Support scale

src/preprocess/scale.jl

@@ -0,0 +1,78 @@
+"""
+    scale(p; kwargs...)
+    scale(X; kwargs...)
+
+Scale each gene to zero mean and unit variance.
+
+# Arguments
+
+- `p::AnnotatedProfile`: The profile object to calculate on.
+- `X::AbstractMatrix`: The count matrix to calculate on.
+
+# Common Keyword arguments
+
+- `max_value::Float64`: Clip to this value after scaling.
+
+# Example
+
+See also [`scale!`](@ref) for inplace operation.
+"""
+function scale end
+
+"""
+    scale!(p; kwargs...)
+    scale!(X; kwargs...)
+
+Scale each gene to zero mean and unit variance.
+
+# Arguments
+
+- `p::AnnotatedProfile`: The profile object to calculate on.
+- `X::AbstractMatrix`: The count matrix to calculate on.
+
+# Common Keyword arguments
+
+- `max_value::Float64`: Clip to this value after scaling.
+
+# Example
+
+See also [`scale`](@ref) for non-inplace operation.
+"""
+function scale! end
+
+
+scale(p::AnnotatedProfile; kwargs...) = scale!(copy(p); kwargs...)
+
+function scale!(p::AnnotatedProfile; max_value=nothing)
+    @info "Scaling each gene:"
+    X = p.RNA.count
+    X = mapcols!(zscore, X)
+
+    if max_value !== nothing
+        @info "Clipping at max_value $(max_value)"
+        X[X.>=max_value] .= max_value
+
+    return p
+end
+
+function scale!(X::AbstractMatrix; max_value=nothing)
+    @info "Scaling each gene:"
+    X = mapcols!(zscore, X)
+
+    if max_value !== nothing
+        @info "Clipping at max_value $(max_value)"
+        X[X.>=max_value] .= max_value
+
+    return X
+end
+
+function scale(X::AbstractMatrix; max_value=nothing)
+    @info "Scaling each gene:"
+    X = mapcols(zscore, X)
+
+    if max_value !== nothing
+        @info "Clipping at max_value $(max_value)"
+        X[X.>=max_value] .= max_value
+
+    return X
+end