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GridCounts
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| Original file line number | Diff line number | Diff line change |
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| module GridCount | ||
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| export GridCounts, crop!, mask!, gridsize, totalrna | ||
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| using Base.Threads: @threads | ||
| using DataFrames: DataFrame, groupby, transform! | ||
| using SparseArrays: SparseMatrixCSC, dropzeros!, findnz, nonzeros, sparse | ||
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| """ | ||
| AbstractGridCounts | ||
| A stack of genes each consisting of a 2D count array of the same size. | ||
| """ | ||
| abstract type AbstractGridCounts end | ||
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| """ | ||
| GridCounts{G,T<:Number} <: AbstractGridCounts | ||
| A stack of genes`::G` each consisting of a 2D count`::T` array of the same size. | ||
| """ | ||
| mutable struct GridCounts{G,T<:Number} <: AbstractGridCounts | ||
| counts::Dict{G,SparseMatrixCSC{T}} | ||
| shape::Tuple{Int,Int} | ||
| @doc """ | ||
| GridCounts(counts::Dict) | ||
| All values of the dict must be arrays of the same size. | ||
| """ | ||
| function GridCounts{G,T}(counts::Dict{G,SparseMatrixCSC{T}}) where {G,T<:Number} | ||
| shape = size(first(values(counts))) | ||
| for (_, c) in counts | ||
| if size(c) != shape | ||
| throw(DimensionMismatch("All `counts` must have the same size")) | ||
| end | ||
| end | ||
| return new{G,T}(counts, shape) | ||
| end | ||
| end | ||
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| function GridCounts(counts::Dict{G,SparseMatrixCSC{T}}) where {G,T<:Number} | ||
| return GridCounts{G,T}(counts) | ||
| end | ||
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| """ | ||
| GridCounts(df::DataFrame) | ||
| Construct from a DataFrame with columns 'x' (`Integer`), 'y' (`Integer`), 'count', and | ||
| 'geneID' (`Pool`). | ||
| """ | ||
| function GridCounts(df::DataFrame) | ||
| transform!(df, [:x, :y] .=> (x -> x .- (minimum(x) - one(eltype(x)))) .=> [:x, :y]) | ||
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| rows = maximum(df.x) | ||
| cols = maximum(df.y) | ||
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| n = length(df.geneID.pool) | ||
| genes = Vector{eltype(df.geneID)}(undef, n) | ||
| counts = Vector{SparseMatrixCSC{eltype(df.count)}}(undef, n) | ||
| @threads for (i, (key, subdf)) in collect(enumerate(pairs(groupby(df, :geneID)))) | ||
| genes[i] = key.geneID | ||
| counts[i] = sparse(subdf.x, subdf.y, subdf.count, rows, cols) | ||
| end | ||
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| return GridCounts(Dict(zip(genes, counts))) | ||
| end | ||
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| """ | ||
| GridCounts(df::DataFrame, binsize::Integer) | ||
| Construct from a DataFrame with columns 'x' (`Real`), 'y' (`Real`), 'count', and | ||
| 'geneID' (`Pool`) binning the data by `binsize`. | ||
| """ | ||
| function GridCounts(df::DataFrame, binsize::Integer) | ||
| transform!(df, [:x, :y] .=> (x -> x .- minimum(x)) .=> [:x, :y]) | ||
| transform!(df, @. [:x, :y] => (x -> div(x, binsize) + 1) => [:x, :y]) | ||
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| return GridCounts(df) | ||
| end | ||
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| Base.iterate(iter::GridCounts) = iterate(iter.counts) | ||
| Base.iterate(iter::GridCounts, state) = iterate(iter.counts, state) | ||
| Base.length(collection::GridCounts) = length(collection.counts) | ||
| Base.eltype(type::GridCounts) = eltype(type.counts) | ||
| Base.haskey(collection::GridCounts, key) = haskey(collection.counts, key) | ||
| Base.getindex(collection::GridCounts, key) = getindex(collection.counts, key) | ||
| Base.get(collection::GridCounts, key, default) = get(collection.counts, key, default) | ||
| Base.delete!(collection::GridCounts, key) = delete!(collection.counts, key) | ||
| Base.pop!(collection::GridCounts) = pop!(collection.counts) | ||
| Base.keys(iterator::GridCounts) = keys(iterator.counts) | ||
| Base.values(iterator::GridCounts) = values(iterator.counts) | ||
| Base.pairs(collection::GridCounts) = pairs(collection.counts) | ||
| Base.keytype(type::GridCounts) = keytype(type.counts) | ||
| Base.valtype(type::GridCounts) = valtype(type.counts) | ||
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| function Base.setindex!(collection::GridCounts, value, key) | ||
| if size(value) == collection.shape | ||
| setindex!(collection.counts, value, key) | ||
| else | ||
| throw(DimensionMismatch("All `counts` must have the same size")) | ||
| end | ||
| end | ||
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| function Base.show(io::IO, x::GridCounts) | ||
| type = "GridCounts{$(keytype(x)),$(eltype(valtype(x)))}" | ||
| return print(io, type, " ", x.shape, " with ", length(x), " genes") | ||
| end | ||
| # Base.show(io::IO, m::MIME"text/plain", x::GridCounts) = print(io, x) | ||
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| """ | ||
| gridsize(counts) | ||
| The size of the grid of each layer. | ||
| """ | ||
| gridsize(counts) = counts.shape | ||
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| """ | ||
| crop!(counts, slice) | ||
| Crop each gene layer in counts by indexing with `slice`. | ||
| """ | ||
| function crop!(counts, slice) | ||
| for (g, c) in counts | ||
| counts.counts[g] = c[slice...] | ||
| end | ||
| counts.shape = size(first(values(counts))) | ||
| return nothing | ||
| end | ||
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| """ | ||
| mask!(counts, mask::AbstractMatrix{Bool}) | ||
| Remove all counts in each gene layer for which `mask` is `false`. | ||
| """ | ||
| function mask!(counts::GridCounts{<:Any,T}, mask::AbstractMatrix{Bool}) where {T<:Any} | ||
| if gridsize(counts) != size(mask) | ||
| throw(DimensionMismatch("Size of `mask` must match gridsize of `counts`")) | ||
| end | ||
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| inv_mask = .!mask | ||
| z = zero(T) | ||
| @threads for c in collect(values(counts)) | ||
| x, y, _ = findnz(c) | ||
| nonzeros(c)[inv_mask[[CartesianIndex(i) for i in zip(x, y)]]] .= z | ||
| dropzeros!(c) | ||
| end | ||
| end | ||
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| """ | ||
| totalrna(counts) | ||
| Caclulate the totalrna as sum of all genes for each pixel. | ||
| """ | ||
| function totalrna(counts) | ||
| n = length(counts) | ||
| x, y, v = Vector{Vector}(undef, n), Vector{Vector}(undef, n), Vector{Vector}(undef, n) | ||
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| @threads for (i, c) in collect(enumerate(values(counts))) | ||
| x[i], y[i], v[i] = findnz(c) | ||
| end | ||
| return sparse((reduce(vcat, i) for i in (x, y, v))..., gridsize(counts)...) | ||
| end | ||
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| end # module GridCount |
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