app object
#' @export
#'
#' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
#' @import shinydashboard
#' @import rintrojs
#' @import shinythemes
#' @importFrom base64enc dataURI
#' @importFrom DT datatable renderDataTable dataTableOutput
#' @importFrom shinyBS bsTooltip
#'
#' @examples
#' out_annofuse <- system.file("extdata", "PutativeDriverAnnoFuse.tsv",
#' package = "annoFuseData"
#' )
#' if (interactive()) {
#' shinyFuse(out_annofuse)
#' }
shinyFuse <- function(out_annofuse = NULL) {
# Checks on the objects provided ---------------------------------------------
if (!is.null(out_annofuse)) {
if (!is(out_annofuse, "character")) {
stop("'out_annofuse' has to be a character string")
}
if (!file.exists(out_annofuse)) {
stop("File specified by 'out_annofuse' not found")
}
}
oopt <- options(spinner.type = 6, spinner.color = "#0092AC")
# play nice with other previously chosen options
on.exit(options(oopt))
# UI definition -----------------------------------------------------------
shinyfuse_ui <- shinydashboard::dashboardPage(
skin = "black",
# header definition -------------------------------------------------------
header = shinydashboard::dashboardHeader(
title = "shinyFuse",
titleWidth = 350,
shinydashboard::dropdownMenu(
type = "tasks",
icon = icon("question-circle fa-1g"),
badgeStatus = NULL,
headerText = "Documentation",
shinydashboard::notificationItem(
text = actionButton(
"interface_overview", "Overview of the interface",
icon("hand-o-right")
),
icon = icon(""), # tricking it to not have additional icon
status = "primary"
)
)
),
# sidebar definition ------------------------------------------------------
sidebar = shinydashboard::dashboardSidebar(
width = 250,
collapsed = !is.null(out_annofuse),
div(
style = "display:inline-block;vertical-align:top;",
actionButton(
inputId = "btn_load_demo",
label = "Load demo data"
)
),
div(
style = "display:inline-block;vertical-align:top;",
actionButton(
"help_format",
label = "",
icon = icon("question-circle"),
style = "color: #0092AC; background-color: #222222; border-color: #222222"
),
shinyBS::bsTooltip(
"help_format",
"How to provide your input data to shinyFuse",
"bottom",
options = list(container = "body")
)
),
uiOutput("choose_annofusedata_file"),
uiOutput("plot_controls"),
uiOutput("plot_filters"),
uiOutput("export_controls")
),
# body definition ---------------------------------------------------------
body = shinydashboard::dashboardBody(
rintrojs::introjsUI(),
## Define output size and style of error messages
shiny::tags$head(
shiny::tags$style(
shiny::HTML(".shiny-output-error-validation {
font-size: 15px;
color: forestgreen;
text-align: center;
}
")
)
),
id = "main-app",
navbarPage(
title = div(),
id = "navbartab",
windowTitle = "shinyfuse",
footer = "",
theme = shinytheme("cosmo"),
selected = "FusionExplorer",
# ui FusionExplorer -----------------------------------------------------
tabPanel(
title = "FusionExplorer", icon = icon("table"),
fluidPage(
fluidRow(
column(
width = 8,
DT::dataTableOutput("table_annofuse")
),
column(
width = 4,
fluidRow(
column(
width = 4,
offset = 4,
actionButton("btn_load_exonsdata", "Load exons")
),
column(
width = 4,
actionButton("btn_load_pfamdata", "Load pfam")
)
),
hr(),
uiOutput("geneinfo_ui"),
uiOutput("geneplots_ui")
)
)
)
),
# ui FusionSummary -----------------------------------------------------
tabPanel(
title = "FusionSummary", icon = icon("dna"),
fluidPage(
fluidRow(
column(
width = 12,
uiOutput("ui_af_summary")
)
),
fluidRow(
column(
width = 6,
withSpinner(
plotOutput("af_recurrentfusions")
),
downloadButton("btn_dl_recufusions",
label = "",
class = "btn btn-success"
)
),
column(
width = 6,
withSpinner(
plotOutput("af_recurrentgenes")
),
downloadButton("btn_dl_recugenes",
label = "",
class = "btn btn-success"
)
)
)
)
),
# ui About page --------------------------------------------------------
tabPanel(
title = "About", icon = icon("info-circle"),
includeMarkdown(
system.file("extdata", "content_about.md", package = "annoFuse")
)
)
)
)
)
# nocov start
# Server definition -------------------------------------------------------
shinyfuse_server <- function(input, output, session) {
# Initializing data storage ------------------------------------------------
values <- reactiveValues()
values$annofuse_tbl <- NULL
values$enhanced_annofuse_tbl <- NULL
values$ann_domain <- NULL
values$data_exons <- NULL
values$data_pfam <- NULL
# Define data file if annoFuse data is not provided ------------------------
if (is.null(out_annofuse)) {
output$choose_annofusedata_file <- renderUI({
menuItem(
icon = icon("file-alt"),
fileInput(
inputId = "annofusedatasel",
label = "Load sample data file (tab-separated)",
accept = c(
"text/tab-separated-values", "text/plain",
".tsv", ".tab", ".txt"
),
multiple = FALSE
)
)
})
} else {
annofuse_tbl <- read.delim(out_annofuse, stringsAsFactors = FALSE)
annofuse_tbl <- .check_annoFuse_calls(annofuse_tbl)
values$annofuse_tbl <- annofuse_tbl
enhanced_annofuse_tbl <- annofuse_tbl
# enhancing the content of the table
# enhanced_annofuse_tbl$Gene1A <- .multilink(enhanced_annofuse_tbl$Gene1A)
# enhanced_annofuse_tbl$Gene1B <- .multilink(enhanced_annofuse_tbl$Gene1B)
values$enhanced_annofuse_tbl <- enhanced_annofuse_tbl
}
# Controls for plot panels -------------------------------------------------
output$plot_controls <- renderUI({
if (is.null(values$annofuse_tbl)) {
return(NULL)
} else {
all_cols <- colnames(values$annofuse_tbl)
cols_groupable <-
all_cols[unlist(lapply(values$annofuse_tbl, class)) %in% c("character", "factor")]
minset_cols <- c(
"Sample", "FusionName",
"Gene1A", "Gene1B",
"LeftBreakpoint", "RightBreakpoint",
"Fusion_Type", "JunctionReadCount", "SpanningFragCount",
"Confidence", "CalledBy"
)
minset_cols <- minset_cols[minset_cols %in% all_cols]
tagList(
selectInput(
inputId = "af_filtercols",
label = "Columns to display",
choices = c("", union(minset_cols, all_cols)),
selectize = TRUE, multiple = TRUE, selected = minset_cols
),
tagList(
menuItem(
"Plot output settings",
icon = icon("paint-brush"),
startExpanded = TRUE,
selectInput(
inputId = "af_cols",
label = "Grouping column",
choices = c("", cols_groupable),
selectize = TRUE, multiple = FALSE, selected = "Fusion_Type"
),
selectInput(
