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inst/shiny/ui.R
In treespace: Statistical Exploration of Landscapes of Phylogenetic Trees
options(rgl.useNULL=TRUE)
## CHECKS ##
require("scatterD3")
require("shiny")
require("rgl")
require("RLumShiny")
require("shinyBS")
## DEFINE UI ##
shinyUI(
navbarPage("",position="fixed-top", collapsible = TRUE,
theme = "bootstrap.simplex.css",
tabPanel("Tree landscape explorer",
tags$link(rel = 'stylesheet', type = 'text/css', href = 'styles.css'),
tags$style(type="text/css", "body {padding-top: 40px;}"),
pageWithSidebar(
## TITLE ##
headerPanel(
img(src="img/logo.png", height="160")
),
## SIDE PANEL CONTENT ##
sidebarPanel(
tags$head(tags$style(
type = 'text/css',
'form.well { max-height: 1600px; overflow-y: auto; }'
)),
## SPECIFIC TO TREE LANDSCAPE EXPLORER ##
conditionalPanel(condition = "$('li.active a').first().html()== 'Tree landscape explorer'",
## INPUT
## choice of type of data source
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Input </font>')),
radioButtons("datatype", HTML('<font size="4"> Choose data source:</font>'),
list("Example: Dengue fever"="exDengue",
"Example: Woodmice"="exWoodmice",
"Input file"="file")),
## choice of dataset if source is a file
conditionalPanel(condition = "input.datatype=='file'",
fileInput("datafile", p(HTML(' <font size="4"> Choose input file:</font>'), br(),
strong("accepted formats:"), br(),
em("- multiphylo"), "saved from R (.RData/.rda/.rds)", br(),
em("- nexus"), "file (.nex/.nexus)")
),
checkboxInput("randSamp","Randomly sample from the trees?", value=TRUE),
bsTooltip("randSamp", "For large sets of trees and/or trees with many tips the app may be slow, so beginning the analysis with a small random sample is recommended.",
placement = "right", trigger = "hover", options = NULL),
conditionalPanel(
condition="input.randSamp",
sliderInput("sampleSize", "Size of random sample:", value=10, min=10, max=300, step=10)
)
),
## ANALYSIS
img(src="img/line.png", width="100%"),
h4(HTML('<font color="#6C6CC4" size="6"> > Analysis </font>')),
## choose metric
selectInput("treemethod", "Choose a tree summary:",
choices=c(
"Kendall Colijn (rooted)" = "metric",
"Billera, Holmes, Vogtmann (rooted, uses branch lengths)" = "BHV",
"Kuhner & Felsenstein branch score distance (unrooted, uses branch lengths)" = "KF",
"Robinson Foulds symmetric difference (unrooted, topological)" = "RF",
"Weighted Robinson Foulds (unrooted, uses branch lengths)" = "wRF",
"Steel & Penny tip-tip distance (unrooted, topological)" = "nNodes",
"Steel & Penny weighted tip-tip distance (unrooted, uses branch lengths)" = "patristic",
"Abouheif test (rooted, topological)" = "Abouheif",
"Sum of direct descendents (rooted, topological)" = "sumDD")),
## lambda, axes
uiOutput("lambda"),
bsTooltip("lambda","When lambda=0 trees are compared topologically; increasing lambda gives more focus to branch lengths"),
conditionalPanel(
condition="input.plotType==1",
uiOutput("naxes")
## Future: highlight median trees (if plotType==1)
#checkboxInput("showMedians", label=strong("Highlight median tree(s)?"), value=FALSE)
),
## show Shepard plot?
checkboxInput("quality", label=strong("Assess quality of projection (Shepard plot)?"), value=FALSE),
bsTooltip("quality","A Shepard plot gives an indication of the quality of the MDS projection. It will be displayed below the main plot.", placement="right"),
## show screeplot?
conditionalPanel(
condition="input.graphics==1",
checkboxInput("scree", label=strong("Show screeplot?"), value=FALSE),
bsTooltip("scree","Display screeplot of the eigenvalues associated with each componenet? It will be displayed below the main plot.", placement="right")
