flex-station-data 0.2.0 → 0.3.0

checksums.yaml

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data/CHANGELOG.md

@@ -0,0 +1,19 @@
+# 0.3.0
+
+* The linear regression analysis report now produces a summary report of the
+  regression for each sample. The sample data can by added by sSpecifying the
+  `--verbose` option.
+
+# 0.2.0
+
+* Adds quality control checks. Samples with values that are saturated,
+  missing, or below a user-specified threshold are suppressed in the output.
+
+# 0.1.1
+
+* Bump the minimum required Ruby version to 2.4.4. On of our gem dependencies
+  relies on this version.
+
+# 0.1.0
+
+* Initial version

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    flex-station-data (0.2.0)
+    flex-station-data (0.3.0)
       activesupport
       linefit
 

data/README.md

@@ -1,8 +1,8 @@
 # FlexStationData
 
-Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/flex_station_data`. To experiment with that code, run `bin/console` for an interactive prompt.
+Tools for reading and analyzing data from the FlexStation microplate reader.
 
-TODO: Delete this and the text above, and describe your gem
+Currently this is somewhere between alpha and beta.
 
 ## Installation
 
@@ -20,15 +20,50 @@ Or install it yourself as:
 
     $ gem install flex-station-data
 
+## Updating
+
+To update your installation, use:
+
+    $ gem update flex-station-data
+
 ## Usage
 
-TODO: Write usage instructions here
+### Viewing the sample data
+
+To view the sample results from a set of plate readings, use the following
+command:
+
+    $ flex-station sample-data <source file> [--threshold=<threshold>]
+
+Where `source file` is the file that you got from the reader. You can specify
+multiple source files. The `threshold` setting is optional. If provided,
+samples with values that are below the `threshold` value will be skipped.
+`threshold` must be a number.
+
+The output is in CSV format. You'll probably want to save it to a file. You
+can do that by piping the output to a file:
+
+    $ flex-station sample-data source-data.csv --threshold=300 > sample-data.csv
+
+### Performing linear regression analysis on the sample data
+
+To perform a linear regression analysis on the sample data, use the following
+command:
+
+    $ flex-station-data liinear-regression <source file> [--threshold=<threshold>] [--verbose] [--min-r-squared=<mininmum R²>]
+
+Note that the `source file` and `threshold` options are the same as for the
+`sample-data` command above. If a `--min-r-squared` value is given, samples
+with a R² value that falls below the threshold will be flagged as "poor fits."
+If no `--min-r-squared` is specified, a default of 0.75 will be used.
 
-## Development
+By default the linear regression tool will produce a summary report giving the
+slope, intercept, and R² values for each sample. However if `--verbose` is
+specified, it will also include the sample data and regressions for each well.
 
-After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+As with the sample data tool, you will probably want to pipe the output to a file:
 
-To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+    $ flex-station linear-regression source-data.csv --threshold=300 > linear-regression.csv
 
 ## Contributing
 

data/bin/flex-station-linear-regression

@@ -1,11 +1,11 @@
 #!/usr/bin/env ruby
 
-#!/usr/bin/env ruby
-
 require "flex_station_data/services/load_plates"
 require "flex_station_data/presenters/plates_csv"
-require "flex_station_data/presenters/plate_csv"
-require "flex_station_data/presenters/sample_linear_regression_csv"
+require "flex_station_data/presenters/linear_regression/plates_hash"
+require "flex_station_data/presenters/linear_regression/verbose_sample_csv"
+
+require "pry"
 
 module FlexStationData
   class LinearRegressionApp
@@ -22,22 +22,23 @@ module FlexStationData
       end
     end
 
-    def threshold
-      name, value = options.reverse.detect { |name, value| name == "threshold" }
-      return nil if name.blank?
+    def option(option_name)
+      name, value = options.reverse.detect { |name, _| name == option_name.to_s }
+      return if name.blank?
 