inputId = "af_countcol",
label = "Counting column",
choices = c("", all_cols),
selectize = TRUE, multiple = FALSE, selected = "Sample"
),
numericInput(
inputId = "af_n_topfusions",
label = "Nr top fusions",
value = 20, min = 1, max = 300, step = 1
)
)
)
)
}
})
output$plot_filters <- renderUI({
if (is.null(values$annofuse_tbl)) {
return(NULL)
} else {
tagList(
menuItem(
"Plot filters settings",
icon = icon("filter"),
startExpanded = TRUE,
if ("Fusion_Type" %in% colnames(values$annofuse_tbl)) {
selectInput(
inputId = "filter_fusion_type",
label = "Filter for fusion type",
choices = c("", unique(values$annofuse_tbl$Fusion_Type)),
selectize = TRUE, multiple = TRUE,
selected = unique(values$annofuse_tbl$Fusion_Type)
)
} else {
""
},
if ("Caller" %in% colnames(values$annofuse_tbl)) {
selectInput(
inputId = "filter_caller",
label = "Filter for caller",
choices = c("", unique(values$annofuse_tbl$Caller)),
selectize = TRUE, multiple = TRUE,
selected = unique(values$annofuse_tbl$Caller)
)
} else {
""
},
if ("Confidence" %in% colnames(values$annofuse_tbl)) {
selectInput(
inputId = "filter_confidence",
label = "Filter for confidence",
choices = c("", unique(values$annofuse_tbl$Confidence)),
selectize = TRUE, multiple = TRUE,
selected = unique(values$annofuse_tbl$Confidence)
)
} else {
""
},
if ("BreakpointLocation" %in% colnames(values$annofuse_tbl)) {
selectInput(
inputId = "filter_bplocation",
label = "Filter for breakpoint location",
choices = c("", unique(values$annofuse_tbl$BreakpointLocation)),
selectize = TRUE, multiple = TRUE,
selected = unique(values$annofuse_tbl$BreakpointLocation)
)
} else {
""
},
if ("SpanningFragCount" %in% colnames(values$annofuse_tbl)) {
numericInput(
inputId = "filter_spanningfragcount",
label = "Filter for spanning frag count",
value = 0,
min = 0, max = max(values$annofuse_tbl$SpanningFragCount)
)
} else {
""
},
if ("JunctionReadCount" %in% colnames(values$annofuse_tbl)) {
numericInput(
inputId = "filter_junctionreadcount",
label = "Filter for junction read count",
value = 0,
min = 0, max = max(values$annofuse_tbl$JunctionReadCount)
)
} else {
""
},
if ("caller_count" %in% colnames(values$annofuse_tbl)) {
numericInput(
inputId = "filter_callercount",
label = "Filter for caller count",
value = 1,
min = 1, max = max(values$annofuse_tbl$caller_count)
)
} else {
""
}
)
)
}
})
output$export_controls <- renderUI({
if (is.null(values$annofuse_tbl)) {
return(NULL)
} else {
tagList(
menuItem(
"Plot export settings",
icon = icon("images"),
startExpanded = TRUE,
numericInput(
inputId = "export_width",
label = "Export width (in)",
value = 20,
min = 4, max = 50
),
numericInput(
inputId = "export_height",
label = "Export height (in)",
value = 12,
min = 4, max = 50
)
)
)
}
})
# Load annoFuse data file --------------------------------------------------
observeEvent(input$annofusedatasel, {
message("Reading in...")
values$annofuse_tbl <- .check_annoFuse_calls(
read.delim(input$annofusedatasel$datapath, stringsAsFactors = FALSE)
)
values$enhanced_annofuse_tbl <- values$annofuse_tbl
# enhancing the content of the table
# values$enhanced_annofuse_tbl$Gene1A <- .multilink(values$enhanced_annofuse_tbl$Gene1A)
# values$enhanced_annofuse_tbl$Gene1B <- .multilink(values$enhanced_annofuse_tbl$Gene1B)
if (!is.null(values$data_pfam)) {
message("Creating domain information...")
values$ann_domain <- annoFuse::get_Pfam_domain(
standardFusioncalls = values$annofuse_tbl,
bioMartDataPfam = values$data_pfam, # must be pre-loaded
# partial overlapping domains are retained == "Partial" with keepPartialAnno=TRUE;
# if keepPartialAnno=FALSE then domain retained status == "No"
keepPartialAnno = TRUE
)
}
})
# Load demo data
observeEvent(input$btn_load_demo, {
message("Loading demo data...")
demodata_location <- system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
values$annofuse_tbl <-
.check_annoFuse_calls(read.delim(demodata_location, stringsAsFactors = FALSE))
values$enhanced_annofuse_tbl <- values$annofuse_tbl
# enhancing the content of the table
# values$enhanced_annofuse_tbl$Gene1A <- .multilink(values$enhanced_annofuse_tbl$Gene1A)
# values$enhanced_annofuse_tbl$Gene1B <- .multilink(values$enhanced_annofuse_tbl$Gene1B)
if (!is.null(values$data_pfam)) {
message("Creating domain information...")
values$ann_domain <- annoFuse::get_Pfam_domain(
standardFusioncalls = values$annofuse_tbl,
bioMartDataPfam = values$data_pfam, # must be pre-loaded
# partial overlapping domains are retained == "Partial" with keepPartialAnno=TRUE;
# if keepPartialAnno=FALSE then domain retained status == "No"
keepPartialAnno = TRUE
)
}
})
# Main interactive table for exploration -----------------------------------
output$table_annofuse <- DT::renderDataTable({
validate(
need(
!is.null(values$annofuse_tbl),
"Please upload the results of annoFuse to start the exploration"
)
)
display_tbl <- values$enhanced_annofuse_tbl
display_tbl <- display_tbl[, input$af_filtercols]
# if("BreakpointLocation" %in% colnames(display_tbl)) {
# display_tbl$BreakpointLocation <- factor(display_tbl$BreakpointLocation)
# }
for (i in seq_len(ncol(display_tbl))) {
if (is.character(display_tbl[[i]])) {
display_tbl[[i]] <- factor(display_tbl[[i]])
}
}
DT::datatable(
display_tbl,
style = "bootstrap",
rownames = FALSE,
filter = "top",
selection = "single",
escape = FALSE,
extensions = c("Buttons", "FixedHeader"),
options = list(
scrollX = TRUE,
scrollY = "800px",
fixedHeader = TRUE,
paging = FALSE,
pageLength = 25,
lengthMenu = c(5, 10, 25, 50, 100, nrow(display_tbl)),
dom = "Bfrtip",
buttons = list(list(
extend = "collection",
buttons = c("csv", "excel", "pdf"),
text = "Download table"
))
)
)
})
# TODO? link to the DB where the info was taken from
# Gene info and plots from FusionExplorer
output$geneinfo_ui <- renderUI({
validate(
need(
length(input$table_annofuse_rows_selected) > 0,
"Please select a row to display additional information"
)
)
row_id <- input$table_annofuse_rows_selected
message(row_id)
gene_for_content <- values$annofuse_tbl[row_id, "Gene1A"]
gene_for_content_2 <- values$annofuse_tbl[row_id, "Gene1B"]
tagList(
h4("External links"),
p(
"Click on the buttons below to open their related page in new tabs ",
"with information retrieved from a number of external databases."