),
## find clusters?
checkboxInput("findClusters", label=strong("Identify clusters?"), value=FALSE),
bsTooltip("findClusters","Statistical tools for choosing an appropriate clustering method and number of clusters will be added to treespace soon.", placement="right"),
conditionalPanel(condition ="input.findClusters",
radioButtons("clusterType", label="Method:",
choices=c("statistically"="stat","by metadata"="meta"), selected="stat"),
conditionalPanel(
condition="input.clusterType=='stat'",
## clustering method
selectInput("clustmethod", "Clustering method:",
choices=c(
"Ward" = "ward.D2",
"Single" = "single",
"Complete" = "complete",
"UPGMA" = "average")),
## number of clusters
uiOutput("nclust")
),
conditionalPanel(
condition="input.clusterType=='meta'",
fileInput("metadatafile", p(HTML(' <font size="4"> Choose input file:</font>'), br(),
strong("accepted formats:"), br(),
em("- object of class factor/numeric/character/list"), "saved from R (.RData/.rda)", br(),
em("- csv file"), "(.csv) (first column will be used)")
)
)
),
## relevant if method = KC metric, allow tip emphasis
conditionalPanel(
condition="input.treemethod=='metric'",
## Emphasise tips
checkboxInput("emphTips", label=strong("Emphasise tips?"), value=FALSE),
bsTooltip("emphTips","Choose tips to emphasise or de-emphasise: the vector elements corresponding to these tips are multiplied by the weight chosen below.", placement="right"),
## if tip emphasis is chosen, provide options:
conditionalPanel(
condition="input.emphTips",
uiOutput("whichTips"),
sliderInput("emphWeight", "Weight of emphasis", value=2,min=0.1,max=100)
)
),
## AESTHETICS
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Aesthetics </font>')),
## tree landscape or compare to single reference tree
conditionalPanel(
condition="input.plot3D==2",
radioButtons("plotType", "View",
choices=c("Full tree landscape"=1,"Distances from a reference tree"=2),
selected=1),
bsTooltip("plotType", "Choose whether to view the relative distances between all trees, or a 1-dimensional plot of their distances from a fixed reference tree")
),
## Dimensions (3D possible if 3 or more axes retained, and full tree landscape)
conditionalPanel(condition="input.naxes>2",
conditionalPanel(
condition="input.plotType==1",
radioButtons("plot3D", "Plot dimensions",
choices=c("2D"=2,"3D"=3),
selected=2)
)
),
conditionalPanel(
condition="(input.plot3D==2)&&(input.plotType==1)",
radioButtons("graphics", "Display using",
choices=c("plotGrovesD3"=1,"plotGroves"=2),
selected=1),
bsTooltip("graphics", "Choose whether to view the tree landscape using plotGrovesD3 which uses scatterD3 (interactive html) or plotGroves which uses adegraphics")
),
# if plotType=1, pick the axes to view:
conditionalPanel(
condition="input.plotType==1",
## select first axis to plot
numericInput("xax", "Indicate the x axis", value=1, min=1, max=3),
## select second axis to plot
numericInput("yax", "Indicate the y axis", value=2, min=1, max=3),
bsTooltip("yax", "If multiple MDS axes have been retained, any combination of axes can be viewed"),
## if in 3D, need a z axis:
conditionalPanel(condition="input.plot3D==3",
numericInput("zax", "Indicate the z axis", value=3, min=1, max=3)
)
),
## aesthetics for tree landscape view
conditionalPanel(
condition="input.plotType==1",
conditionalPanel(
condition="(input.plot3D==2)&&(input.graphics==1)",
## Animate transitions?
checkboxInput("transitions", label="Animate transitions?", value=TRUE)
),
conditionalPanel(
condition="(input.plot3D==2)&&(input.graphics==2)",
## convex hulls or ellipses when clusters identified
conditionalPanel(
condition="input.findClusters",
radioButtons("scattertype", "Type of scatterplot",
choices=c("chull","ellipse"),
selected="chull")
),
selectInput("screemds", "Position of the MDS screeplot:",
choices=c("None" = "none",
"Bottom right" = "bottomright",
"Bottom left" = "bottomleft",
"Top right" = "topright",
"Top left" = "topleft"),
selected="bottomleft")
),
## symbol size
sliderInput("pointsize", "Size of the points", value=2, min=0, max=10, step=0.2),
conditionalPanel(
condition="(input.plot3D==2)&&(input.graphics==1)",
## symbol size
sliderInput("pointopacity", "Opacity of the points", value=0.6, min=0, max=1, step=0.05)
),
conditionalPanel(
condition="input.plot3D==2",
## display labels
checkboxInput("showlabels", label="Display tree labels?", value=FALSE),
conditionalPanel(
condition="input.showlabels",
## label size
sliderInput("labelsize", "Size of the labels", value=1, min=0, max=10, step=1),
conditionalPanel(
condition="input.graphics==2",
checkboxInput("optimlabels", label="Optimize label position?", value=FALSE)
)
)
)
),
# if plotType=2, option to stretch
conditionalPanel(
condition="input.plotType==2",
uiOutput("selectedRefTree"),
sliderInput("stretch", "Height of plot (pixels)", value=1600, min=800, max=12800, step=200)
),
## choose color palette (if clusters detected)
conditionalPanel(
## condition
condition="input.findClusters",
selectInput("palette", "Palette for the clusters",
choices=c("funky", "spectral",
"seasun", "lightseasun", "deepseasun",
"rainbow", "azur", "wasp"),
selected="funky")
),
conditionalPanel(
condition="input.plotType==1",
## choose label colors
jscolorInput("labcol", "Label / point color", value="#1B2266", close=TRUE)
),
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
width=4)), # end conditional panel and sidebarPanel; width is out of 12
## MAIN PANEL
mainPanel("",