-      Float(value)
+      value.nil? || value
     end
 
-    def value_quality_control
-      @value_quality_control ||= begin
-        value_threshold = threshold
-        ->(value) { ValueQuality.call(value, threshold: value_threshold) }
-      end
+    def threshold
+      Float(option(:threshold)) rescue nil
     end
 
-    def sample_quality_control
-      ->(sample) { SampleQuality.call(sample, value_quality_control: value_quality_control) }
+    def verbose?
+      option(:verbose)
+    end
+
+    def min_r_squared
+      Float(option("min-r-squared")) rescue 0.75
     end
 
     def files
@@ -50,16 +51,57 @@ module FlexStationData
       end
     end
 
-    def csv
+    def verbose_csv
+      plates.flat_map do |file, file_plates|
+        Presenters::PlatesCsv.present(
+          file,
+          file_plates,
+          sample_presenter: Presenters::LinearRegression::VerboseSampleCsv,
+          threshold:        threshold,
+          min_r_squared:    min_r_squared
+        )
+      end
+    end
+
+    def summary_hashes
       plates.flat_map do |file, file_plates|
-        Presenters::PlatesCsv.present(file, file_plates) do |plate|
-          Presenters::PlateCsv.present(plate) do |times, sample|
-            Presenters::SampleLinearRegressionCsv.present(times, sample, quality_control: sample_quality_control)
+        Presenters::LinearRegression::PlatesHash.present(
+          file,
+          file_plates,
+          threshold:     threshold,
+          min_r_squared: min_r_squared
+        )
+      end
+    end
+
+    def clean_values(values)
+      values.each_with_object([]) do |value, memo|
+        memo << ((value != memo.compact.last) ? value : nil)
+      end
+    end
+
+    def summary_hash
+      @summary_hash ||= begin
+        result = summary_hashes.each_with_object({}) do |hash, memo|
+          hash.each do |header, value|
+            memo[header] ||= []
+            memo[header] << value
           end
         end
+        result["file"] = clean_values(result["file"])
+        result["plate"] = clean_values(result["plate"])
+        result
       end
     end
 
+    def summary_csv
+      [ summary_hash.keys, *summary_hash.values.transpose ]
+    end
+
+    def csv
+      verbose? ? verbose_csv : summary_csv
+    end
+
     def call
       CSV do |out|
         csv.each do |row|

data/bin/flex-station-sample-data

@@ -25,17 +25,6 @@ module FlexStationData
       Float(value)
     end
 
-    def value_quality_control
-      @value_quality_control ||= begin
-        value_threshold = threshold
-        ->(value) { ValueQuality.call(value, threshold: value_threshold) }
-      end
-    end
-
-    def sample_quality_control
-      ->(sample) { SampleQuality.call(sample, value_quality_control: value_quality_control) }
-    end
-
     def files
       @files ||= args.map { |arg| Pathname(arg) }
     end
@@ -48,11 +37,7 @@ module FlexStationData
 
     def csv
       plates.flat_map do |file, file_plates|
-        Presenters::PlatesCsv.present(file, file_plates) do |plate|
-          Presenters::PlateCsv.present(plate) do |times, sample|
-            Presenters::SampleCsv.present(times, sample, quality_control: sample_quality_control)
-          end
-        end
+        Presenters::PlatesCsv.present(file, file_plates, threshold: threshold)
       end
     end
 

data/lib/flex_station_data/linear_regression.rb

@@ -3,11 +3,12 @@ require "linefit"
 
 module FlexStationData
   class LinearRegression
-    attr_reader :x, :y
+    attr_reader :x, :y, :min_r_squared
 
-    def initialize(x, y)
+    def initialize(x, y, min_r_squared: 0.0, **)
       @x = x
       @y = y
+      @min_r_squared = min_r_squared.to_f
     end
 
     def slope
@@ -24,6 +25,10 @@ module FlexStationData
       nil
     end
 
+    def quality
+      "poor fit" if r_squared.present? && r_squared < min_r_squared
+    end
+
     private
 
     def coefficients

data/lib/flex_station_data/presenters/linear_regression/plate_hash.rb

@@ -0,0 +1,27 @@
+require "flex_station_data/presenters/linear_regression/sample_hash"
+
+module FlexStationData
+  module Presenters
+    module LinearRegression
+      class PlateHash
+        include Concerns::Presenter
+
+        attr_reader :plate, :sample_presenter, :options
+
+        delegate :times, :samples, to: :plate
+
+        def initialize(plate, sample_presenter: SampleHash, **options)
+          @plate = plate
+          @sample_presenter = sample_presenter
+          @options = options
+        end
+
+        def present
+          samples.map do |sample|
+            { "plate" => plate.label }.merge(sample_presenter.present(times, sample, **options))
+          end
+        end
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/linear_regression/plates_hash.rb