),
doublegeneinfo_2_html(gene_for_content, gene_for_content_2)
)
})
output$geneplots_ui <- renderUI({
validate(
need(
length(input$table_annofuse_rows_selected) > 0,
message = ""
)
)
tagList(
hr(),
h4("Fusion specific plots"),
radioButtons("bp_plot_mode",
label = "Breakpoint plot type:",
choices = c(
"Breakpoint specific" = "bp_bp",
"Sample specific" = "bp_sample",
"All samples" = "bp_allsamples"
),
inline = TRUE,
selected = "bp_bp"
),
tabsetPanel(
tabPanel(
"Plot left",
withSpinner(
plotOutput("geneplots_left"),
type = 6, color = "#0092AC"
),
downloadButton("btn_dl_bpleft",
label = "",
class = "btn btn-success"
)
),
tabPanel(
"Plot right",
withSpinner(
plotOutput("geneplots_right"),
type = 6, color = "#0092AC"
),
downloadButton("btn_dl_bpright",
label = "",
class = "btn btn-success"
)
),
tabPanel(
"Plot both",
withSpinner(
plotOutput("geneplots_both"),
type = 6, color = "#0092AC"
),
downloadButton("btn_dl_bpboth",
label = "",
class = "btn btn-success"
)
)
)
)
})
# Breakpoint plots ---------------------------------------------------------
output$geneplots_right <- renderPlot({
validate(
need(
(!is.null(values$data_exons) & !is.null(values$data_pfam)),
"Please load the exons and the pfam information via the buttons above to display the plot"
)
)
row_id <- input$table_annofuse_rows_selected
message(row_id)
fusion_for_content <- values$annofuse_tbl[row_id, "FusionName"]
rightfused_for_content <- values$annofuse_tbl[row_id, "Gene1B"]
samplespec <- values$annofuse_tbl[row_id, "Sample"]
breakpointspec_right <- values$annofuse_tbl[row_id, "RightBreakpoint"]
if (input$bp_plot_mode == "bp_bp") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
sampleid = samplespec,
rightBreakpoint = breakpointspec_right,
fusionname = fusion_for_content
)
}
if (input$bp_plot_mode == "bp_sample") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
fusionname = fusion_for_content,
sampleid = samplespec
)
}
if (input$bp_plot_mode == "bp_allsamples") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
fusionname = fusion_for_content
)
}
values$plotobj_breakpoint_right <- p
print(p)
})
output$geneplots_left <- renderPlot({
validate(
need(
(!is.null(values$data_exons) & !is.null(values$data_pfam)),
"Please load the exons and the pfam information via the buttons above to display the plot"
)
)
row_id <- input$table_annofuse_rows_selected
message(row_id)
fusion_for_content <- values$annofuse_tbl[row_id, "FusionName"]
leftfused_for_content <- values$annofuse_tbl[row_id, "Gene1A"]
samplespec <- values$annofuse_tbl[row_id, "Sample"]
breakpointspec_left <- values$annofuse_tbl[row_id, "LeftBreakpoint"]
if (input$bp_plot_mode == "bp_bp") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
sampleid = samplespec,
leftBreakpoint = breakpointspec_left,
fusionname = fusion_for_content
)
}
if (input$bp_plot_mode == "bp_sample") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
fusionname = fusion_for_content,
sampleid = samplespec
)
}
if (input$bp_plot_mode == "bp_allsamples") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
fusionname = fusion_for_content
)
}
values$plotobj_breakpoint_left <- p
print(p)
})
output$geneplots_both <- renderPlot({
validate(
need(
(!is.null(values$data_exons) & !is.null(values$data_pfam)),
"Please load the exons and the pfam information via the buttons above to display the plot"
)
)
# common part
row_id <- input$table_annofuse_rows_selected
message(row_id)
fusion_for_content <- values$annofuse_tbl[row_id, "FusionName"]
samplespec <- values$annofuse_tbl[row_id, "Sample"]
breakpointspec_left <- values$annofuse_tbl[row_id, "LeftBreakpoint"]
breakpointspec_right <- values$annofuse_tbl[row_id, "RightBreakpoint"]
# left plot
leftfused_for_content <- values$annofuse_tbl[row_id, "Gene1A"]
if (input$bp_plot_mode == "bp_bp") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
sampleid = samplespec,
leftBreakpoint = breakpointspec_left,
fusionname = fusion_for_content
)
}
if (input$bp_plot_mode == "bp_sample") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
fusionname = fusion_for_content,
sampleid = samplespec
)
}
if (input$bp_plot_mode == "bp_allsamples") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
fusionname = fusion_for_content
)
}
values$plotobj_breakpoint_left <- p
# right plot
rightfused_for_content <- values$annofuse_tbl[row_id, "Gene1B"]
if (input$bp_plot_mode == "bp_bp") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
sampleid = samplespec,
rightBreakpoint = breakpointspec_right,
fusionname = fusion_for_content
)
}
if (input$bp_plot_mode == "bp_sample") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
fusionname = fusion_for_content,
sampleid = samplespec
)
}
if (input$bp_plot_mode == "bp_allsamples") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
fusionname = fusion_for_content
)
}
values$plotobj_breakpoint_right <- p
pboth <- ggpubr::ggarrange(
values$plotobj_breakpoint_left,
values$plotobj_breakpoint_right,
align = "h"
)
values$plotobj_breakpoint_both <- pboth
print(pboth)
})
# FusionSummary panel -------------------------------------------
output$ui_af_summary <- renderUI({
tagList(
box(
title = "annoFuse summary",
status = "success",
width = 12,
collapsible = TRUE,
collapsed = TRUE,
withSpinner(
plotOutput("af_overview"),
type = 6, color = "#0092AC"
),
downloadButton("btn_dl_summary",
label = "",
class = "btn btn-success"
)
)
)
})
output$af_overview <- renderPlot({
withProgress(
{
p <- plot_summary(values$annofuse_tbl, base_size = 10)
},
message = "Rendering summary..."
)
values$plotobj_summary <- p
print(p)
})
output$af_recurrentfusions <- renderPlot({
validate(
need(
!is.null(values$annofuse_tbl),
"Please provide the results of annoFuse to display the plot"
)
)
subset_to_plot <- values$annofuse_tbl
if (!is.null(input$filter_fusion_type)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Fusion_Type %in% input$filter_fusion_type,
]
}
if (!is.null(input$filter_caller)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Caller %in% input$filter_caller,
]
}
if (!is.null(input$filter_confidence)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Confidence %in% input$filter_confidence,
]
}
if (!is.null(input$filter_bplocation)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$BreakpointLocation %in% input$filter_bplocation,
]
}
if (!is.null(input$filter_spanningfragcount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$SpanningFragCount >= input$filter_spanningfragcount,
]
}
if (!is.null(input$filter_junctionreadcount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$JunctionReadCount >= input$filter_junctionreadcount,
]
}
if (!is.null(input$filter_callercount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$caller_count >= input$filter_callercount,
]
}
message(paste0("nr rows", nrow(subset_to_plot)))
validate(
need(
nrow(subset_to_plot) > 0,
"Please changing the filtering criteria, current table has no record"
)
)
gby_rf <- input$af_cols
plotn_rf <- input$af_n_topfusions
cid_rf <- input$af_countcol
p <- plot_recurrent_fusions(subset_to_plot,
groupby = gby_rf,
plotn = plotn_rf,
countID = cid_rf
)
values$plotobj_recufusions <- p
print(p)
})
output$af_recurrentgenes <- renderPlot({
validate(
need(
!is.null(values$annofuse_tbl),
"Please provide the results of annoFuse to display the plot"
)
)
subset_to_plot <- values$annofuse_tbl
if (!is.null(input$filter_fusion_type)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Fusion_Type %in% input$filter_fusion_type,
]
}
if (!is.null(input$filter_caller)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Caller %in% input$filter_caller,
]
}
if (!is.null(input$filter_confidence)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Confidence %in% input$filter_confidence,
]
}
if (!is.null(input$filter_bplocation)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$BreakpointLocation %in% input$filter_bplocation,
]
}
if (!is.null(input$filter_spanningfragcount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$SpanningFragCount >= input$filter_spanningfragcount,
]
}
if (!is.null(input$filter_junctionreadcount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$JunctionReadCount >= input$filter_junctionreadcount,
]
}
if (!is.null(input$filter_callercount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$caller_count >= input$filter_callercount,
]
}
message(paste0("nr rows", nrow(subset_to_plot)))
validate(
need(
nrow(subset_to_plot) > 0,
"Please changing the filtering criteria, current table has no record"
)
)
gby_rg <- input$af_cols
plotn_rg <- input$af_n_topfusions
cid_rg <- input$af_countcol
p <- plot_recurrent_genes(subset_to_plot,
groupby = gby_rg,
plotn = plotn_rg,
countID = cid_rg
)
values$plotobj_recugenes <- p
print(p)
})
# Tour trigger -------------------------------------------------------------
observeEvent(input$interface_overview, {
tour <- read.delim(system.file("extdata", "annoFuse_overview.txt",
package = "annoFuse"
),
sep = ";", stringsAsFactors = FALSE,
row.names = NULL, quote = ""
)
rintrojs::introjs(session, options = list(steps = tour))
})
# Load data via buttons ----------------------------------------------------
observeEvent(input$btn_load_pfamdata, {
if (is.null(values$data_pfam)) {
message("Loading pfam data...")
