Update to ChemistryQuantitativeAnalysis v0.3.0

Project.toml

@@ -30,6 +30,7 @@ UnitfulMoles = "999f2bd7-36bf-5ba7-9bc1-c9473aa75374"
 AnovaGLM = "0.2"
 CSV = "0.10"
 Clustering = "0.15"
+ChemistryQuantitativeAnalysis = "0.3"
 DataPipes = "0.3"
 Dictionaries = "0.3"
 MLStyle = "0.4"

src/SphingolipidsID.jl

@@ -51,7 +51,7 @@ export SPDB, LIBRARY_POS, FRAGMENT_POS, ADDUCTCODE, CLASSDB,
  nfrags, @cpdsc, @score, calc_score, apply_score!, calc_threshold, apply_threshold!, w_rank, w_nfrags, w_rank_log, w_rank_exp, 
  normalized_sig_diff, abs_sig_diff,
  # Transition
- analyte_map_mrm, transitiontable, concurrent_transition, write_transition, 
+ analytetable_mrm, transitiontable, concurrent_transition, write_transition, 
  read_transition, union_transition!, union_transition, diff_transition!, diff_transition,
  # Quantification
  quantification_mrm, set_quantification_mrm!, set_qcdata_mrm!, qcdata_mrm, qcdata_mrm!, 
@@ -221,11 +221,11 @@ struct AnalyteID <: AbstractAnalyteID
  rt::Float64
 end
 """
- TransitionID <: AbstractAnalyteID
+ TransitionID
 
 A type represents a transition of an analyte and whether it is a quantifier. 
 """
-struct TransitionID <: AbstractAnalyteID
+struct TransitionID
  compound::SPID
  quantifier::Bool
 end
@@ -290,7 +290,9 @@ Multiple reaction monitoring data.
  * `area`: peak area.
  * `FWHM`: Full width at half maximum.
  * `symmetry`: peak symmetry.
- * `error`: signal error.
+ * `error`: signal error, optinal.
+ * `raw_id`: `id` of original table, optional.
+ * `match_id`: `id` of matched transition from `project.quantification`.
 * `mz2`: `Vector{Float64}`, m/z of fragments.
 * `polarity`: `Bool`; `true` for positive ion mode; `false` for negative ion mode.
 * `config`: `Dictionary` containing config information.
@@ -304,18 +306,24 @@ Multiple reaction monitoring data.
  * `:other_fn`: `Dictionary`. Stores functions for calculating other signal information.
 """
 struct MRM <: AbstractRawData
- table::Table # id, mz1, mz2_id, height, area, collision_energy, FWHM, symmetry, error
+ table::Table
  mz2::Vector{Float64}
  polarity::Bool
  config::Dictionary
 end
 
 """
  QuantData{T} <: AbstractQuantData{T}
+
+Type containing raw data and tables related to quantification. 
+
+* `raw`: raw data.
+* `table`: `AnalysisTable`, data for quantification (`table.area` or `table.height`), and quantification result (`table.estimated_concentration`).
+* `config`: `Dictionary` containing config information.
 """
 struct QuantData{T} <: AbstractQuantData{T}
  raw::T
- table::AnalysisTable # id, analyte, FWHM, symmetry, estimate, error, raw_id
+ table::AnalysisTable
  config::Dictionary
 end
 
@@ -330,6 +338,12 @@ propertynames(dt::QuantData) = Tuple(unique((:raw, :table, :config, propertyname
 
 """
  QCData{T} <: AbstractQuantData{T}
+
+Type for QC samples containing raw data and tables related to quantification. 
+
+* `raw`: raw data.
+* `table`: `AnalysisTable`, data for quantification (`table.area` or `table.height`), and quantification result (`table.estimated_concentration`).
+* `config`: `Dictionary` containing config information.
 """
 struct QCData{T} <: AbstractQuantData{T}
  raw::T
@@ -348,10 +362,16 @@ propertynames(qc::QCData) = Tuple(unique((:raw, :table, :config, propertynames(g
 #QCData(raw::T, table::Table, config::Dictionary) where {T <: Data} = QCData{T}(raw, table, config)
 """
  SerialDilution{T} <: AbstractQuantData{T}
+
+Type for serial dilution samples containing raw data and calibration data. 
+
+* `raw`: raw data.
+* `batch`: `Batch` containg analyte settings and calibration curves.
+* `config`: `Dictionary` containing config information.
 """
 struct SerialDilution{T} <: AbstractQuantData{T}
- raw::T # id, mz1, mz2, height, area, collision_energy, FWHM, symmetry, level
- batch::Batch # id, analyte, raw_id, r2, model, data_id
+ raw::T
+ batch::Batch
  config::Dictionary
 end
 
@@ -367,6 +387,11 @@ propertynames(sd::SerialDilution) = Tuple(unique((:raw, :batch, :config, propert
 
