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app.R
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suppressPackageStartupMessages({
library(shiny)
library(shinyBS)
library(shinyjs)
library(pedtools)
library(ribd)
library(verbalisr)
library(ggplot2)
library(ggrepel)
library(glue)
library(lubridate)
})
VERSION = "4.2.0"
DEBUG = F; debugCounter = 0
.debug <<- function(msg) if(DEBUG) cat(debugCounter <<- debugCounter+1, msg, "\n")
ui = fluidPage(
includeCSS("www/custom.css"),
tags$head(includeHTML("GA.html")),
tags$head(tags$link(rel = "stylesheet", href = "https://fonts.googleapis.com/css2?family=Lobster&display=swap")),
useShinyjs(),
# tags$div(id = "banner",
# p(id="big-text", "New app design!"),
# p("Discover the ", mylink("new features", href="https://github.com/magnusdv/quickped/blob/master/NEWS.md", style = "font-weight:bold;")),
# p(id="small-text", "Or stay with the old version: ", mylink("QuickPed3", href="https://magnusdv.shinyapps.io/quickped-32/"))
# ),
# Application title
h2(id = "title-h2", "QuickPed: An Interactive Pedigree Creator"),
tags$style(HTML("#title-h2 {background-color: #f0f4f7; color: #505050; padding: 15px}")),
p(bold("Purpose: "), style = "margin: 0 0 5px",
"QuickPed lets you rapidly create attractive pedigree plots, save them as images or text files, and analyse the relationships within them."),
p(bold("Instructions: "), style = "margin: 0 0 5px",
"Choose a suitable start pedigree and modify it by clicking on individuals and using appropriate buttons.
For example, to add a male child, select the parent(s) and press the ",
img(src = "add-son.svg", height = "18px", width = "18px", style="border: 1px solid gray; border-radius: 3px;"), "icon.",
"Check out the ",
mylink("online user manual", "https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html"),
" for various tips and tricks, including an introduction to relatedness coefficients."),
p(bold("Citation: "), style = "margin: 0 0 10px",
"If you use QuickPed in a publication, please cite this paper: ",
"Vigeland MD (2022). QuickPed: an online tool for drawing pedigrees and analysing relatedness. ",
ital("BMC Bioinformatics"), ", ", bold("23"), ". DOI:",
mylink("10.1186/s12859-022-04759-y", "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04759-y"),
"."),
fluidRow(
# Sidebar
column(width = 4, style = "width:450px",
fluidRow(
# First control column
column(width = 6,
wellPanel(style = "height:430px; width:210px",
bigHeading("Quick start"),
selectInput("startped", "Built-in pedigree", selected = "Trio", choices = BUILTIN_CHOICES, width = "100%"),
br(),
fluidRow(
column(5, hr(style = "border-top: 1px solid #000000; margin-top: 7px; margin-bottom: 12px")),
column(2, "or", style = "padding-left:10px;"),
column(5, hr(style = "border-top: 1px solid #000000; margin-top: 7px; margin-bottom: 12px")),
),
br(),
fileInput("loadped", label = "Load a ped file", buttonLabel = icon("folder-open"),
accept = c(".ped", ".txt", ".csv", ".tsv"),
width = "100%", placeholder = NULL),
fluidRow(
column(5, hr(style = "border-top: 1px solid #000000; margin-top: 15px; margin-bottom: 20px")),
column(2, "or", style = "padding-left:10px; margin-top: 5px"),
column(5, hr(style = "border-top: 1px solid #000000; margin-top: 15px; margin-bottom: 20px")),
),
br(),
pedButton("randomped", "Random pedigree"),
br(),
actionButton("reset", "Reset all", class = "btn btn-danger",
style = "position: absolute; bottom:30px; width: 170px")
),
),
# Second control column
column(width = 6,
wellPanel(style = "height:430px; width:210px",
div(style = "display: flex; flex-wrap: nowrap; align-items: center; width: 100%; justify-content: space-between;",
bigHeading("Modify"),
actionButton("clearsel", label = NULL,
icon = icon(name = NULL, class = "custom_icon",
style = "background-image: url('hand-pointer-strikethrough.svg'); width: 20px; aspect-ratio: 1/1;"),
class = "icon_button",
style = "float:left"),
bsTooltip("clearsel", HTML("Deselect<br>all")),
),
midHeading("Add", style = "margin-top: 2.5px"),