showNotification("Loading pfam data...", type = "message")
values$data_pfam <- readRDS(system.file("extdata", "pfamDataBioMart.RDS", package = "annoFuseData"))
showNotification("Done loading pfam data!", type = "message")
if (!is.null(values$annofuse_tbl)) {
showNotification("Correctly created domain information!", type = "message")
values$ann_domain <- annoFuse::get_Pfam_domain(
standardFusioncalls = values$annofuse_tbl,
bioMartDataPfam = values$data_pfam, # must be pre-loaded
# partial overlapping domains are retained == "Partial" with keepPartialAnno=TRUE;
# if keepPartialAnno=FALSE then domain retained status == "No"
keepPartialAnno = TRUE
)
}
} else {
showNotification("pfam data already loaded", type = "default")
}
})
observeEvent(input$btn_load_exonsdata, {
if (is.null(values$data_exons)) {
message("Loading exons data...")
showNotification("Loading exons data...", type = "message", duration = 10)
values$data_exons <- readRDS(system.file("extdata", "exonsToPlot.RDS", package = "annoFuseData"))
showNotification("Done loading exons data!", type = "message")
} else {
showNotification("exons data already loaded", type = "default")
}
})
# Defining behaviors for downloading the plots -----------------------------
output$btn_dl_bpleft <- downloadHandler(
filename = "annofuse_bpleft.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_breakpoint_left,
width = input$export_width,
height = input$export_height,
units = "in"
)
}
)
output$btn_dl_bpright <- downloadHandler(
filename = "annofuse_bpright.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_breakpoint_right,
width = input$export_width,
height = input$export_height,
units = "in"
)
}
)
output$btn_dl_bpboth <- downloadHandler(
filename = "annofuse_bpboth.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_breakpoint_both,
width = input$export_width,
height = input$export_height,
units = "in"
)
}
)
output$btn_dl_summary <- downloadHandler(
filename = "annofuse_summary.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_summary,
width = input$export_width,
height = input$export_height,
units = "in"
)
}
)
output$btn_dl_recufusions <- downloadHandler(
filename = "annofuse_recurrent_fusions.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_recufusions # ,
# width = input$export_width,
# height = input$export_height, units = "cm"
)
}
)
output$btn_dl_recugenes <- downloadHandler(
filename = "annofuse_recurrent_genes.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_recugenes # ,
# width = input$export_width,
# height = input$export_height, units = "cm"
)
}
)
observeEvent(input$help_format, {
showModal(
modalDialog(
title = "Format specifications for shinyFuse",
includeMarkdown(
system.file("extdata", "howto_datainput.md", package = "annoFuse")
),
h4("Example:"),
tags$img(
src = base64enc::dataURI(
file = system.file("www", "help_dataformats_minimalexample.png", package = "annoFuse"), mime = "image/png"
),
width = "100%"
),
easyClose = TRUE,
footer = NULL,
size = "l"
)
)
})
}
# nocov end
shinyApp(ui = shinyfuse_ui, server = shinyfuse_server)
}
.actionbutton_biocstyle <- "color: #ffffff; background-color: #0092AC"
## ENSEMBL? needs species info
# Helper functions --------------------------------------------------------
#' Link to NCBI database
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2ncbi <- function(val) {
sprintf(
'<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-database"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
#' Link to the GTEx Portal
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2gtex <- function(val) {
sprintf(
'<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-dna"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
#' Link to the Uniprot Portal
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2uniprot <- function(val) {
sprintf(
'<a href = "https://www.uniprot.org/uniprot/?query=%s&sort=score" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-spinner"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
#' Link to human protein atlas Portal
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2hpa <- function(val) {
sprintf(
'<a href = "https://www.proteinatlas.org/search/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-cubes"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
#' Link to the COSMIC Portal
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2cosmic <- function(val) {
sprintf(
'<a href = "https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-book-medical"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
.multilink <- function(val) {
b1 <- sprintf(
'<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-database"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
b2 <- sprintf(
'<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-dna"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
return(paste(b1, b2))
}
geneinfo_2_html <- function(gene_id) {
gene_ncbi_button <- .link2ncbi(gene_id)
gene_gtex_button <- .link2gtex(gene_id)
gene_uniprot_button <- .link2uniprot(gene_id)
gene_hpa_button <- .link2hpa(gene_id)
mycontent <- paste0(
shiny::tags$b(gene_id), shiny::tags$br(),
"Link to the NCBI Gene database: ", gene_ncbi_button, shiny::tags$br(),
"Link to the GTEx Portal: ", gene_gtex_button, shiny::tags$br(),
"Link to the Uniprot Portal: ", gene_uniprot_button, shiny::tags$br(),
"Link to the Human Protein Atlas: ", gene_hpa_button, shiny::tags$br()
)
return(HTML(mycontent))
}
doublegeneinfo_2_html <- function(gene_id1, gene_id2) {
gene_ncbi_button_1 <- .link2ncbi(gene_id1)
gene_gtex_button_1 <- .link2gtex(gene_id1)
gene_uniprot_button_1 <- .link2uniprot(gene_id1)
gene_hpa_button_1 <- .link2hpa(gene_id1)
gene_cosmic_button_1 <- .link2cosmic(gene_id1)
gene_ncbi_button_2 <- .link2ncbi(gene_id2)
gene_gtex_button_2 <- .link2gtex(gene_id2)
gene_uniprot_button_2 <- .link2uniprot(gene_id2)
gene_hpa_button_2 <- .link2hpa(gene_id2)
gene_cosmic_button_2 <- .link2cosmic(gene_id2)
mycontent <- paste0(
"<table><tr>",
'<td width="33%">', "NCBI", "</td>",
'<td width="33%">', gene_ncbi_button_1, "</td>",
'<td width="33%">', gene_ncbi_button_2, "</td>",
"</tr></table>",
"<table><tr>",
'<td width="33%">', "GTEx", "</td>",
'<td width="33%">', gene_gtex_button_1, "</td>",
'<td width="33%">', gene_gtex_button_2, "</td>",
"</tr></table>",
"<table><tr>",
'<td width="33%">', "UniProt", "</td>",
'<td width="33%">', gene_uniprot_button_1, "</td>",
'<td width="33%">', gene_uniprot_button_2, "</td>",
"</tr></table>",
"<table><tr>",
'<td width="33%">', "HPA", "</td>",
'<td width="33%">', gene_hpa_button_1, "</td>",
'<td width="33%">', gene_hpa_button_2, "</td>",
"</tr></table>",
"<table><tr>",
'<td width="33%">', "COSMIC", "</td>",
'<td width="33%">', gene_cosmic_button_1, "</td>",
'<td width="33%">', gene_cosmic_button_2, "</td>",
"</tr></table>"
)
return(HTML(mycontent))
}
## TODO? these functions can be directly used also to simply create a report, whose content is just the table with the nicely enhanced many buttons and co.!
d3b-center/annoFuse documentation built on Oct. 2, 2024, 4:17 a.m.
R Package Documentation
Browse R Packages
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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 doublegeneinfo_2_html geneinfo_2_html .multilink .link2cosmic .link2hpa .link2uniprot .link2gtex .link2ncbi shinyFuse
Documented in shinyFuse
#' shinyFuse
#'
#' Exploring interactively the results of the annoFuse pipeline
#'
#' The application can also be started without specifying the location of the data,
#' which can be provided (via upload) at runtime.
