lcsb-biocore / gigascatter.jl Goto Github PK

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the current type signature uses Matrix{Float64} for points and colors positional arguments which is too restrictive and does not allow for useful color formats such as ::Array{Normed{UInt8,8},2} or views into larger arrays such as ::SubArray. Would recommend using AbstractMatrix{<:Number} instead

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Using Julia 1.6.1

Precompiling project...
  ✗ GigaScatter v0.1.5
  0 dependencies successfully precompiled in 8 seconds (95 already precompiled)

ERROR: The following 1 direct dependency failed to precompile:
GigaScatter [9213d8c3-915d-41ea-a218-6d7652ffb8c6]

┌ Warning: Replacing module `ImageCore`
└ @ Base loading.jl:937
┌ Warning: Module ImageCore with build ID 61615909826018 is missing from the cache.
│ This may mean ImageCore [a09fc81d-aa75-5fe9-8630-4744c3626534] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1008
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for ImageMetadata [bc367c6b-8a6b-528e-b4bd-a4b897500b49]
│   exception = Required dependency ImageCore [a09fc81d-aa75-5fe9-8630-4744c3626534] failed to load from a cache file.
└ @ Base loading.jl:1033
WARNING: both ImageCore and ImageAxes export "ImageCore"; uses of it in module ImageMetadata must be qualified
ERROR: LoadError: LoadError: LoadError: UndefVarError: ImageCore not defined

We would like a getTile(x,y,z) type method that will eventually be called by some sort of front end such as OpenLayers that will allow us to zoom in and out of the beautiful SOM Embeddings. Making this work with the Makie plotting ecosystem with both GLMakie and WGLMakie backends would be ideal. Otherwise JSServe.jl can be used to connect to OpenLayers. Things to consider:

• Inplace Rasterisation vs Caching Do we keep all results in ram (presumably always a the size of the viewing window) or do we cache results on disk, creating a z/x/y.png folder structure?
• Triggering re-reasterisation for updating colours, marker sizes etc

I would like to more precisely control the dynamic range of the expressionPalette. For example my expressions range from -2 to 7, but the interesting region lies from -1 to 1. I want to adjust my colour range so any expression values outside of the limits [-1,1] are clipped to the boundary colours.

It is possible to to this by pre-processing the input data, which would re-calculate the inputs each time I change the colour range which doesn't seem to be necessary. It makes more sense to have to colour representation change, not the underlying data.

As you can imagine, this will eventually be used in an interactive figure :)