fluidRow(style = "margin-left:0px; width: 170px",
iconButton("addson", icon = "add-son.svg"),
iconButton("adddaughter", icon = "add-daughter.svg"),
iconButton("addsibRight", icon = "add-sib.svg"),
iconButton("addsibLeft", icon = "add-sib-left.svg"),
iconButton("addparents", icon = "add-parents.svg"),
),
bsTooltip("addson", "Add son"),
bsTooltip("adddaughter", "Add daughter"),
bsTooltip("addsibRight", "Add sibling to the right"),
bsTooltip("addsibLeft", "Add sibling to the left"),
bsTooltip("addparents", "Add parents"),
midHeading("Sex"),
fluidRow(style = "margin-left:0px; width: 170px",
iconButton("sex1", icon = "sex-male.svg"),
iconButton("sex2", icon = "sex-female.svg"),
iconButton("sex0", icon = "sex-unknown.svg"),
iconButton("sex3", icon = "sex-miscarriage.svg"),
bsTooltip("sex1", "Male"),
bsTooltip("sex2", "Female"),
bsTooltip("sex0", "Unknown"),
bsTooltip("sex3", "Miscarriage"),
),
midHeading("Style"),
fluidRow(style = "margin-left:0px; width: 170px",
iconButton("clean", icon = "open.svg"),
iconButton("hatched", icon = "hatched.svg"),
iconButton("carrier", icon = "carrier.svg"),
iconButton("deceased", icon = "deceased.svg"),
iconButton("dashed", icon = "dashed.svg"),
),
midHeading("Fill"),
fluidRow(style = "margin-left:0px; width: 170px",
iconButton("fill-white", icon = "fill-white.svg"),
iconButton("fill-black", icon = "fill-black.svg"),
iconButton("fill-red", icon = "fill-red.svg"),
iconButton("fill-green", icon = "fill-green.svg"),
iconButton("fill-blue", icon = "fill-blue.svg"),
),
fluidRow(style = "margin-left:0px; width: 170px",
iconButton("fill-pink", icon = "fill-pink.svg"),
iconButton("fill-cyan", icon = "fill-cyan.svg"),
iconButton("fill-magenta", icon = "fill-magenta.svg"),
iconButton("fill-yellow", icon = "fill-yellow.svg"),
iconButton("fill-gray", icon = "fill-gray.svg"),
),
fluidRow(
column(6,
midHeading("Twins"),
actionButton("twinstatus", "MZ / DZ", width = "100%",
style = "padding-top: 5px; padding-bottom: 5px; padding-left: 0px; padding-right: 3px"),
bsTooltip("twinstatus", HTML("Change twin status"), placement = "top"),
),
column(6,
midHeading("Remove"),
fluidRow(
pedButton("removeDown", NULL, icon("arrow-down"), side = "left"),
pedButton("removeUp", NULL, icon("arrow-up"), side = "right"),
bsTooltip("removeDown", HTML("Remove selected + descendants"), placement = "top"),
bsTooltip("removeUp", HTML("Remove selected + ancestors"), placement = "top"),
),
),
),
disabled(actionButton("undo", "Undo", class = "btn btn-warning",
style = "position: absolute; bottom:30px; width: 170px")),
),
)
),
# Relationship descriptions
wellPanel(style = "height:210px; width:435px",
fluidRow(
column(width = 4, bigHeading("Relationships")),
column(width = 2, actionButton("describe", icon("comment"), class = "btn btn-success", onclick = "buttonClick('describe')")),
column(width = 2, actionButton("coeffs", icon("calculator"), class = "btn btn-success"), onclick = "buttonClick('coeffs')"),
column(width = 2, actionButton("triangle", icon("chart-area"), class = "btn btn-success"), onclick = "buttonClick('triangle')"),
column(width = 2, actionButton("coeffTable", icon("list"), class = "btn btn-success"), onclick = "buttonClick('coeffTable')"),
),
bsTooltip("describe", "Describe relationship", placement = "top"),
bsTooltip("coeffs", "Calculate coefficients", placement = "top"),
bsTooltip("triangle", "Plot kappa coefficients", placement = "top"),
bsTooltip("coeffTable", "Table of coefficients", placement = "top"),
verbatimTextOutput("description", placeholder = TRUE),
tags$head(tags$style("#description{height:145px;padding-bottom:2px;}"))
)
),
# Plot window
column(width = 4, style = "margin-bottom: 15px",
plotOutput("plot", click = "ped_click", dblclick = "ped_dblclick", width = "auto", height = "auto"),
p("Double-click on an individual to add text", style = "width: 100%; font-size: smaller; text-align: left;")
),
# Settings
column(width = 4, style = "float:right; width:420px;",
fluidRow(
column(width = 6,