#'
#' @param out_annofuse The character string specifying the location of the file
#' output by the annoFuse pipeline. This file needs to be structured with the set
#' of columns required for the later exploration steps in the interactive app.
#'
#' @return A Shiny app object
#' @export
#'
#' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
#' @import shinydashboard
#' @import rintrojs
#' @import shinythemes
#' @importFrom base64enc dataURI
#' @importFrom DT datatable renderDataTable dataTableOutput
#' @importFrom shinyBS bsTooltip
#'
#' @examples
#' out_annofuse <- system.file("extdata", "PutativeDriverAnnoFuse.tsv",
#' package = "annoFuseData"
#' )
#' if (interactive()) {
#' shinyFuse(out_annofuse)
#' }
shinyFuse <- function(out_annofuse = NULL) {
# Checks on the objects provided ---------------------------------------------
if (!is.null(out_annofuse)) {
if (!is(out_annofuse, "character")) {
stop("'out_annofuse' has to be a character string")
}
if (!file.exists(out_annofuse)) {
stop("File specified by 'out_annofuse' not found")
}
}
oopt <- options(spinner.type = 6, spinner.color = "#0092AC")
# play nice with other previously chosen options
on.exit(options(oopt))
# UI definition -----------------------------------------------------------
shinyfuse_ui <- shinydashboard::dashboardPage(
skin = "black",
# header definition -------------------------------------------------------
header = shinydashboard::dashboardHeader(
title = "shinyFuse",
titleWidth = 350,
shinydashboard::dropdownMenu(
type = "tasks",
icon = icon("question-circle fa-1g"),
badgeStatus = NULL,
headerText = "Documentation",
shinydashboard::notificationItem(
text = actionButton(
"interface_overview", "Overview of the interface",
icon("hand-o-right")
),
icon = icon(""), # tricking it to not have additional icon
status = "primary"
)
)
),
# sidebar definition ------------------------------------------------------
sidebar = shinydashboard::dashboardSidebar(
width = 250,
collapsed = !is.null(out_annofuse),
div(
style = "display:inline-block;vertical-align:top;",
actionButton(
inputId = "btn_load_demo",
label = "Load demo data"
)
),
div(
style = "display:inline-block;vertical-align:top;",
actionButton(
"help_format",
label = "",
icon = icon("question-circle"),
style = "color: #0092AC; background-color: #222222; border-color: #222222"
),
shinyBS::bsTooltip(
"help_format",
"How to provide your input data to shinyFuse",
"bottom",
options = list(container = "body")
)
),
uiOutput("choose_annofusedata_file"),
uiOutput("plot_controls"),
uiOutput("plot_filters"),
uiOutput("export_controls")
),
# body definition ---------------------------------------------------------
body = shinydashboard::dashboardBody(
rintrojs::introjsUI(),
## Define output size and style of error messages
shiny::tags$head(
shiny::tags$style(
shiny::HTML(".shiny-output-error-validation {
font-size: 15px;
color: forestgreen;
text-align: center;
}
")
)
),
id = "main-app",
navbarPage(
title = div(),
id = "navbartab",
windowTitle = "shinyfuse",
footer = "",
theme = shinytheme("cosmo"),
selected = "FusionExplorer",
# ui FusionExplorer -----------------------------------------------------
tabPanel(
title = "FusionExplorer", icon = icon("table"),
fluidPage(
fluidRow(
column(
width = 8,
DT::dataTableOutput("table_annofuse")
),
column(
width = 4,
fluidRow(
column(
width = 4,
offset = 4,
actionButton("btn_load_exonsdata", "Load exons")
),
column(
width = 4,
actionButton("btn_load_pfamdata", "Load pfam")
)
),
hr(),
uiOutput("geneinfo_ui"),
uiOutput("geneplots_ui")
)
)
)
),
# ui FusionSummary -----------------------------------------------------
tabPanel(
title = "FusionSummary", icon = icon("dna"),
fluidPage(
fluidRow(
column(
width = 12,
uiOutput("ui_af_summary")
)
),
fluidRow(
column(
width = 6,
withSpinner(
plotOutput("af_recurrentfusions")
),
downloadButton("btn_dl_recufusions",
label = "",
class = "btn btn-success"
)
),
column(
width = 6,
withSpinner(
plotOutput("af_recurrentgenes")
),
downloadButton("btn_dl_recugenes",
label = "",
class = "btn btn-success"
)
)
)
)
),
# ui About page --------------------------------------------------------
tabPanel(
title = "About", icon = icon("info-circle"),
includeMarkdown(
system.file("extdata", "content_about.md", package = "annoFuse")
)
)
)
)
)
# nocov start
# Server definition -------------------------------------------------------
shinyfuse_server <- function(input, output, session) {
# Initializing data storage ------------------------------------------------
values <- reactiveValues()
values$annofuse_tbl <- NULL
values$enhanced_annofuse_tbl <- NULL
values$ann_domain <- NULL
values$data_exons <- NULL
values$data_pfam <- NULL
# Define data file if annoFuse data is not provided ------------------------
if (is.null(out_annofuse)) {
output$choose_annofusedata_file <- renderUI({
menuItem(
icon = icon("file-alt"),
fileInput(
inputId = "annofusedatasel",
label = "Load sample data file (tab-separated)",
accept = c(
"text/tab-separated-values", "text/plain",
".tsv", ".tab", ".txt"
),
multiple = FALSE
)
)
})
} else {
annofuse_tbl <- read.delim(out_annofuse, stringsAsFactors = FALSE)
annofuse_tbl <- .check_annoFuse_calls(annofuse_tbl)
values$annofuse_tbl <- annofuse_tbl
enhanced_annofuse_tbl <- annofuse_tbl
# enhancing the content of the table
# enhanced_annofuse_tbl$Gene1A <- .multilink(enhanced_annofuse_tbl$Gene1A)
# enhanced_annofuse_tbl$Gene1B <- .multilink(enhanced_annofuse_tbl$Gene1B)
values$enhanced_annofuse_tbl <- enhanced_annofuse_tbl
}
# Controls for plot panels -------------------------------------------------
output$plot_controls <- renderUI({
if (is.null(values$annofuse_tbl)) {
return(NULL)
} else {
all_cols <- colnames(values$annofuse_tbl)
cols_groupable <-
all_cols[unlist(lapply(values$annofuse_tbl, class)) %in% c("character", "factor")]
minset_cols <- c(
"Sample", "FusionName",
"Gene1A", "Gene1B",
"LeftBreakpoint", "RightBreakpoint",
"Fusion_Type", "JunctionReadCount", "SpanningFragCount",
"Confidence", "CalledBy"
)
minset_cols <- minset_cols[minset_cols %in% all_cols]
tagList(
selectInput(
inputId = "af_filtercols",
label = "Columns to display",
choices = c("", union(minset_cols, all_cols)),
selectize = TRUE, multiple = TRUE, selected = minset_cols
),
tagList(
menuItem(
"Plot output settings",
icon = icon("paint-brush"),
startExpanded = TRUE,
selectInput(
inputId = "af_cols",