# TITLE #
h2(HTML('<font color="#6C6CC4" size="6"> Tree landscape explorer </font>')),
br(),br(),
## function I was using for testing:
#verbatimTextOutput("plot_click"),
# Removed:
#verbatimTextOutput("caption"),
conditionalPanel(
condition="input.plot3D==2",
uiOutput("treespacePlot")
),
conditionalPanel(
condition="input.plot3D==3",
rglwidgetOutput("treespacePlot3D", width="800px")
),
conditionalPanel(
condition="(input.plotType==1)&&(input.plot3D==2)&&(input.graphics==1)",
tags$p(actionButton("scatterD3-reset-zoom", HTML("<span class='glyphicon glyphicon-search' aria-hidden='true'></span> Reset Zoom")))
),
conditionalPanel(
condition="input.quality",
uiOutput("shep")
),
conditionalPanel(
condition="(input.scree)&&(input.graphics==1)",
uiOutput("scree")
),
br(), br(),
## OUTPUT (save)
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Output </font>')),
## save MDS plot
conditionalPanel(
condition="(input.plotType==1)&&(input.plot3D==2)&&(input.graphics==1)",
tags$p(tags$a(id = "scatterD3-svg-export", href = "#",
class = "btn btn-default", HTML("<span class='glyphicon glyphicon-save' aria-hidden='true'></span> Save treespace plot as svg"))),
downloadButton("downloadMDS2Dhtml", "Save treespace plot as interactive html")
),
conditionalPanel(
condition="(input.plotType==1)&&(input.plot3D==2)&&(input.graphics==2)",
downloadButton("downloadMDS", "Save treespace image as png file")
),
conditionalPanel(
condition="input.plot3D==3",
downloadButton("downloadMDS3Dhtml", "Save treespace 3D plot as interactive html")
),
conditionalPanel(
condition="input.quality",
downloadButton("downloadShep", "Save Shepard plot as png file")
),
conditionalPanel(
condition="input.scree",
downloadButton("downloadScree", "Save screeplot as png file")
),
## save trees to nexus file
downloadButton('exporttrees', "Save trees to nexus file"),
## save results to csv
downloadButton('exportrestocsv', "Save results (MDS+clusters) to csv file"),
## save results to RData
downloadButton('exportrestordata', "Save results (MDS+clusters) to R object")
) # end mainPanel
) # end page with sidebar
), # end tabPanel
tabPanel("Tree viewer",
tags$link(rel = 'stylesheet', type = 'text/css', href = 'styles.css'),
tags$style(type="text/css", "body {padding-top: 40px;}"),
pageWithSidebar(
## TITLE ##
headerPanel(
img(src="img/logo.png", height="160")
),
## SIDE PANEL CONTENT ##
sidebarPanel(
tags$head(tags$style(
type = 'text/css',
'form.well { max-height: 1600px; overflow-y: auto; }'
)),
## INPUT
## choice of tree type
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Input </font>')),
h2(HTML('<font color="#6C6CC4" size="4"> >> Tree view </font>')),
radioButtons("treePlotType", "View",
choices=c("Single tree"=1,"Two tree comparison"=2),
selected=1, width="100%"),
bsTooltip("treePlotType", "Choose whether to view a single tree or two trees side by side with their differences highlighted."),
h2(HTML('<font color="#6C6CC4" size="4"> >> Tree selection </font>')),
conditionalPanel(condition = "input.treePlotType==1",
radioButtons("treeChoice", "Selection",
choices=c("Median tree"="med","General tree selection"="gen"),
selected="med", width="100%"),
bsTooltip("treeChoice", "A geometric median tree is plotted by default. If clusters have been identified, the median for each can be viewed. Alternatively, any individual tree can be plotted."),
conditionalPanel(condition = "input.treeChoice=='med'",
selectInput("selectedMedTree", "Median tree from:",
choices=c("All trees"="all"))
),
conditionalPanel(condition = "input.treeChoice=='gen'",
uiOutput("selectedGenTree")
)
), # end single tree choice
conditionalPanel(condition = "input.treePlotType==2",
radioButtons("treeChoice1", "Select first tree",
choices=c("Median tree"="med","General tree selection"="gen"),
selected="med", width="100%"),
bsTooltip("treeChoice1", "Plot a geometric median tree or any individual tree"),
conditionalPanel(condition = "input.treeChoice1=='med'",
selectInput("selectedMedTree1", "Median tree from:",
choices=c("All trees"="all"))
),
conditionalPanel(condition = "input.treeChoice1=='gen'",
uiOutput("selectedGenTree1")
),
radioButtons("treeChoice2", "Select second tree",
choices=c("Median tree"="med","General tree selection"="gen"),
selected="med", width="100%"),
bsTooltip("treeChoice2", "Plot a geometric median tree or any individual tree"),
conditionalPanel(condition = "input.treeChoice2=='med'",
selectInput("selectedMedTree2", "Median tree from:",
choices=c("All trees"="all"))
),
conditionalPanel(condition = "input.treeChoice2=='gen'",
uiOutput("selectedGenTree2")
),
checkboxInput("showTipDiffTable", label="Display table of tip differences?", value=FALSE)
), # end tree comparison choices
## TREE AESTHETICS
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Aesthetics </font>')),
## condition on tree being displayed
conditionalPanel(condition = "input.selectedTree!=''",
## use edge lengths?
checkboxInput("edgelengths", label="Use original branch lengths?", value=TRUE),
## ladderize
checkboxInput("ladderize", label="Ladderize the tree(s)?", value=TRUE),
## type of tree
radioButtons("treetype", "Type of tree",
choices=c("phylogram","cladogram", "fan", "unrooted", "radial"),
selected="phylogram", width="100%"),
conditionalPanel(condition = "input.treePlotType==1",
## tree direction
radioButtons("treedirection", "Direction of the tree",
choices=c("rightwards", "leftwards", "upwards", "downwards"),
selected="rightwards", width="100%")