wellPanel(
style = "min-height:100%; width:200px",
bigHeading("Labels"),
fluidRow(
column(width = 6, align = "left", style = "padding-right:5px; padding-bottom:7px;",
actionButton("labs123", "1, 2, 3, ..", width = "100%", style = "background-color: lightgray;")),
column(width = 6, align = "right", style = "padding-left:5px; padding-bottom:7px;",
actionButton("labsGen", "I-1, I-2, ..", width = "100%",style = "background-color: lightgray;"))
),
radioButtons("showlabs", label = NULL, choices = c("Show all" = "show", "Hide all" = "hide"),
inline = TRUE, selected = "show", width = "100%"),
uiOutput("labels"),
actionButton("updateLabs", "Update", width = "100%",
class = "btn btn-success", style = "margin-top: 10px;"),
),
),
# Rightmost column: Settings and save
column(width = 6,
wellPanel(style = "height:430px; width:180px",
bigHeading("Plot settings"),
fluidRow(class = "num-input-row",
column(6, numericInput("width", "Width", value = 430, min = 100, max = 1200, step = 10)),
column(6, numericInput("height", "Height", value = 430, min = 100, max = 1200, step = 10))
),
fluidRow(class = "num-input-row",
column(6, numericInput("cex", "Cex", value = 1.4, min = 0.5, max = 3, step = 0.1)),
column(6, numericInput("symbolsize", "Symbols", value = 1, min = 0.5, max = 3, step = 0.1))
),
fluidRow(class = "num-input-row",
column(12, numericInput("mar", "Margins", value = 3, min = 0.1, max = 10, step = 0.1))
),
br(),
checkboxGroupInput("settings", "Other options (beta)", selected = NULL,
c("Straight legs" = "straightlegs", "Arrows" = "arrows")),
actionButton("rcode", "R code", style = "background: lightgoldenrodyellow; font-family:monospace; font-weight: bolder; padding:0px; width: 100%;"),
fluidRow(style = "position: absolute; top:375px",
column(width = 6, align = "left", style = "padding-right:5px;",
downloadButton("savePlotPng", "PNG", class = "btn btn-info", style = "padding-inline:8px; width:100%;"),
),
column(width = 6, align = "right", style = "padding-left:5px;",
downloadButton("savePlotPdf", "PDF", class = "btn btn-info", style = "padding-inline:8px; width:100%;"),
)
)
),
# Save ped file
wellPanel(style = "height:210px; width:180px",
bigHeading("Ped file"),
checkboxGroupInput("include", "Include", selected = "head",
c("Headers" = "head", "Family ID" = "famid", "Affection status" = "aff")),
downloadButton("savePed", "Save ped file", class="btn btn-info", style = "width: 100%;"),
)
),
)
),
),
p("This is QuickPed version", VERSION, "(",
mylink("changelog", "https://github.com/magnusdv/quickped/blob/master/NEWS.md"), ").",
"QuickPed is powered by the ",
mylink("pedsuite", "https://magnusdv.github.io/pedsuite/"),
" and uses ",
mylink("kinship2", "https://cran.r-project.org/package=kinship2"),
" for alignment calculations.",
"If you find something that isn't working properly, please file a bug report at ",
mylink("https://github.com/magnusdv/quickped/issues"), "."),
)
server = function(input, output, session) {
pedigree = reactiveValues(ped = nuclearPed(1), twins = NULL, miscarriage = NULL)
styles = reactiveValues(hatched = NULL, carrier = NULL, deceased = NULL,
dashed = NULL, fill = NULL)
textAnnot = reactiveVal(NULL)
sel = reactiveVal(character(0))
relText = reactiveVal(NULL)
# Stack of previous states ------------------------------------------------
previousStack = reactiveVal(list())
observe(switch(length(previousStack()) + 1, disable("undo"), enable("undo")))
addCurrentToStack = function() { .debug("add to stack")
stack = previousStack()
n = length(stack)
# Collect state of current reactives in static list
curr = c(reactiveValuesToList(pedigree), reactiveValuesToList(styles),
list(textAnnot = textAnnot()))
# If new: add
if(n == 0 || !identical(curr, stack[[n]]))
previousStack(c(stack, list(curr)))
}
# Main updating function --------------------------------------------------
updatePed = function(..., addToStack = TRUE, clearSel = NULL,
clearStart = NULL, clearRel = NULL) { .debug("updateped")
if(!length(args <- list(...)))