label = "Grouping column",
choices = c("", cols_groupable),
selectize = TRUE, multiple = FALSE, selected = "Fusion_Type"
),
selectInput(
inputId = "af_countcol",
label = "Counting column",
choices = c("", all_cols),
selectize = TRUE, multiple = FALSE, selected = "Sample"
),
numericInput(
inputId = "af_n_topfusions",
label = "Nr top fusions",
value = 20, min = 1, max = 300, step = 1
)
)
)
)
}
})
output$plot_filters <- renderUI({
if (is.null(values$annofuse_tbl)) {
return(NULL)
} else {
tagList(
menuItem(
"Plot filters settings",
icon = icon("filter"),
startExpanded = TRUE,
if ("Fusion_Type" %in% colnames(values$annofuse_tbl)) {
selectInput(
inputId = "filter_fusion_type",
label = "Filter for fusion type",
choices = c("", unique(values$annofuse_tbl$Fusion_Type)),
selectize = TRUE, multiple = TRUE,
selected = unique(values$annofuse_tbl$Fusion_Type)
)
} else {
""
},
if ("Caller" %in% colnames(values$annofuse_tbl)) {
selectInput(
inputId = "filter_caller",
label = "Filter for caller",
choices = c("", unique(values$annofuse_tbl$Caller)),
selectize = TRUE, multiple = TRUE,
selected = unique(values$annofuse_tbl$Caller)
)
} else {
""
},
if ("Confidence" %in% colnames(values$annofuse_tbl)) {
selectInput(
inputId = "filter_confidence",
label = "Filter for confidence",
choices = c("", unique(values$annofuse_tbl$Confidence)),
selectize = TRUE, multiple = TRUE,
selected = unique(values$annofuse_tbl$Confidence)
)
} else {
""
},
if ("BreakpointLocation" %in% colnames(values$annofuse_tbl)) {
selectInput(
inputId = "filter_bplocation",
label = "Filter for breakpoint location",
choices = c("", unique(values$annofuse_tbl$BreakpointLocation)),
selectize = TRUE, multiple = TRUE,
selected = unique(values$annofuse_tbl$BreakpointLocation)
)
} else {
""
},
if ("SpanningFragCount" %in% colnames(values$annofuse_tbl)) {
numericInput(
inputId = "filter_spanningfragcount",
label = "Filter for spanning frag count",
value = 0,
min = 0, max = max(values$annofuse_tbl$SpanningFragCount)
)
} else {
""
},
if ("JunctionReadCount" %in% colnames(values$annofuse_tbl)) {
numericInput(
inputId = "filter_junctionreadcount",
label = "Filter for junction read count",
value = 0,
min = 0, max = max(values$annofuse_tbl$JunctionReadCount)
)
} else {
""
},
if ("caller_count" %in% colnames(values$annofuse_tbl)) {
numericInput(
inputId = "filter_callercount",
label = "Filter for caller count",
value = 1,
min = 1, max = max(values$annofuse_tbl$caller_count)
)
} else {
""
}
)
)
}
})
output$export_controls <- renderUI({
if (is.null(values$annofuse_tbl)) {
return(NULL)
} else {
tagList(
menuItem(
"Plot export settings",
icon = icon("images"),
startExpanded = TRUE,
numericInput(
inputId = "export_width",
label = "Export width (in)",
value = 20,
min = 4, max = 50
),
numericInput(
inputId = "export_height",
label = "Export height (in)",
value = 12,
min = 4, max = 50
)
)
)
}
})
# Load annoFuse data file --------------------------------------------------
observeEvent(input$annofusedatasel, {
message("Reading in...")
values$annofuse_tbl <- .check_annoFuse_calls(
read.delim(input$annofusedatasel$datapath, stringsAsFactors = FALSE)
)
values$enhanced_annofuse_tbl <- values$annofuse_tbl
# enhancing the content of the table
# values$enhanced_annofuse_tbl$Gene1A <- .multilink(values$enhanced_annofuse_tbl$Gene1A)
# values$enhanced_annofuse_tbl$Gene1B <- .multilink(values$enhanced_annofuse_tbl$Gene1B)
if (!is.null(values$data_pfam)) {
message("Creating domain information...")
values$ann_domain <- annoFuse::get_Pfam_domain(
standardFusioncalls = values$annofuse_tbl,
bioMartDataPfam = values$data_pfam, # must be pre-loaded
# partial overlapping domains are retained == "Partial" with keepPartialAnno=TRUE;
# if keepPartialAnno=FALSE then domain retained status == "No"
keepPartialAnno = TRUE
)
}
})
# Load demo data
observeEvent(input$btn_load_demo, {
message("Loading demo data...")
demodata_location <- system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
values$annofuse_tbl <-
.check_annoFuse_calls(read.delim(demodata_location, stringsAsFactors = FALSE))
values$enhanced_annofuse_tbl <- values$annofuse_tbl
# enhancing the content of the table
# values$enhanced_annofuse_tbl$Gene1A <- .multilink(values$enhanced_annofuse_tbl$Gene1A)
# values$enhanced_annofuse_tbl$Gene1B <- .multilink(values$enhanced_annofuse_tbl$Gene1B)
if (!is.null(values$data_pfam)) {
message("Creating domain information...")
values$ann_domain <- annoFuse::get_Pfam_domain(
standardFusioncalls = values$annofuse_tbl,
bioMartDataPfam = values$data_pfam, # must be pre-loaded
# partial overlapping domains are retained == "Partial" with keepPartialAnno=TRUE;
# if keepPartialAnno=FALSE then domain retained status == "No"
keepPartialAnno = TRUE
)
}
})
# Main interactive table for exploration -----------------------------------
output$table_annofuse <- DT::renderDataTable({
validate(
need(
!is.null(values$annofuse_tbl),
"Please upload the results of annoFuse to start the exploration"
)
)
display_tbl <- values$enhanced_annofuse_tbl
display_tbl <- display_tbl[, input$af_filtercols]
# if("BreakpointLocation" %in% colnames(display_tbl)) {
# display_tbl$BreakpointLocation <- factor(display_tbl$BreakpointLocation)
# }
for (i in seq_len(ncol(display_tbl))) {
if (is.character(display_tbl[[i]])) {
display_tbl[[i]] <- factor(display_tbl[[i]])
}
}
DT::datatable(
display_tbl,
style = "bootstrap",
rownames = FALSE,
filter = "top",
selection = "single",
escape = FALSE,
extensions = c("Buttons", "FixedHeader"),
options = list(
scrollX = TRUE,
scrollY = "800px",
fixedHeader = TRUE,
paging = FALSE,
pageLength = 25,
lengthMenu = c(5, 10, 25, 50, 100, nrow(display_tbl)),
dom = "Bfrtip",
buttons = list(list(
extend = "collection",
buttons = c("csv", "excel", "pdf"),
text = "Download table"
))
)
)
})
# TODO? link to the DB where the info was taken from
# Gene info and plots from FusionExplorer
output$geneinfo_ui <- renderUI({
validate(
need(
length(input$table_annofuse_rows_selected) > 0,
"Please select a row to display additional information"
)
)
row_id <- input$table_annofuse_rows_selected
message(row_id)
gene_for_content <- values$annofuse_tbl[row_id, "Gene1A"]
gene_for_content_2 <- values$annofuse_tbl[row_id, "Gene1B"]
tagList(
h4("External links"),
p(
"Click on the buttons below to open their related page in new tabs ",
"with information retrieved from a number of external databases."