),
conditionalPanel(condition = "input.treePlotType==2",
## trees facing?
radioButtons("treesFacing", "Direction of trees",
choices=c("facing"=T, "rightwards"=F),
selected=T, width="100%")
),
## tip labels
checkboxInput("showtiplabels", label="Display tip labels?", value=TRUE),
conditionalPanel(condition="input.showtiplabels",
## tip label font
selectInput("tiplabelfont", "Tip label font",
choices=c("Plain"=1,"Bold"=2,"Italic"=3,"Bold italic"=4), selected=1),
## tip label size
sliderInput("tiplabelsize", "Size of the tip labels", value=1, min=0, max=5, step=0.1),
conditionalPanel(condition="input.treePlotType==1",
## tip label colour
jscolorInput("tiplabelcolour", "Tip label colour", value="#000000", close=TRUE)
),
conditionalPanel(condition="input.treePlotType==2",
selectInput("colourMethod", "Colouring method",
choices=c("Gradual colour ramp"=1,"Palette from adegenet"=2),
selected=1),
## basic tip label colour
jscolorInput("basetiplabelcolour", "Label colour for tips with same ancestry", value="#BEBEBE", close=TRUE),
conditionalPanel(condition="input.colourMethod==1",
## basic tip label colour
jscolorInput("minortiplabelcolour", "Label colour for tips with smaller ancestral differences", value="#FFDAB9", close=TRUE),
## basic tip label colour
jscolorInput("majortiplabelcolour", "Label colour for tips with greater ancestral differences", value="#EE0000", close=TRUE)
),
conditionalPanel(condition="input.colourMethod==2",
selectInput("tipPalette", "Palette",
choices=c("funky"=1, "spectral"=2,
"seasun"=3, "lightseasun"=4, "deepseasun"=5,
"rainbow"=6, "azur"=7, "wasp"=8),
selected=2)
)
)
),
## edge width
sliderInput("edgewidth", "Width of the edges", value=2, min=1, max=20, step=0.2),
## edge colour
jscolorInput("edgecolor", "Edge colour", value="#000000", close=TRUE),
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
width=4)), # end conditional panel and sidebarPanel; width is out of 12
## MAIN PANEL
mainPanel("",
# TITLE #
h2(HTML('<font color="#6C6CC4" size="6"> Tree viewer </font>')),
br(),br(),
## conditional panel: plot single tree if needed
conditionalPanel(condition = "(input.treePlotType==1)&&(input.selectedTree!='')",
plotOutput("tree", height = "800px"),
br(), br(),
## OUTPUT (save)
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Output </font>')),
downloadButton("downloadTree", "Save tree image"),
br(), br()
), # end single tree conditional panel
## conditional panel: plot tree comparison if needed
conditionalPanel(condition = "(input.treePlotType==2)&&(input.selectedTree1!='')&&(input.selectedTree2!='')",
plotOutput("treeDiff", height = "800px"),
# conditional panel: show tip differences table:
conditionalPanel(condition = "input.showTipDiffTable",
tableOutput("tipDiffTable")
),
br(), br(),
## OUTPUT (save)
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Output </font>')),
downloadButton("downloadTreeDiff", "Save tree comparison image"),
# conditional panel: show tip differences table:
conditionalPanel(condition = "input.showTipDiffTable",
downloadButton("downloadTipDiffTable", "Save tip differences table")
),
br(), br()
), # end tree comparison conditional panel
## Repeat of treespace plot, for reference
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Copy of scatter plot </font>')),
br(), br(),
uiOutput("treespacePlotTreeTab")
) # end mainPanel
) # end page with sidebar
), # end tabPanel "Tree Viewer"
tabPanel("densiTree viewer",
tags$link(rel = 'stylesheet', type = 'text/css', href = 'styles.css'),
tags$style(type="text/css", "body {padding-top: 40px;}"),
pageWithSidebar(
## TITLE ##
headerPanel(
img(src="img/logo.png", height="160")
),
## SIDE PANEL CONTENT ##
sidebarPanel(
tags$head(tags$style(
type = 'text/css',
'form.well { max-height: 1600px; overflow-y: auto; }'
)),
## INPUT
## choice of tree type
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Input </font>')),
## add densiTree selector (gets updated to number of clusters by )
selectInput("selectedDensiTree", "Choose collection of trees to view in densiTree plot",
choices=c("Choose one"="","All trees"="all"), width="100%"),
#h2(HTML('<font color="#6C6CC4" size="2"> Note: this can be slow for large sets of trees </font>')),
bsTooltip("selectedDensiTree", "View all trees together in a densiTree plot. If clusters have been identified, the set of trees from a single cluster can be plotted. Note this function can be slow if many trees are included.", placement="bottom"),
## DENSITREE AESTHETICS
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Aesthetics </font>')),
conditionalPanel(condition = "input.selectedDensiTree!=''",
## alpha (semitransparency of edges)
sliderInput("alpha", "Transparency of edges", value=0.5, min=0, max=1, step=0.05),
