dynamic colorbar limits

Project.toml

@@ -1,7 +1,7 @@
 name = "FlowAtlas"
 uuid = "ef7debb3-0d09-4604-8960-6109d4c5b3e0"
 authors = ["gszep <[email protected]>"]
-version = "0.1.6"
+version = "0.1.7"
 
 [deps]
 CSVFiles = "5d742f6a-9f54-50ce-8119-2520741973ca"

src/FlowAtlas.jl

@@ -53,10 +53,12 @@ const extensions = JSServe.Dependency( :extensions, map(  extension -> joinpath(
 
 function run( path::String; files::String=joinpath(dirname(path),"*.fcs"), transform::Function=x->asinh(x/250),
         port::Int = 3141, url::String = "http://localhost:$port", cols::Symbol=:union, drop::Union{Vector{String},Nothing}=String[],
-        nlevels::Int=10, channelRange = range(-3,7,length=50), channelScheme=reverse(ColorSchemes.matter), labelScheme=ColorSchemes.seaborn_colorblind,
+        nlevels::Int=10, nbins::Int=50, p::Real=0.1, channelScheme=reverse(ColorSchemes.matter), labelScheme=ColorSchemes.seaborn_colorblind,
         perplexity::Number=300, maxIter::Integer=10000, hold::Bool=true )
 
-    indexTransform(x::AbstractVector{<:Union{Number,Missing}}) = toIndex(x, channelRange; nlevels=nlevels)
+    indexTransform(x::AbstractVector{<:Union{Number,Missing}}) = toIndex(x; nlevels=nlevels)
+    channelRange(x::AbstractVector{<:Union{Number,Missing}}) = range(quantile(skipmissing(x),(p,1-p))...,length=nlevels)
+
 
     @info "Loading FCS files..."
     data, labels, groups, gating = FlowWorkspace.load( path; files=files, transform=transform, cols=cols)
@@ -88,14 +90,16 @@ function run( path::String; files::String=joinpath(dirname(path),"*.fcs"), trans
 
         ),
         channels = (
-            levels = range(extrema(channelRange)...,length=nlevels),
+            range =  Dict([ col => channelRange(data[!,col]) for col ∈ Base.names(data) ]),
             rows = combine(data, [ col => indexTransform => col for col ∈ Base.names(data) ]),
             colors = channelview([map(x->RGBA(get(channelScheme, x)),range(0,1,length=nlevels)); RGBA(0,0,0,0)]),
             hex = map(x->'#'*hex(x),colorview(RGB,view(channelview(map(x->RGBA(get(channelScheme, x)),range(0,1,length=nlevels))),1:3,:)))
 
         )
     )
 
+    channelMin = minimum(map(col->minimum(skipmissing(data[!,col])),Base.names(data)))
+    channelMax = maximum(map(col->maximum(skipmissing(data[!,col])),Base.names(data)))
     for (name,color) ∈ colors.labels.names colors!( Dict(["name"=>name,"color"=>color]),labels,groups,colors) end
 
     ##################################################### initalise filter settings
@@ -127,7 +131,7 @@ function run( path::String; files::String=joinpath(dirname(path),"*.fcs"), trans
                 r"/\d+/\d+/\d+.png" => x->tile(x,embedding,selections,colors,names),
                 r"/colors" => x->colors!(x,labels,groups,colors), r"/selection" => x->selection!(x,selections,names),
 
-                r"/gate" => x->gate(x,data,embedding,selections;channelRange=channelRange),
+                r"/gate" => x->gate(x,data,embedding,selections;channelRange=range(channelMin,channelMax,length=nbins)),
                 r"/count" => x->count(x,selections),
 
                 r"/favicon.ico" => context -> HTTP.Response(500),

src/assets/style.css

@@ -117,7 +117,6 @@ top: 10;
 
 svg.colorbar {
   position: absolute;
-  visibility: hidden;
   z-index: 1;
   transform: translate(-50%,-50%);
   top: 50%;

src/lib/colors.jl

@@ -19,9 +19,9 @@ function colors!(label::Dict,labels::DataFrame,groups::DataFrame,colors::NamedTu
 	return colors
 end
 
-function toIndex(x::AbstractVector{<:Union{Number,Missing}},channelRange::AbstractVector{<:Number};nlevels::Int=10)
+function toIndex(x::AbstractVector{<:Union{Number,Missing}};nlevels::Int=10,p::Real=0.1)
 
-	min,max = extrema(channelRange)
+	min,max = quantile(skipmissing(x),(p,1-p))
 	scaled = ( x .- min ) / ( max - min )
 
 	@. scaled[(scaled<0)&(~ismissing(scaled))] = 0

src/lib/map.jl

@@ -4,9 +4,6 @@ function olMap(extrema::Array{<:Tuple}, colors::NamedTuple; port::Int = 3141)
     return js"""
         function (container){
 
-            var colorScale = $d3.scaleLinear().domain($(colors.channels.levels)).range($(colors.channels.hex))
-            $d3.select("#map").call( colorbar( colorScale, height=300, width=20, origin={x:40,y:10} ))
-
             ////////////////////////////////////////////////// tile layer
             var projection = new $ol.proj.Projection({
                 code: 'raster',

src/lib/sidebar.jl

@@ -198,7 +198,16 @@ function sidebar(session::Session, names::NamedTuple, colors::NamedTuple; port::
 
                     "Colour by",
                     DOM.select( DOM.option.(["Labels";names.channels]), id="channel", onchange = js"""
-                        document.querySelector('svg.colorbar').style.visibility = document.getElementById('channel').value == 'Labels' ? 'hidden' : 'visible'
+                        var channel = document.getElementById('channel').value
+                        var channelRange = $(colors.channels.range)
+
+                        document.querySelector('svg.colorbar') ? document.querySelector('svg.colorbar').remove() : null
+                        if (channel != 'Labels'){
+
+                            var colorScale = $d3.scaleLinear().domain(channelRange[channel]).range($(colors.channels.hex))
+                            $d3.select("#map").call( colorbar( colorScale, height=300, width=20, origin={x:40,y:10} ))
+                        }
+
                         document.getElementById("map").tiles.refresh()
                     """)
                 ),