),
doublegeneinfo_2_html(gene_for_content, gene_for_content_2)
)
})
output$geneplots_ui <- renderUI({
validate(
need(
length(input$table_annofuse_rows_selected) > 0,
message = ""
)
)
tagList(
hr(),
h4("Fusion specific plots"),
radioButtons("bp_plot_mode",
label = "Breakpoint plot type:",
choices = c(
"Breakpoint specific" = "bp_bp",
"Sample specific" = "bp_sample",
"All samples" = "bp_allsamples"
),
inline = TRUE,
selected = "bp_bp"
),
tabsetPanel(
tabPanel(
"Plot left",
withSpinner(
plotOutput("geneplots_left"),
type = 6, color = "#0092AC"
),
downloadButton("btn_dl_bpleft",
label = "",
class = "btn btn-success"
)
),
tabPanel(
"Plot right",
withSpinner(
plotOutput("geneplots_right"),
type = 6, color = "#0092AC"
),
downloadButton("btn_dl_bpright",
label = "",
class = "btn btn-success"
)
),
tabPanel(
"Plot both",
withSpinner(
plotOutput("geneplots_both"),
type = 6, color = "#0092AC"
),
downloadButton("btn_dl_bpboth",
label = "",
class = "btn btn-success"
)
)
)
)
})
# Breakpoint plots ---------------------------------------------------------
output$geneplots_right <- renderPlot({
validate(
need(
(!is.null(values$data_exons) & !is.null(values$data_pfam)),
"Please load the exons and the pfam information via the buttons above to display the plot"
)
)
row_id <- input$table_annofuse_rows_selected
message(row_id)
fusion_for_content <- values$annofuse_tbl[row_id, "FusionName"]
rightfused_for_content <- values$annofuse_tbl[row_id, "Gene1B"]
samplespec <- values$annofuse_tbl[row_id, "Sample"]
breakpointspec_right <- values$annofuse_tbl[row_id, "RightBreakpoint"]
if (input$bp_plot_mode == "bp_bp") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
sampleid = samplespec,
rightBreakpoint = breakpointspec_right,
fusionname = fusion_for_content
)
}
if (input$bp_plot_mode == "bp_sample") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
fusionname = fusion_for_content,
sampleid = samplespec
)
}
if (input$bp_plot_mode == "bp_allsamples") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
fusionname = fusion_for_content
)
}
values$plotobj_breakpoint_right <- p
print(p)
})
output$geneplots_left <- renderPlot({
validate(
need(
(!is.null(values$data_exons) & !is.null(values$data_pfam)),
"Please load the exons and the pfam information via the buttons above to display the plot"
)
)
row_id <- input$table_annofuse_rows_selected
message(row_id)
fusion_for_content <- values$annofuse_tbl[row_id, "FusionName"]
leftfused_for_content <- values$annofuse_tbl[row_id, "Gene1A"]
samplespec <- values$annofuse_tbl[row_id, "Sample"]
breakpointspec_left <- values$annofuse_tbl[row_id, "LeftBreakpoint"]
if (input$bp_plot_mode == "bp_bp") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
sampleid = samplespec,
leftBreakpoint = breakpointspec_left,
fusionname = fusion_for_content
)
}
if (input$bp_plot_mode == "bp_sample") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
fusionname = fusion_for_content,
sampleid = samplespec
)
}
if (input$bp_plot_mode == "bp_allsamples") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
fusionname = fusion_for_content
)
}
values$plotobj_breakpoint_left <- p
print(p)
})
output$geneplots_both <- renderPlot({
validate(
need(
(!is.null(values$data_exons) & !is.null(values$data_pfam)),
"Please load the exons and the pfam information via the buttons above to display the plot"
)
)
# common part
row_id <- input$table_annofuse_rows_selected
message(row_id)
fusion_for_content <- values$annofuse_tbl[row_id, "FusionName"]
samplespec <- values$annofuse_tbl[row_id, "Sample"]
breakpointspec_left <- values$annofuse_tbl[row_id, "LeftBreakpoint"]
breakpointspec_right <- values$annofuse_tbl[row_id, "RightBreakpoint"]
# left plot
leftfused_for_content <- values$annofuse_tbl[row_id, "Gene1A"]
if (input$bp_plot_mode == "bp_bp") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
sampleid = samplespec,
leftBreakpoint = breakpointspec_left,
fusionname = fusion_for_content
)
}
if (input$bp_plot_mode == "bp_sample") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
fusionname = fusion_for_content,
sampleid = samplespec
)
}
if (input$bp_plot_mode == "bp_allsamples") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Left",
fusionname = fusion_for_content
)
}
values$plotobj_breakpoint_left <- p
# right plot
rightfused_for_content <- values$annofuse_tbl[row_id, "Gene1B"]
if (input$bp_plot_mode == "bp_bp") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
sampleid = samplespec,
rightBreakpoint = breakpointspec_right,
fusionname = fusion_for_content
)
}
if (input$bp_plot_mode == "bp_sample") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
fusionname = fusion_for_content,
sampleid = samplespec
)
}
if (input$bp_plot_mode == "bp_allsamples") {
p <- plot_breakpoints(
domainDataFrame = values$ann_domain,
exons = values$data_exons,
geneposition = "Right",
fusionname = fusion_for_content
)
}
values$plotobj_breakpoint_right <- p
pboth <- ggpubr::ggarrange(
values$plotobj_breakpoint_left,
values$plotobj_breakpoint_right,
align = "h"
)
values$plotobj_breakpoint_both <- pboth
print(pboth)
})
# FusionSummary panel -------------------------------------------
output$ui_af_summary <- renderUI({
tagList(
box(
title = "annoFuse summary",
status = "success",
width = 12,
collapsible = TRUE,
collapsed = TRUE,
withSpinner(
plotOutput("af_overview"),
type = 6, color = "#0092AC"
),
downloadButton("btn_dl_summary",
label = "",
class = "btn btn-success"
)
)
)
})
output$af_overview <- renderPlot({
withProgress(
{
p <- plot_summary(values$annofuse_tbl, base_size = 10)
},
message = "Rendering summary..."
)
values$plotobj_summary <- p
print(p)
})
output$af_recurrentfusions <- renderPlot({
validate(
need(
!is.null(values$annofuse_tbl),
"Please provide the results of annoFuse to display the plot"
)
)
subset_to_plot <- values$annofuse_tbl
if (!is.null(input$filter_fusion_type)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Fusion_Type %in% input$filter_fusion_type,
]
}
if (!is.null(input$filter_caller)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Caller %in% input$filter_caller,
]
}
if (!is.null(input$filter_confidence)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Confidence %in% input$filter_confidence,
]
}
if (!is.null(input$filter_bplocation)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$BreakpointLocation %in% input$filter_bplocation,
]
}
if (!is.null(input$filter_spanningfragcount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$SpanningFragCount >= input$filter_spanningfragcount,
]
}
if (!is.null(input$filter_junctionreadcount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$JunctionReadCount >= input$filter_junctionreadcount,
]
}
if (!is.null(input$filter_callercount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$caller_count >= input$filter_callercount,
]
}
message(paste0("nr rows", nrow(subset_to_plot)))
validate(
need(
nrow(subset_to_plot) > 0,
"Please changing the filtering criteria, current table has no record"
)
)
gby_rf <- input$af_cols
plotn_rf <- input$af_n_topfusions
cid_rf <- input$af_countcol
p <- plot_recurrent_fusions(subset_to_plot,
groupby = gby_rf,
plotn = plotn_rf,
countID = cid_rf
)
values$plotobj_recufusions <- p
print(p)
})
output$af_recurrentgenes <- renderPlot({
validate(
need(
!is.null(values$annofuse_tbl),
"Please provide the results of annoFuse to display the plot"
)
)
subset_to_plot <- values$annofuse_tbl
if (!is.null(input$filter_fusion_type)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Fusion_Type %in% input$filter_fusion_type,
]
}
if (!is.null(input$filter_caller)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Caller %in% input$filter_caller,
]
}
if (!is.null(input$filter_confidence)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$Confidence %in% input$filter_confidence,
]
}
if (!is.null(input$filter_bplocation)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$BreakpointLocation %in% input$filter_bplocation,
]
}
if (!is.null(input$filter_spanningfragcount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$SpanningFragCount >= input$filter_spanningfragcount,
]
}
if (!is.null(input$filter_junctionreadcount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$JunctionReadCount >= input$filter_junctionreadcount,
]
}
if (!is.null(input$filter_callercount)) {
subset_to_plot <- subset_to_plot[
subset_to_plot$caller_count >= input$filter_callercount,
]
}
message(paste0("nr rows", nrow(subset_to_plot)))
validate(
need(
nrow(subset_to_plot) > 0,
"Please changing the filtering criteria, current table has no record"
)
)
gby_rg <- input$af_cols
plotn_rg <- input$af_n_topfusions
cid_rg <- input$af_countcol
p <- plot_recurrent_genes(subset_to_plot,
groupby = gby_rg,
plotn = plotn_rg,
countID = cid_rg
)
values$plotobj_recugenes <- p
print(p)
})
# Tour trigger -------------------------------------------------------------
observeEvent(input$interface_overview, {
tour <- read.delim(system.file("extdata", "annoFuse_overview.txt",
package = "annoFuse"
),
sep = ";", stringsAsFactors = FALSE,
row.names = NULL, quote = ""
)
rintrojs::introjs(session, options = list(steps = tour))
})
# Load data via buttons ----------------------------------------------------
observeEvent(input$btn_load_pfamdata, {
if (is.null(values$data_pfam)) {
message("Loading pfam data...")