checkboxInput("scaleX", label="Scale trees to equal heights?", value=FALSE),
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
width=4)), # end conditional panel and sidebarPanel; width is out of 12
## MAIN PANEL
mainPanel("",
# TITLE #
h2(HTML('<font color="#6C6CC4" size="6"> densiTree viewer </font>')),
br(),br(),
## conditional panel: plot tree if needed
conditionalPanel(condition = "input.selectedDensiTree!=''",
plotOutput("densiTree", height = "800px"),
br(), br(),
## OUTPUT (save)
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Output </font>')),
downloadButton("downloadDensiTree", "Save densiTree image"),
br(), br(), br(), br(), br(), br()
) # end densiTree conditional panel
) # end of main panel "Multi-tree viewer"
) # end of page with sidebar
),# end of tabPanel "densiTree viewer"
## HELP SECTION
tabPanel("Help",
tags$style(type="text/css", "body {padding-top: 40px;}"),
HTML(paste(readLines("www/html/help.html"), collapse=" "))
),
## SERVER INFO ##
tabPanel("System info",
tags$style(type="text/css", "body {padding-top: 40px;}"),
verbatimTextOutput("systeminfo"))
) # end of tabsetPanel
) # end of Shiny UI
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options(rgl.useNULL=TRUE)
## CHECKS ##
require("scatterD3")
require("shiny")
require("rgl")
require("RLumShiny")
require("shinyBS")
## DEFINE UI ##
shinyUI(
navbarPage("",position="fixed-top", collapsible = TRUE,
theme = "bootstrap.simplex.css",
tabPanel("Tree landscape explorer",
tags$link(rel = 'stylesheet', type = 'text/css', href = 'styles.css'),
tags$style(type="text/css", "body {padding-top: 40px;}"),
pageWithSidebar(
## TITLE ##
headerPanel(
img(src="img/logo.png", height="160")
),
## SIDE PANEL CONTENT ##
sidebarPanel(
tags$head(tags$style(
type = 'text/css',
'form.well { max-height: 1600px; overflow-y: auto; }'
)),
## SPECIFIC TO TREE LANDSCAPE EXPLORER ##
conditionalPanel(condition = "$('li.active a').first().html()== 'Tree landscape explorer'",
## INPUT
## choice of type of data source
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Input </font>')),
radioButtons("datatype", HTML('<font size="4"> Choose data source:</font>'),
list("Example: Dengue fever"="exDengue",
"Example: Woodmice"="exWoodmice",
"Input file"="file")),
## choice of dataset if source is a file
conditionalPanel(condition = "input.datatype=='file'",
fileInput("datafile", p(HTML(' <font size="4"> Choose input file:</font>'), br(),
strong("accepted formats:"), br(),
em("- multiphylo"), "saved from R (.RData/.rda/.rds)", br(),
em("- nexus"), "file (.nex/.nexus)")
),
checkboxInput("randSamp","Randomly sample from the trees?", value=TRUE),
bsTooltip("randSamp", "For large sets of trees and/or trees with many tips the app may be slow, so beginning the analysis with a small random sample is recommended.",
placement = "right", trigger = "hover", options = NULL),
conditionalPanel(
condition="input.randSamp",
sliderInput("sampleSize", "Size of random sample:", value=10, min=10, max=300, step=10)
)
),
## ANALYSIS
img(src="img/line.png", width="100%"),
h4(HTML('<font color="#6C6CC4" size="6"> > Analysis </font>')),
## choose metric
selectInput("treemethod", "Choose a tree summary:",
choices=c(
"Kendall Colijn (rooted)" = "metric",
"Billera, Holmes, Vogtmann (rooted, uses branch lengths)" = "BHV",
"Kuhner & Felsenstein branch score distance (unrooted, uses branch lengths)" = "KF",
"Robinson Foulds symmetric difference (unrooted, topological)" = "RF",
"Weighted Robinson Foulds (unrooted, uses branch lengths)" = "wRF",
"Steel & Penny tip-tip distance (unrooted, topological)" = "nNodes",
"Steel & Penny weighted tip-tip distance (unrooted, uses branch lengths)" = "patristic",
"Abouheif test (rooted, topological)" = "Abouheif",
"Sum of direct descendents (rooted, topological)" = "sumDD")),
## lambda, axes
uiOutput("lambda"),
bsTooltip("lambda","When lambda=0 trees are compared topologically; increasing lambda gives more focus to branch lengths"),
conditionalPanel(
condition="input.plotType==1",
uiOutput("naxes")
## Future: highlight median trees (if plotType==1)
#checkboxInput("showMedians", label=strong("Highlight median tree(s)?"), value=FALSE)
),
## show Shepard plot?
checkboxInput("quality", label=strong("Assess quality of projection (Shepard plot)?"), value=FALSE),
bsTooltip("quality","A Shepard plot gives an indication of the quality of the MDS projection. It will be displayed below the main plot.", placement="right"),
## show screeplot?
conditionalPanel(
condition="input.graphics==1",
checkboxInput("scree", label=strong("Show screeplot?"), value=FALSE),
bsTooltip("scree","Display screeplot of the eigenvalues associated with each componenet? It will be displayed below the main plot.", placement="right")