 """
  Quantification
+
+Type containg information of analyte settings, calibration data, qc data, serial dilution data, and sample data.
+
+* `batch`: `Batch` containg analyte settings, calibration data, and sample data.
+* `config`: `Dictionary` containing config information. `config[:qcdata]` stores a `QCData`, `config[:serialdilution]` stores a `SerialDilution`, and `config[:quantdata]` stores a `QuantData` (sample data).
 """
 struct Quantification
  batch::Batch
@@ -386,6 +411,14 @@ propertynames(quant::Quantification) = (:batch, :config, propertynames(getfield(
 
 """
  RTCorrection
+
+Type holding rt data and regression line for correcting rt from old batch (data for identification) to new batch (data for quantification).
+
+* `data`: raw data from new batch.
+* `table`: old transition table generated from `project.analye` and function `analytetable_mrm`.
+* `fn`: `Dictionary` containg regression coefficents for each class.
+
+This is a callable object taking a class and rt or vector of class and a vector of rt as input, and returning new rt or a vector of new rt. If the class is not in `fn`, it will return the original rt. 
 """
 struct RTCorrection
  data::AbstractRawData
@@ -420,22 +453,33 @@ mutable struct Project <: AbstractProject
  analyte::Vector{AnalyteSP}
  data::Vector{AbstractData}
  quantification::Quantification
- #anion::Symbol
- #cluster::Dictionary
- #alignment::Int
  appendix::Dictionary
 end
 """
  Project(; kwargs...)
 
-Create an empty `Project`. All keyword arguments will be put into `project.appendix`. By default, `project.appendix[:anion]` will be `:acetate`; `project.appendix[:signal]` will be `:area`
+Create an empty `Project`. All keyword arguments will be put into `project.appendix`. By default, `project.appendix[:anion]` will be `:acetate`; `project.appendix[:signal]` will be `:area`.
 """
 function Project(; kwargs...)
  appendix = Dictionary{Symbol, Any}(kwargs)
  get!(appendix, :anion, :acetate)
  get!(appendix, :signal, :area)
  Project(AnalyteSP[], AbstractData[], Quantification(), appendix)
 end
+"""
+ Project(qt::Quantification; kwargs...)
+
+Create a `Project` from `Quantification`. All keyword arguments will be put into `project.appendix`. By default, `project.appendix[:anion]` will be `:acetate`; `project.appendix[:signal]` will be `:area`.
+"""
+function Project(qt::Quantification; kwargs...)
+ appendix = Dictionary{Symbol, Any}(kwargs)
+ get!(appendix, :anion, get(qt.appendix, :anion, :acetate))
+ get!(appendix, :signal, get(qt.appendix, :signal, :area))
+ analyte = isa(qt.analyte, Vector{AnalyteSP}) ? qt.analyte : map(qt.analyte, qt.batch.analytetable.rt) do ana, rt
+ isa(ana, AnalyteSP) ? ana : AnalyteSP([CompoundSP(class(ana), chain(ana))], rt)
+ end
+ Project(analyte, AbstractData[], qt, appendix)
+end
 """
  AbstractQuery
 

src/interface.jl

@@ -242,9 +242,20 @@ end
 
 getproperty(reusable::ReusableQuery, sym::Symbol) = sym ≡ :query ? getfield(reusable, :query) : getfield(getfield(reusable, :query), sym)
 
+convert(::Type{CompoundSP}, cpd::CompoundSP) = cpd
+convert(::Type{CompoundSPVanilla}, cpd::CompoundSPVanilla) = cpd
+convert(::Type{SPID}, cpd::SPID) = cpd
 convert(::Type{CompoundSPVanilla}, cpd::CompoundSP) = CompoundSPVanilla(cpd.class, cpd.chain, cpd.fragment)
 convert(::Type{CompoundSP}, cpd::CompoundSPVanilla) = CompoundSP(cpd.class, cpd.chain, cpd.fragment)
-convert(::Type{SPID}, cpd::SPID) = cpd
+convert(::Type{SPID}, cpd::CompoundSP) = SPID(cpd.calss, cpd.chain)
+convert(::Type{CompoundSP}, cpd::SPID) = CompoundSP(cpd.calss, cpd.chain)
+convert(::Type{SPID}, cpd::CompoundSPVanilla) = SPID(cpd.calss, cpd.chain)
+convert(::Type{CompoundSPVanilla}, cpd::SPID) = CompoundSPVanilla(cpd.calss, cpd.chain)
+convert(::Type{AnalyteSP}, analyte::AnalyteSP) = analyte
+convert(::Type{AnalyteID}, analyte::AnalyteID) = analyte
+convert(::Type{TransitionID}, analyte::TransitionID) = analyte
+convert(::Type{AnalyteSP}, analyte::AnalyteID) = AnalyteSP(analyte.compound, analyte.rt)
+convert(::Type{AnalyteID}, analyte::AnalyteSP) = AnalyteID(analyte.compound, analyte.rt)
 
 # variant of interface
 # iscomponent: whether ion is a component of cpd