return()
# Push current state to stack
if(addToStack)
addCurrentToStack()
# Update only given attributes
argnames = names(args)
# Convert empty vectors to explicit NULLs
args = lapply(args, function(b) if(length(b)) b else NULL)
# Update reactives
for(a in .myintersect(argnames, c("ped", "twins", "miscarriage")))
pedigree[[a]] = args[[a]]
for(a in .myintersect(argnames, names(styles)))
styles[[a]] = args[[a]]
if("textAnnot" %in% argnames)
textAnnot(args$textAnnot)
# Clear stuff
if(clearSel %||% ("textAnnot" %in% argnames))
sel(character(0))
if(clearRel %||% any(c("ped", "twins") %in% argnames))
relText(NULL)
if(clearStart %||% any(c("ped", "twins") %in% argnames))
updateSelectInput(session, "startped", selected = "")
codeTxt(NULL)
}
# Reset with a new pedigree -----------------------------------------------
resetPed = function(ped, ...) { .debug("resetped")
cleanArgs = list(twins = NULL, miscarriage = NULL, hatched = NULL,
carrier = NULL, dashed = NULL,
deceased = NULL, fill = NULL, textAnnot = NULL)
args = modifyList(cleanArgs, list(ped = ped, ...), keep.null = TRUE)
do.call(updatePed, args)
}
# Startped/load -----------------------------------------------------------
observeEvent(input$startped, { .debug("startped")
choice = req(input$startped)
params = paramsBuiltin(choice)
updateNumericInput(session, "width", value = params$width)
updateNumericInput(session, "height", value = params$height)
updateNumericInput(session, "cex", value = params$cex)
updateNumericInput(session, "symbolsize", value = params$symbolsize)
updateNumericInput(session, "mar", value = params$mar)
y = req(BUILTIN_PEDS[[choice]])
args = list(ped = y$ped %||% y,
fill = modifyVec(NULL, y$aff, val = 1),
carrier = y$carrier,
clearStart = FALSE)
do.call(resetPed, args)
}, ignoreInit = TRUE)
observeEvent(input$loadped, { .debug("loadped")
file = req(input$loadped$datapath)
y = tryCatch(readPed2(file), error = errModal, warning = errModal)
resetPed(ped = y$ped, fill = modifyVec(NULL, y$aff, val = 1))
})
observeEvent(input$randomped, { .debug("random ped")
n = sample(5:15, size = 1) # total pedigree size
f = sample(2:floor((n+1)/2), size = 1) # number of founders
ped = NULL
while(is.null(ped)) {
ped = tryCatch(randomPed(n, f, maxDirectGap = 0) |> relabel(),
error = function(e) NULL, warning = function(e) NULL)
}
resetPed(ped = ped)
})
# Modify pedigree ---------------------------------------------------------
observeEvent(input$addson, { .debug("add son")
id = req(sel())
tryCatch({
if(any(id %in% pedigree$miscarriage))
stop2("Cannot add children to a miscarriage")
updatePed(ped = addSon(pedigree$ped, id, verbose = FALSE))
}, error = errModal)
})
observeEvent(input$adddaughter, { .debug("add daughter")
id = req(sel())
tryCatch({
if(any(id %in% pedigree$miscarriage))
stop2("Cannot add children to a miscarriage")
updatePed(ped = addDaughter(pedigree$ped, id, verbose = FALSE))
}, error = errModal)
})
observeEvent(input$addsibRight, { .debug("add right sib")
id = req(sel())
tryCatch({
updatePed(ped = addSib(pedigree$ped, id, side = "right"))
}, error = errModal)
})
observeEvent(input$addsibLeft, { .debug("add left sib")
id = req(sel())
tryCatch({
updatePed(ped = addSib(pedigree$ped, id, side = "left"))
}, error = errModal)
})
observeEvent(input$addparents, { .debug("add parents")
ids = req(sel()) # If multiple, the first is interpreted as child, followed by parents
ok = FALSE
tryCatch({
updatePed(ped = addPar(pedigree$ped, ids))
ok = TRUE
}, error = errModal)
if(ok && length(ids) %in% 2:3 && !isTRUE(input$suppressParentMessage))
showModal(parentMessage)
})
observeEvent(input$sex1, { .debug("sex1")
id = req(sel())
tryCatch({
ped = changeSex(pedigree$ped, id, sex = 1, twins = pedigree$twins)
updatePed(ped = ped, miscarriage = .mysetdiff(pedigree$miscarriage, id))