),
## find clusters?
checkboxInput("findClusters", label=strong("Identify clusters?"), value=FALSE),
bsTooltip("findClusters","Statistical tools for choosing an appropriate clustering method and number of clusters will be added to treespace soon.", placement="right"),
conditionalPanel(condition ="input.findClusters",
radioButtons("clusterType", label="Method:",
choices=c("statistically"="stat","by metadata"="meta"), selected="stat"),
conditionalPanel(
condition="input.clusterType=='stat'",
## clustering method
selectInput("clustmethod", "Clustering method:",
choices=c(
"Ward" = "ward.D2",
"Single" = "single",
"Complete" = "complete",
"UPGMA" = "average")),
## number of clusters
uiOutput("nclust")
),
conditionalPanel(
condition="input.clusterType=='meta'",
fileInput("metadatafile", p(HTML(' <font size="4"> Choose input file:</font>'), br(),
strong("accepted formats:"), br(),
em("- object of class factor/numeric/character/list"), "saved from R (.RData/.rda)", br(),
em("- csv file"), "(.csv) (first column will be used)")
)
)
),
## relevant if method = KC metric, allow tip emphasis
conditionalPanel(
condition="input.treemethod=='metric'",
## Emphasise tips
checkboxInput("emphTips", label=strong("Emphasise tips?"), value=FALSE),
bsTooltip("emphTips","Choose tips to emphasise or de-emphasise: the vector elements corresponding to these tips are multiplied by the weight chosen below.", placement="right"),
## if tip emphasis is chosen, provide options:
conditionalPanel(
condition="input.emphTips",
uiOutput("whichTips"),
sliderInput("emphWeight", "Weight of emphasis", value=2,min=0.1,max=100)
)
),
## AESTHETICS
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Aesthetics </font>')),
## tree landscape or compare to single reference tree
conditionalPanel(
condition="input.plot3D==2",
radioButtons("plotType", "View",
choices=c("Full tree landscape"=1,"Distances from a reference tree"=2),
selected=1),
bsTooltip("plotType", "Choose whether to view the relative distances between all trees, or a 1-dimensional plot of their distances from a fixed reference tree")
),
## Dimensions (3D possible if 3 or more axes retained, and full tree landscape)
conditionalPanel(condition="input.naxes>2",
conditionalPanel(
condition="input.plotType==1",
radioButtons("plot3D", "Plot dimensions",
choices=c("2D"=2,"3D"=3),
selected=2)
)
),
conditionalPanel(
condition="(input.plot3D==2)&&(input.plotType==1)",
radioButtons("graphics", "Display using",
choices=c("plotGrovesD3"=1,"plotGroves"=2),
selected=1),
bsTooltip("graphics", "Choose whether to view the tree landscape using plotGrovesD3 which uses scatterD3 (interactive html) or plotGroves which uses adegraphics")
),
# if plotType=1, pick the axes to view:
conditionalPanel(
condition="input.plotType==1",
## select first axis to plot
numericInput("xax", "Indicate the x axis", value=1, min=1, max=3),
## select second axis to plot
numericInput("yax", "Indicate the y axis", value=2, min=1, max=3),
bsTooltip("yax", "If multiple MDS axes have been retained, any combination of axes can be viewed"),
## if in 3D, need a z axis:
conditionalPanel(condition="input.plot3D==3",
numericInput("zax", "Indicate the z axis", value=3, min=1, max=3)
)
),
## aesthetics for tree landscape view
conditionalPanel(
condition="input.plotType==1",
conditionalPanel(
condition="(input.plot3D==2)&&(input.graphics==1)",
## Animate transitions?
checkboxInput("transitions", label="Animate transitions?", value=TRUE)
),
conditionalPanel(
condition="(input.plot3D==2)&&(input.graphics==2)",
## convex hulls or ellipses when clusters identified
conditionalPanel(
condition="input.findClusters",
radioButtons("scattertype", "Type of scatterplot",
choices=c("chull","ellipse"),
selected="chull")
),
selectInput("screemds", "Position of the MDS screeplot:",
choices=c("None" = "none",
"Bottom right" = "bottomright",
"Bottom left" = "bottomleft",
"Top right" = "topright",
"Top left" = "topleft"),
selected="bottomleft")
),
## symbol size
sliderInput("pointsize", "Size of the points", value=2, min=0, max=10, step=0.2),
conditionalPanel(
condition="(input.plot3D==2)&&(input.graphics==1)",
## symbol size
sliderInput("pointopacity", "Opacity of the points", value=0.6, min=0, max=1, step=0.05)
),
conditionalPanel(
condition="input.plot3D==2",
## display labels
checkboxInput("showlabels", label="Display tree labels?", value=FALSE),
conditionalPanel(
condition="input.showlabels",
## label size
sliderInput("labelsize", "Size of the labels", value=1, min=0, max=10, step=1),
conditionalPanel(
condition="input.graphics==2",
checkboxInput("optimlabels", label="Optimize label position?", value=FALSE)
)
)
)
),
# if plotType=2, option to stretch
conditionalPanel(
condition="input.plotType==2",
uiOutput("selectedRefTree"),
sliderInput("stretch", "Height of plot (pixels)", value=1600, min=800, max=12800, step=200)
),
## choose color palette (if clusters detected)
conditionalPanel(
## condition
condition="input.findClusters",
selectInput("palette", "Palette for the clusters",
choices=c("funky", "spectral",
"seasun", "lightseasun", "deepseasun",
"rainbow", "azur", "wasp"),
selected="funky")
),
conditionalPanel(
condition="input.plotType==1",
## choose label colors
jscolorInput("labcol", "Label / point color", value="#1B2266", close=TRUE)
),
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
width=4)), # end conditional panel and sidebarPanel; width is out of 12
## MAIN PANEL
mainPanel("",