showNotification("Loading pfam data...", type = "message")
values$data_pfam <- readRDS(system.file("extdata", "pfamDataBioMart.RDS", package = "annoFuseData"))
showNotification("Done loading pfam data!", type = "message")
if (!is.null(values$annofuse_tbl)) {
showNotification("Correctly created domain information!", type = "message")
values$ann_domain <- annoFuse::get_Pfam_domain(
standardFusioncalls = values$annofuse_tbl,
bioMartDataPfam = values$data_pfam, # must be pre-loaded
# partial overlapping domains are retained == "Partial" with keepPartialAnno=TRUE;
# if keepPartialAnno=FALSE then domain retained status == "No"
keepPartialAnno = TRUE
)
}
} else {
showNotification("pfam data already loaded", type = "default")
}
})
observeEvent(input$btn_load_exonsdata, {
if (is.null(values$data_exons)) {
message("Loading exons data...")
showNotification("Loading exons data...", type = "message", duration = 10)
values$data_exons <- readRDS(system.file("extdata", "exonsToPlot.RDS", package = "annoFuseData"))
showNotification("Done loading exons data!", type = "message")
} else {
showNotification("exons data already loaded", type = "default")
}
})
# Defining behaviors for downloading the plots -----------------------------
output$btn_dl_bpleft <- downloadHandler(
filename = "annofuse_bpleft.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_breakpoint_left,
width = input$export_width,
height = input$export_height,
units = "in"
)
}
)
output$btn_dl_bpright <- downloadHandler(
filename = "annofuse_bpright.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_breakpoint_right,
width = input$export_width,
height = input$export_height,
units = "in"
)
}
)
output$btn_dl_bpboth <- downloadHandler(
filename = "annofuse_bpboth.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_breakpoint_both,
width = input$export_width,
height = input$export_height,
units = "in"
)
}
)
output$btn_dl_summary <- downloadHandler(
filename = "annofuse_summary.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_summary,
width = input$export_width,
height = input$export_height,
units = "in"
)
}
)
output$btn_dl_recufusions <- downloadHandler(
filename = "annofuse_recurrent_fusions.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_recufusions # ,
# width = input$export_width,
# height = input$export_height, units = "cm"
)
}
)
output$btn_dl_recugenes <- downloadHandler(
filename = "annofuse_recurrent_genes.pdf",
content = function(file) {
ggsave(file,
plot = values$plotobj_recugenes # ,
# width = input$export_width,
# height = input$export_height, units = "cm"
)
}
)
observeEvent(input$help_format, {
showModal(
modalDialog(
title = "Format specifications for shinyFuse",
includeMarkdown(
system.file("extdata", "howto_datainput.md", package = "annoFuse")
),
h4("Example:"),
tags$img(
src = base64enc::dataURI(
file = system.file("www", "help_dataformats_minimalexample.png", package = "annoFuse"), mime = "image/png"
),
width = "100%"
),
easyClose = TRUE,
footer = NULL,
size = "l"
)
)
})
}
# nocov end
shinyApp(ui = shinyfuse_ui, server = shinyfuse_server)
}
.actionbutton_biocstyle <- "color: #ffffff; background-color: #0092AC"
## ENSEMBL? needs species info
# Helper functions --------------------------------------------------------
#' Link to NCBI database
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2ncbi <- function(val) {
sprintf(
'<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-database"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
#' Link to the GTEx Portal
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2gtex <- function(val) {
sprintf(
'<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-dna"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
#' Link to the Uniprot Portal
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2uniprot <- function(val) {
sprintf(
'<a href = "https://www.uniprot.org/uniprot/?query=%s&sort=score" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-spinner"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
#' Link to human protein atlas Portal
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2hpa <- function(val) {
sprintf(
'<a href = "https://www.proteinatlas.org/search/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-cubes"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
#' Link to the COSMIC Portal
#'
#' @param val Character, the gene symbol
#'
#' @return HTML for an action button
#' @noRd
.link2cosmic <- function(val) {
sprintf(
'<a href = "https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-book-medical"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
}
.multilink <- function(val) {
b1 <- sprintf(
'<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-database"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
b2 <- sprintf(
'<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-dna"></i>%s</a>',
val,
.actionbutton_biocstyle,
val
)
return(paste(b1, b2))
}
geneinfo_2_html <- function(gene_id) {
gene_ncbi_button <- .link2ncbi(gene_id)
gene_gtex_button <- .link2gtex(gene_id)
gene_uniprot_button <- .link2uniprot(gene_id)
gene_hpa_button <- .link2hpa(gene_id)
mycontent <- paste0(
shiny::tags$b(gene_id), shiny::tags$br(),
"Link to the NCBI Gene database: ", gene_ncbi_button, shiny::tags$br(),
"Link to the GTEx Portal: ", gene_gtex_button, shiny::tags$br(),
"Link to the Uniprot Portal: ", gene_uniprot_button, shiny::tags$br(),
"Link to the Human Protein Atlas: ", gene_hpa_button, shiny::tags$br()
)
return(HTML(mycontent))
}
doublegeneinfo_2_html <- function(gene_id1, gene_id2) {
gene_ncbi_button_1 <- .link2ncbi(gene_id1)
gene_gtex_button_1 <- .link2gtex(gene_id1)
gene_uniprot_button_1 <- .link2uniprot(gene_id1)
gene_hpa_button_1 <- .link2hpa(gene_id1)
gene_cosmic_button_1 <- .link2cosmic(gene_id1)
gene_ncbi_button_2 <- .link2ncbi(gene_id2)
gene_gtex_button_2 <- .link2gtex(gene_id2)
gene_uniprot_button_2 <- .link2uniprot(gene_id2)
gene_hpa_button_2 <- .link2hpa(gene_id2)
gene_cosmic_button_2 <- .link2cosmic(gene_id2)
mycontent <- paste0(
"<table><tr>",
'<td width="33%">', "NCBI", "</td>",
'<td width="33%">', gene_ncbi_button_1, "</td>",
'<td width="33%">', gene_ncbi_button_2, "</td>",
"</tr></table>",
"<table><tr>",
'<td width="33%">', "GTEx", "</td>",
'<td width="33%">', gene_gtex_button_1, "</td>",
'<td width="33%">', gene_gtex_button_2, "</td>",
"</tr></table>",
"<table><tr>",
'<td width="33%">', "UniProt", "</td>",
'<td width="33%">', gene_uniprot_button_1, "</td>",
'<td width="33%">', gene_uniprot_button_2, "</td>",
"</tr></table>",
"<table><tr>",
'<td width="33%">', "HPA", "</td>",
'<td width="33%">', gene_hpa_button_1, "</td>",
'<td width="33%">', gene_hpa_button_2, "</td>",
"</tr></table>",
"<table><tr>",
'<td width="33%">', "COSMIC", "</td>",
'<td width="33%">', gene_cosmic_button_1, "</td>",
'<td width="33%">', gene_cosmic_button_2, "</td>",
"</tr></table>"
)
return(HTML(mycontent))
}
## TODO? these functions can be directly used also to simply create a report, whose content is just the table with the nicely enhanced many buttons and co.!
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