}, error = errModal)
})
observeEvent(input$sex2, { .debug("sex2")
id = req(sel())
tryCatch({
ped = changeSex(pedigree$ped, id, sex = 2, twins = pedigree$twins)
updatePed(ped = ped, miscarriage = .mysetdiff(pedigree$miscarriage, id))
}, error = errModal)
})
observeEvent(input$sex0, { .debug("sex0")
id = req(sel())
tryCatch({
ped = changeSex(pedigree$ped, id, sex = 0, twins = pedigree$twins)
updatePed(ped = ped, miscarriage = .mysetdiff(pedigree$miscarriage, id))
}, error = errModal)
})
observeEvent(input$sex3, { .debug("miscarriage")
id = req(sel())
tryCatch({
if(!all(id %in% leaves(pedigree$ped)))
stop2("A parent cannot be a miscarriage")
updatePed(miscarriage = union(pedigree$miscarriage, id), clearSel = TRUE)
}, error = errModal)
})
observeEvent(input$clean, { .debug("clear styles")
id = req(sel())
addCurrentToStack()
styles$hatched = setdiff(styles$hatched, id)
styles$carrier = setdiff(styles$carrier, id)
styles$deceased = setdiff(styles$deceased, id)
styles$dashed = setdiff(styles$dashed, id)
})
observeEvent(input$hatched, { .debug("hatched")
updatePed(hatched = union(styles$hatched, req(sel())))
})
observeEvent(input$carrier, { .debug("carrier")
updatePed(carrier = union(styles$carrier, req(sel())))
})
observeEvent(input$deceased, { .debug("deceased")
updatePed(deceased = union(styles$deceased, req(sel())))
})
observeEvent(input$dashed, { .debug("dashed")
updatePed(dashed = union(styles$dashed, req(sel())))
})
COLS = c(white = 0, black = 1, red = 2, green = 3, blue = 4, cyan = 5,
magenta = 6, yellow = 7, gray = 8, pink = "pink")
for(cc in names(COLS)) local({
thisCol = cc
tag = paste0("fill-", thisCol)
observeEvent(input[[tag]], { .debug(tag)
fill = modifyVec(styles$fill, req(sel()), val = COLS[[thisCol]])
updatePed(fill = fill)
})
})
# Remove individuals ------------------------------------------------------
observeEvent(input$removeDown, { .debug("remove down")
ids = req(sel())
dat = c(reactiveValuesToList(pedigree), reactiveValuesToList(styles),
list(textAnnot = textAnnot()))
tryCatch({
newdat = removeSel(dat, ids = ids, updown = "descendants")
do.call(updatePed, newdat)
}, error = errModal)
})
observeEvent(input$removeUp, { .debug("remove down")
ids = req(sel())
dat = c(reactiveValuesToList(pedigree), reactiveValuesToList(styles),
list(textAnnot = textAnnot()))
tryCatch({
newdat = removeSel(dat, ids = ids, updown = "ancestors")
do.call(updatePed, newdat)
}, error = errModal)
})
observeEvent(input$twinstatus, { .debug("twinstatus")
ids = req(sel())
tryCatch({
updatePed(twins = updateTwins(pedigree$ped, pedigree$twins, ids))
}, error = errModal)
})
observeEvent(input$clearsel, sel(character(0)))
# Undo/reset --------------------------------------------------------------
observeEvent(input$undo, { .debug("undo")
stack = previousStack()
len = length(stack)
if(len == 0)
return()
args = c(stack[[len]], list(addToStack = FALSE))
do.call(updatePed, args)
previousStack(stack[-len])
})
observeEvent(input$reset, { .debug("reset")
if(input$startped == "Trio")
updateSelectInput(session, "startped", selected = "")
updateSelectInput(session, "startped", selected = "Trio")
# Show labels
updateRadioButtons(session, "showlabs", selected = "show")
# Reset settings (main plot settings reset in 'startped')
updateCheckboxGroupInput(session, "settings", selected = character(0))
updateCheckboxGroupInput(session, "include", selected = "head")
})
# Labels ------------------------------------------------------------------
output$labels = renderUI({ .debug("labelsUI")
labs = labels(pedigree$ped)
n = length(labs)
fields = paste0("lab", seq_len(n))
h = if(n < 10) 24 else if (n < 20) 21 else 18
lapply(seq_along(labs), function(i) textInput2(fields[i], value = labs[i], height = h))
})
observeEvent(input$labs123, { # New labels: 1, 2, ...