# TITLE #
h2(HTML('<font color="#6C6CC4" size="6"> Tree landscape explorer </font>')),
br(),br(),
## function I was using for testing:
#verbatimTextOutput("plot_click"),
# Removed:
#verbatimTextOutput("caption"),
conditionalPanel(
condition="input.plot3D==2",
uiOutput("treespacePlot")
),
conditionalPanel(
condition="input.plot3D==3",
rglwidgetOutput("treespacePlot3D", width="800px")
),
conditionalPanel(
condition="(input.plotType==1)&&(input.plot3D==2)&&(input.graphics==1)",
tags$p(actionButton("scatterD3-reset-zoom", HTML("<span class='glyphicon glyphicon-search' aria-hidden='true'></span> Reset Zoom")))
),
conditionalPanel(
condition="input.quality",
uiOutput("shep")
),
conditionalPanel(
condition="(input.scree)&&(input.graphics==1)",
uiOutput("scree")
),
br(), br(),
## OUTPUT (save)
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Output </font>')),
## save MDS plot
conditionalPanel(
condition="(input.plotType==1)&&(input.plot3D==2)&&(input.graphics==1)",
tags$p(tags$a(id = "scatterD3-svg-export", href = "#",
class = "btn btn-default", HTML("<span class='glyphicon glyphicon-save' aria-hidden='true'></span> Save treespace plot as svg"))),
downloadButton("downloadMDS2Dhtml", "Save treespace plot as interactive html")
),
conditionalPanel(
condition="(input.plotType==1)&&(input.plot3D==2)&&(input.graphics==2)",
downloadButton("downloadMDS", "Save treespace image as png file")
),
conditionalPanel(
condition="input.plot3D==3",
downloadButton("downloadMDS3Dhtml", "Save treespace 3D plot as interactive html")
),
conditionalPanel(
condition="input.quality",
downloadButton("downloadShep", "Save Shepard plot as png file")
),
conditionalPanel(
condition="input.scree",
downloadButton("downloadScree", "Save screeplot as png file")
),
## save trees to nexus file
downloadButton('exporttrees', "Save trees to nexus file"),
## save results to csv
downloadButton('exportrestocsv', "Save results (MDS+clusters) to csv file"),
## save results to RData
downloadButton('exportrestordata', "Save results (MDS+clusters) to R object")
) # end mainPanel
) # end page with sidebar
), # end tabPanel
tabPanel("Tree viewer",
tags$link(rel = 'stylesheet', type = 'text/css', href = 'styles.css'),
tags$style(type="text/css", "body {padding-top: 40px;}"),
pageWithSidebar(
## TITLE ##
headerPanel(
img(src="img/logo.png", height="160")
),
## SIDE PANEL CONTENT ##
sidebarPanel(
tags$head(tags$style(
type = 'text/css',
'form.well { max-height: 1600px; overflow-y: auto; }'
)),
## INPUT
## choice of tree type
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Input </font>')),
h2(HTML('<font color="#6C6CC4" size="4"> >> Tree view </font>')),
radioButtons("treePlotType", "View",
choices=c("Single tree"=1,"Two tree comparison"=2),
selected=1, width="100%"),
bsTooltip("treePlotType", "Choose whether to view a single tree or two trees side by side with their differences highlighted."),
h2(HTML('<font color="#6C6CC4" size="4"> >> Tree selection </font>')),
conditionalPanel(condition = "input.treePlotType==1",
radioButtons("treeChoice", "Selection",
choices=c("Median tree"="med","General tree selection"="gen"),
selected="med", width="100%"),
bsTooltip("treeChoice", "A geometric median tree is plotted by default. If clusters have been identified, the median for each can be viewed. Alternatively, any individual tree can be plotted."),
conditionalPanel(condition = "input.treeChoice=='med'",
selectInput("selectedMedTree", "Median tree from:",
choices=c("All trees"="all"))
),
conditionalPanel(condition = "input.treeChoice=='gen'",
uiOutput("selectedGenTree")
)
), # end single tree choice
conditionalPanel(condition = "input.treePlotType==2",
radioButtons("treeChoice1", "Select first tree",
choices=c("Median tree"="med","General tree selection"="gen"),
selected="med", width="100%"),
bsTooltip("treeChoice1", "Plot a geometric median tree or any individual tree"),
conditionalPanel(condition = "input.treeChoice1=='med'",
selectInput("selectedMedTree1", "Median tree from:",
choices=c("All trees"="all"))
),
conditionalPanel(condition = "input.treeChoice1=='gen'",
uiOutput("selectedGenTree1")
),
radioButtons("treeChoice2", "Select second tree",
choices=c("Median tree"="med","General tree selection"="gen"),
selected="med", width="100%"),
bsTooltip("treeChoice2", "Plot a geometric median tree or any individual tree"),
conditionalPanel(condition = "input.treeChoice2=='med'",
selectInput("selectedMedTree2", "Median tree from:",
choices=c("All trees"="all"))
),
conditionalPanel(condition = "input.treeChoice2=='gen'",
uiOutput("selectedGenTree2")
),
checkboxInput("showTipDiffTable", label="Display table of tip differences?", value=FALSE)
), # end tree comparison choices
## TREE AESTHETICS
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Aesthetics </font>')),
## condition on tree being displayed
conditionalPanel(condition = "input.selectedTree!=''",
## use edge lengths?
checkboxInput("edgelengths", label="Use original branch lengths?", value=TRUE),
## ladderize
checkboxInput("ladderize", label="Ladderize the tree(s)?", value=TRUE),
## type of tree
radioButtons("treetype", "Type of tree",
choices=c("phylogram","cladogram", "fan", "unrooted", "radial"),
selected="phylogram", width="100%"),
conditionalPanel(condition = "input.treePlotType==1",
## tree direction
radioButtons("treedirection", "Direction of the tree",
choices=c("rightwards", "leftwards", "upwards", "downwards"),
selected="rightwards", width="100%")
