ui.R

library(shiny)
library(rgl)

templateList <- list("Choose a brain" = "Choose a brain", "T1 (Yu et al. 2010, Dickson, IMP)" = "T1", "IS2 (Cachero & Ostrovsky et al. 2010, Jefferis, MRC LMB)" = "IS2", "IBNWB (Ito et al. 2014, Insect Brain Name Working Group)" = "IBNWB", "FCWB (Costa et al. 2016, Jefferis, MRC LMB)" = "FCWB", "JFRC2 (HHMI/VFB)" = "JFRC2")

shinyUI(navbarPage("Bridging on-the-fly",

tabPanel("Tracing",
sidebarLayout(
	sidebarPanel(
		h2("Instructions"),
		HTML("Select your source and target template brains and upload a tracing below. A zip archive of multiple neurons can also be uploaded. The original neuron(s) will be displayed in 3D below, with the bridged neurons to the right."),
		br(),
		br(),
		selectInput("from", "From:", templateList, selected="Choose a brain"),
		selectInput("to", "To:", templateList, selected="Choose a brain"),
		checkboxInput("mirror", "Mirror?", value=FALSE),
		fileInput('file1', 'Neuron/surface file:'),
		submitButton("Bridge"),
		HTML('<script type="text/javascript">document.getElementById("bridge_button").onclick = function() { document.getElementById("bridge_button").click(); document.getElementById("bridge_submit").click(); }</script>'),

		h2("Original neuron(s)"),
		rglwidgetOutput("originalPlot", width="400px", height="400px")
	),

	mainPanel(
		h2("Transformed neuron(s)"),
		rglwidgetOutput("transformedPlot", width="800px", height="800px")
	)
)),


tabPanel("Points",
sidebarLayout(
	sidebarPanel(
		h2("Instructions"),
		HTML("Select your source and target template brains and enter 3D coordinates below. The original points will be displayed in 3D below, with the bridged points to the right."),
		br(),
		br(),
		selectInput("fromPts", "From:", templateList, selected="Choose a brain"),
		selectInput("toPts", "To:", templateList, selected="Choose a brain"),
		h2("Original points"),
		HTML('<textarea id="input_points" rows="8" cols=40>100 200 50
400 100 10</textarea>'),
		checkboxInput("mirror_points", "Mirror?", value=FALSE),
		submitButton("Bridge"),
		br(),
		h3("In 3D"),
		rglwidgetOutput("originalPtsPlot", width="400px", height="400px")
	),

	mainPanel(
		h2("Transformed points"),
		h3("In 3D"),
		rglwidgetOutput("transformedPtsPlot", width="800px", height="800px"),
		tableOutput("transformedPts")
	)
)),


tabPanel("About",
	HTML("This web app accompanies <a href='https://doi.org/10.7554/eLife.53350'>Bates & Manton et al. (2020) The natverse, a versatile toolbox for combining and analysing neuroanatomical data</a> and acts as a demonstration of the bridging/mirroring approach for <i>Drosophila</i> brains (as implemented in the R package <a href='https://github.com/natverse/nat.flybrains'>nat.flybrains</a>), along with some features of the <a href='https://github.com/natverse/nat'>NeuroAnatomy Toolbox</a>. For more information, see <a href='http://flybrain.mrc-lmb.cam.ac.uk/si/bridging/www/about/'>here</a>."),
  h2("Source code"),
  HTML("The full code for this web app can be downloaded from <a href='https://github.com/jefferislab/bridging_on-the-fly'>GitHub</a>.")
)

))