newdat = updateLabelsData(pedigree, styles, textAnnot(), new = "asPlot", .alignment = plotAlignment())
newdat$clearSel = newdat$clearRel = TRUE
do.call(updatePed, newdat)
})
observeEvent(input$labsGen, { # New labels: I-1, I-2, ...
newdat = updateLabelsData(pedigree, styles, textAnnot(), new = "generations", .alignment = plotAlignment())
newdat$clearSel = newdat$clearRel = TRUE
do.call(updatePed, newdat)
})
observeEvent(input$updateLabs, { .debug("updatelabs")
oldlabs = labels(pedigree$ped)
fields = paste0("lab", seq_along(oldlabs))
newlabs = vapply(fields, function(s) input[[s]], FUN.VALUE = "1") |>
as.character() |> trimws()
if(identical(oldlabs, newlabs))
return()
tryCatch({
newdat = updateLabelsData(pedigree, styles, textAnnot(), new = newlabs)
newdat$clearSel = newdat$clearRel = TRUE
do.call(updatePed, newdat)
}, error = errModal)
})
# Plot --------------------------------------------------------------------
plotLabs = reactive({ .debug("plotlabs")
ped = pedigree$ped
switch(input$showlabs, show = breakLabs(ped), hide = NULL)
})
plotAlignment = reactive({ .debug("align")
arrows = "arrows" %in% input$settings
straight = "straightlegs" %in% input$settings
# Safety check (should be avoided elsewhere)
if(is.pedList(pedigree$ped))
stop2("Disconnected pedigree")
.pedAlignment(pedigree$ped, twins = pedigree$twins, arrows = arrows,
miscarriage = pedigree$miscarriage,
align = if(straight) c(0,0) else c(1.5,2))
})
plotAnnotation = reactive({ .debug("annot")
.pedAnnotation(req(pedigree$ped),
labs = plotLabs(),
hatched = styles$hatched, hatchDensity = 20,
carrier = styles$carrier,
deceased = styles$deceased,
textAnnot = formatAnnot(textAnnot(), input$cex - 0.2),
col = list(red = sel()),
fill = styles$fill %||% NA,
lty = list(dashed = styles$dashed),
lwd = list(`3` = sel(),
`1.5` = .mysetdiff(styles$dashed, sel())))
})
plotScaling = reactive({ .debug("scaling")
checknum(input$width, "Width", min = 100, max = Inf)
checknum(input$height, "Heigth", min = 100, max = Inf)
align = req(plotAlignment())
annot = list(textUnder = plotLabs())
cex = checknum(input$cex, "Cex", min = 0.01, max = 10)
symsize = checknum(input$symbolsize, "Symbols", min = 0.01, max = 10)
mar = checknum(input$mar, "Margins", min = 0, max = 10)
.pedScaling(align, annot, cex = cex, symbolsize = symsize, margins = rep(mar, 4))
})
output$plot = renderPlot({ .debug("plot")
# Plot, but catch various errors & warnings
dat = tryCatch({
align = withCallingHandlers(
plotAlignment(),
warning = function(w) {
if(startsWith(w$message, "Unexpected result in autohint"))
invokeRestart("muffleWarning")
}
)
if(anyNA(align$x))
stop2("Sorry, for some reason this pedigree did align properly.")
scale = plotScaling()
annot = plotAnnotation()
drawPed(align, annotation = annot, scaling = scale)
},
error = errModal) |> req()
box("outer", col = 1)
},
execOnResize = TRUE, res = 72, # default; seems OK in practice
width = function() max(c(100, abs(input$width)), na.rm = TRUE),
height = function() max(c(100, abs(input$height)), na.rm = TRUE)
)
positionDf = reactive({ .debug("position")
align = req(plotAlignment())
scale = plotScaling()
mat = cbind(x = align$xall,
y = align$yall + scale$boxh/2,
idInt = align$plotord)
as.data.frame(mat)
})
# Single click: Text annotation -------------------------------------------
observeEvent(input$ped_click, { .debug("pedclick")
posDf = positionDf()
idInt = nearPoints(posDf, input$ped_click, xvar = "x", yvar = "y",
threshold = 20, maxpoints = 1)$idInt |> req()
id = labels(pedigree$ped)[idInt]
currSel = sel()
newSel = if(id %in% currSel) .mysetdiff(currSel, id) else c(currSel, id)
sel(newSel)
})