),
conditionalPanel(condition = "input.treePlotType==2",
## trees facing?
radioButtons("treesFacing", "Direction of trees",
choices=c("facing"=T, "rightwards"=F),
selected=T, width="100%")
),
## tip labels
checkboxInput("showtiplabels", label="Display tip labels?", value=TRUE),
conditionalPanel(condition="input.showtiplabels",
## tip label font
selectInput("tiplabelfont", "Tip label font",
choices=c("Plain"=1,"Bold"=2,"Italic"=3,"Bold italic"=4), selected=1),
## tip label size
sliderInput("tiplabelsize", "Size of the tip labels", value=1, min=0, max=5, step=0.1),
conditionalPanel(condition="input.treePlotType==1",
## tip label colour
jscolorInput("tiplabelcolour", "Tip label colour", value="#000000", close=TRUE)
),
conditionalPanel(condition="input.treePlotType==2",
selectInput("colourMethod", "Colouring method",
choices=c("Gradual colour ramp"=1,"Palette from adegenet"=2),
selected=1),
## basic tip label colour
jscolorInput("basetiplabelcolour", "Label colour for tips with same ancestry", value="#BEBEBE", close=TRUE),
conditionalPanel(condition="input.colourMethod==1",
## basic tip label colour
jscolorInput("minortiplabelcolour", "Label colour for tips with smaller ancestral differences", value="#FFDAB9", close=TRUE),
## basic tip label colour
jscolorInput("majortiplabelcolour", "Label colour for tips with greater ancestral differences", value="#EE0000", close=TRUE)
),
conditionalPanel(condition="input.colourMethod==2",
selectInput("tipPalette", "Palette",
choices=c("funky"=1, "spectral"=2,
"seasun"=3, "lightseasun"=4, "deepseasun"=5,
"rainbow"=6, "azur"=7, "wasp"=8),
selected=2)
)
)
),
## edge width
sliderInput("edgewidth", "Width of the edges", value=2, min=1, max=20, step=0.2),
## edge colour
jscolorInput("edgecolor", "Edge colour", value="#000000", close=TRUE),
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
width=4)), # end conditional panel and sidebarPanel; width is out of 12
## MAIN PANEL
mainPanel("",
# TITLE #
h2(HTML('<font color="#6C6CC4" size="6"> Tree viewer </font>')),
br(),br(),
## conditional panel: plot single tree if needed
conditionalPanel(condition = "(input.treePlotType==1)&&(input.selectedTree!='')",
plotOutput("tree", height = "800px"),
br(), br(),
## OUTPUT (save)
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Output </font>')),
downloadButton("downloadTree", "Save tree image"),
br(), br()
), # end single tree conditional panel
## conditional panel: plot tree comparison if needed
conditionalPanel(condition = "(input.treePlotType==2)&&(input.selectedTree1!='')&&(input.selectedTree2!='')",
plotOutput("treeDiff", height = "800px"),
# conditional panel: show tip differences table:
conditionalPanel(condition = "input.showTipDiffTable",
tableOutput("tipDiffTable")
),
br(), br(),
## OUTPUT (save)
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Output </font>')),
downloadButton("downloadTreeDiff", "Save tree comparison image"),
# conditional panel: show tip differences table:
conditionalPanel(condition = "input.showTipDiffTable",
downloadButton("downloadTipDiffTable", "Save tip differences table")
),
br(), br()
), # end tree comparison conditional panel
## Repeat of treespace plot, for reference
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Copy of scatter plot </font>')),
br(), br(),
uiOutput("treespacePlotTreeTab")
) # end mainPanel
) # end page with sidebar
), # end tabPanel "Tree Viewer"
tabPanel("densiTree viewer",
tags$link(rel = 'stylesheet', type = 'text/css', href = 'styles.css'),
tags$style(type="text/css", "body {padding-top: 40px;}"),
pageWithSidebar(
## TITLE ##
headerPanel(
img(src="img/logo.png", height="160")
),
## SIDE PANEL CONTENT ##
sidebarPanel(
tags$head(tags$style(
type = 'text/css',
'form.well { max-height: 1600px; overflow-y: auto; }'
)),
## INPUT
## choice of tree type
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Input </font>')),
## add densiTree selector (gets updated to number of clusters by )
selectInput("selectedDensiTree", "Choose collection of trees to view in densiTree plot",
choices=c("Choose one"="","All trees"="all"), width="100%"),
#h2(HTML('<font color="#6C6CC4" size="2"> Note: this can be slow for large sets of trees </font>')),
bsTooltip("selectedDensiTree", "View all trees together in a densiTree plot. If clusters have been identified, the set of trees from a single cluster can be plotted. Note this function can be slow if many trees are included.", placement="bottom"),
## DENSITREE AESTHETICS
img(src="img/line.png", width="100%"),
h2(HTML('<font color="#6C6CC4" size="6"> > Aesthetics </font>')),
conditionalPanel(condition = "input.selectedDensiTree!=''",
## alpha (semitransparency of edges)
sliderInput("alpha", "Transparency of edges", value=0.5, min=0, max=1, step=0.05),
checkboxInput("scaleX", label="Scale trees to equal heights?", value=FALSE),
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
br(),br(),br(),br(),br(),br(),br(), # add some blank space at the end of side panel
width=4)), # end conditional panel and sidebarPanel; width is out of 12
## MAIN PANEL
mainPanel("",
# TITLE #
h2(HTML('<font color="#6C6CC4" size="6"> densiTree viewer </font>')),
br(),br(),
## conditional panel: plot tree if needed
conditionalPanel(condition = "input.selectedDensiTree!=''",
plotOutput("densiTree", height = "800px"),
br(), br(),
## OUTPUT (save)
img(src="img/line.png", width="400px"),
h2(HTML('<font color="#6C6CC4" size="6"> > Output </font>')),
downloadButton("downloadDensiTree", "Save densiTree image"),
br(), br(), br(), br(), br(), br()
) # end densiTree conditional panel
) # end of main panel "Multi-tree viewer"
) # end of page with sidebar
),# end of tabPanel "densiTree viewer"
## HELP SECTION
tabPanel("Help",
tags$style(type="text/css", "body {padding-top: 40px;}"),
HTML(paste(readLines("www/html/help.html"), collapse=" "))
),
## SERVER INFO ##
tabPanel("System info",
tags$style(type="text/css", "body {padding-top: 40px;}"),
verbatimTextOutput("systeminfo"))
) # end of tabsetPanel
) # end of Shiny UI
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