# Double click: Text annotation -------------------------------------------
# Temp copy of textAnnot, to be used in the module.
# Could use textAnnot directly, but want to go via pedUpdate (stack etc)
textAnnotTemp = reactiveVal()
observeEvent(input$ped_dblclick, { .debug("dblclick")
posDf = positionDf()
idInt = nearPoints(posDf, input$ped_dblclick, xvar = "x", yvar = "y",
threshold = 20, maxpoints = 1)$idInt |> req()
id = labels(pedigree$ped)[idInt]
isolate(textAnnotTemp(textAnnot()))
showAnnotationModal(input, output, session, id, textAnnotTemp)
})
observeEvent(textAnnotTemp(), { .debug("textAnnotTemp")
updatePed(textAnnot = textAnnotTemp())})
# Save --------------------------------------------------------------------
output$savePed = downloadHandler(
filename = "quickped.ped",
content = function(con) {
inclHead = "head" %in% input$include
inclFamid = "famid" %in% input$include
inclAff = "aff" %in% input$include
ped = pedigree$ped
df = as.data.frame(ped)
if(inclFamid)
df = cbind(famid = 1, df)
if(inclAff) {
aff = union(styles$hatched, names(styles$fill))
df = cbind(df, aff = ifelse(labels(ped) %in% aff, 2, 1))
}
write.table(df, file = con, col.names = inclHead, row.names = FALSE,
quote = FALSE, sep = "\t", fileEncoding = "UTF-8")
}
)
output$savePlotPng = downloadHandler(
filename = "quickped.png",
content = function(con)
tryCatch({
align = plotAlignment()
scale = plotScaling()
annot = plotAnnotation()
png(con, width = input$width, height = input$height)
drawPed(align, annotation = annot, scaling = scale)
dev.off()
},
error = errModal),
contentType = "image/png"
)
output$savePlotPdf = downloadHandler(
filename = "quickped.pdf",
content = function(file)
tryCatch({
align = plotAlignment()
scale = plotScaling()
annot = plotAnnotation()
cairo_pdf(file, width = input$width/72, height = input$height/72)
drawPed(align, annotation = annot, scaling = scale)
dev.off()
},
error = errModal),
contentType = "application/pdf"
)
# Relationships ------------------------------------------------
dlg = modalDialog(
h3(id = "title-h3", "Download table of pairwise coefficients"),
tags$style(HTML("#title-h3 {background-color: gray; color: white; padding: 15px}")),
textInput("coeffIds", label = "Individuals:", value = "", width = "100%"),
br(),
fluidRow(
column(width = 6,
checkboxGroupInput("coeffSelect", "Coefficients:",
c("Inbreeding" = "f",
"Kinship" = "phi",
"Degree" = "deg",
"IBD (kappa)" = "kappa",
"Identity (condensed)" = "identity",
"Identity (detailed)" = "detailed"
),
selected = c("f", "phi", "deg", "kappa"))
),
column(width = 6,
checkboxGroupInput("coeffChrom", "Chromosome:",
c("Autosomal" = "aut",
"X-chromosomal" = "X"
),
selected = c("aut")),
checkboxGroupInput("coeffInclude", "Include:",
c("Self relationships" = "self"),
selected = NULL)
)
),
easyClose = TRUE,
footer = tagList(
modalButton("Cancel"),
downloadButton("saveCoeffTable", "Download", class = "btn btn-info")
)
)
observeEvent(input$coeffTable, { .debug("coeffTable")
if(1 %in% pedigree$twins$code) {
relText("This feature does not support MZ twin pedigrees.")
return()
}
ped = pedigree$ped
ids = sel()
if(!length(ids))
ids = labels(ped)
updateTextInput(session, "coeffIds", value = toString(sortIds(ped, ids)))
tryCatch(showModal(dlg), error = errModal)
})
# Action when clicking "Download" in the modal dialog
output$saveCoeffTable = downloadHandler(
filename = "quickped-relatedness.txt",
content = function(file) {
idsTxt = req(input$coeffIds)
tryCatch({
ids = trimws(strsplit(idsTxt, ",")[[1]])
coeff = input$coeffSelect # coefficients selected
self = "self" %in% input$coeffInclude
if(!length(chr <- input$coeffChrom))
stop2("Please select chromosome type")
Xchrom = if(length(chr) == 2) NA else chr == "X"
# Compute table
tab = coeffTable(pedigree$ped, ids, coeff = coeff, Xchrom = Xchrom, self = self)
write.table(tab, file = file, col.names = TRUE, row.names = FALSE,
quote = FALSE, sep = "\t", fileEncoding = "UTF-8")
removeModal()
},
error = errModal)
}
)
### Triangle plot
observeEvent(input$triangle, { .debug("triangle")
if(1 %in% pedigree$twins$code) {
relText("This feature does not support MZ twin pedigrees.")
return()
}
ped = pedigree$ped
ids = sel()
if(!length(ids))
ids = labels(ped)
if(length(ids) == 1) {
relText("Please select at least 2 individuals (or none).")
return()
}
if(any(ribd::inbreeding(ped, ids) > 0))
relText(c("Note: Kappa undefined for inbred individuals"))
showModal(modalDialog(
h3("Relatedness triangle", align = "center"),
plotOutput("plotTriangle", width = "560px", height = "480px"),
footer = tags$div(
tags$div(
style = "float: left; margin-left:10px; margin-top:5px",
radioButtons("trianglemode", NULL, inline = TRUE, selected = "noninbred",
choices = c("Noninbred (κ)" = "noninbred",
"Inbred (Δ)" = "inbred")),
),
tags$div(
style = "float: right",
modalButton("Cancel"),
downloadButton("saveTriangle", "Download", class = "btn btn-info")
)
),
size = "m",
easyClose = TRUE
))
})
output$plotTriangle = renderPlot(
plotKappa(pedigree$ped, ids = sel(), mode = input$trianglemode,
arrows = "arrows" %in% input$settings, miscarriage = pedigree$miscarriage),
width = 560, height = 480,
res = 72 # too low, but increasing it disturbs everything else
)
output$saveTriangle = downloadHandler(
filename = "triangle.png",
content = function(file) {
png(file, width = 560*2, height = 480*2, res = 72*2)
plotKappa(pedigree$ped, ids = sel(), mode = input$trianglemode,
arrows = "arrows" %in% input$settings, miscarriage = pedigree$miscarriage)
dev.off()
},
contentType = "image/png"
)
observeEvent(input$describe, { .debug("describe")
ped = req(pedigree$ped)
if(1 %in% pedigree$twins$code) {
relText("This feature does not support MZ twin pedigrees.")
return()
}
ids = sortIds(ped, ids = sel())
if(length(ids) != 2) {
relText("Please select exactly 2 individuals.")
return()
}
paths = verbalisr::verbalise(ped, ids)
txt = format(paths)
txt = gsub("([[:graph:]]) ([[:graph:]])", "\\1 \\2", txt) # remove double spaces
relText(txt)
})
observeEvent(input$coeffs, { .debug("coeffs")
if(1 %in% pedigree$twins$code) {
relText("This feature does not support MZ twin pedigrees.")
return()
}
ped = req(pedigree$ped)
ids = sortIds(ped, ids = sel())
N = length(ids)
if(!N %in% 1:2) {
relText(c("Please select 1 or 2 individuals.",
"(Or click the Table button for more options.)"))
return()
}
if(N == 1) {
txt = c(sprintf("Inbreeding coefficient for individual %s:", ids),
sprintf("* f = %g", ribd::inbreeding(ped, ids)))
relText(txt)
return()
}
### N = 2
txt = sprintf("Relatedness coefficients for %s and %s:", ids[1], ids[2])
# Inbreeding
inb = ribd::inbreeding(ped, ids)
txt = c(txt,
sprintf("* Inbreeding: f1 = %.4g", inb[1]),
sprintf(" f2 = %.4g", inb[2]))
# Kinship
phi = ribd::kinship(ped, ids)
txt = c(txt,
sprintf("* Kinship: phi = %.4g", phi))
# Degree
deg = ribd::kin2deg(phi, unrelated = NA)
txt = c(txt,
sprintf("* Degree: deg = %.4g", deg))
# Kappa (if both outbred) or Delta
if(all(inb == 0)) {
kap = ribd::kappaIBD(ped, ids, simplify = TRUE) # simplify to vector of len 3
kap = sprintf("%.4g", round(kap, 4))
txt = c(txt,
sprintf("* IBD: kappa = (%s)", toString(kap)))
}
else {
delta = ribd::condensedIdentity(ped, ids)
delta = sprintf("%.4g", round(delta, 4))
len = nchar(toString(delta))
if(len <= 50)
s = sprintf("* Condensed identity =\n (%s)", toString(delta))
else
s = sprintf("* Condensed identity = (%s\n %s)",
toString(delta[1:3]), toString(delta[4:9]))
txt = c(txt, s)
}
relText(txt)
})
output$description = renderText(req(relText()), sep = "\n")
# Generate R code----------------------------------------------------------
codeTxt = reactiveVal(NULL)
# Render in modal dialog, created with createCodeModal when pressing rcode button (see below)
output$showCode = renderText(req(codeTxt()))