@@ -0,0 +1,28 @@
+require "flex_station_data/presenters/linear_regression/plate_hash"
+
+module FlexStationData
+  module Presenters
+    module LinearRegression
+      class PlatesHash
+        include Concerns::Presenter
+
+        attr_reader :file, :plates, :plate_presenter, :options
+
+        def initialize(file, plates, plate_presenter: PlateHash, **options)
+          @file = file
+          @plates = plates
+          @plate_presenter = plate_presenter
+          @options = options
+        end
+
+        def present
+          plates.flat_map do |plate|
+            plate_presenter.present(plate, **options).map do |plate_hash|
+              { "file" => file.basename.to_s }.merge(plate_hash)
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/linear_regression/sample_hash.rb

@@ -0,0 +1,47 @@
+require "flex_station_data/presenters/sample_csv"
+require "flex_station_data/presenters/linear_regression/sample_regression_hash"
+
+module FlexStationData
+  module Presenters
+    module LinearRegression
+      class SampleHash
+        include Concerns::Presenter
+
+        attr_reader :times, :sample, :quality_control, :options
+
+        def initialize(times, sample, quality_control: SampleQuality, **options)
+          @times = times
+          @sample = sample
+          @quality_control = quality_control
+          @options = options
+        end
+
+        def errors
+          @errors ||= quality_control.call(sample, **options).reject(&:good?)
+        end
+
+        def errors?
+          errors.present?
+        end
+
+        def errors_hash
+          { "error" => errors.first&.to_s }
+        end
+
+        def wells_hash
+          { "wells" => sample.readings.map(&:label).join(", ") }
+        end
+
+        def regression_hash
+          return SampleRegressionHash.headers.zip([]).to_h if errors?
+
+          SampleRegressionHash.present(times, sample.mean.values, **options).transform_values(&:first)
+        end
+
+        def present
+          { "sample" => sample.label }.merge(wells_hash).merge(errors_hash).merge(regression_hash)
+        end
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/linear_regression/sample_regression_hash.rb

@@ -0,0 +1,43 @@
+require "flex_station_data/linear_regression"
+
+module FlexStationData
+  module Presenters
+    module LinearRegression
+      class SampleRegressionHash
+        include Concerns::Presenter
+
+        PRODUCTS = {
+          slope:     "slope",
+          intercept: "intercept",
+          r_squared: "R²",
+          quality:   "quality"
+        }.freeze
+
+        attr_reader :times, :sample_values, :min_r_squared, :options
+
+        def initialize(times, *sample_values, min_r_squared: nil, **options)
+          @times = times
+          @sample_values = sample_values
+          @min_r_squared = min_r_squared
+          @options = options
+        end
+
+        def sample_regressions
+          @sample_regressions ||= sample_values.map do |values|
+            FlexStationData::LinearRegression.new(times, values, min_r_squared: min_r_squared)
+          end
+        end
+
+        def present
+          PRODUCTS.each_with_object({}) do |(method, label), memo|
+            memo[label] = sample_regressions.map(&method)
+          end
+        end
+
+        def self.headers
+          PRODUCTS.values
+        end
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/linear_regression/verbose_sample_csv.rb

@@ -0,0 +1,28 @@
+require "flex_station_data/presenters/sample_csv"
+require "flex_station_data/presenters/linear_regression/sample_regression_hash"
+
+module FlexStationData
+  module Presenters
+    module LinearRegression
+      class VerboseSampleCsv < Presenters::SampleCsv
+        include Concerns::Presenter
+
+        def sample_values
+          [ *sample.readings, sample.mean ].map(&:values)
+        end
+
+        def regressions_hash
+          SampleRegressionHash.present(times, *sample_values, **options)
+        end
+
+        def regressions_csv
+          regressions_hash.to_a.map(&:flatten)
+        end
+
+        def values_csv
+          super + regressions_csv
+        end
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/plate_csv.rb

@@ -5,18 +5,24 @@ module FlexStationData
     class PlateCsv
       include Concerns::Presenter
 
-      attr_reader :plate
+      attr_reader :plate, :sample_presenter, :options
 
       delegate :times, :samples, to: :plate
 
-      def initialize(plate)
+      def initialize(plate, sample_presenter: SampleCsv, **options)
         @plate = plate
+        @sample_presenter = sample_presenter
+        @options = options
       end
 
-      def present(&sample_presenter)
-        sample_presenter ||= SampleCsv
-        sample_presenter = sample_presenter.curry(2)[times]
-        [ ["Plate #{plate.label}"], *samples.flat_map(&sample_presenter) ]
+      def samples_csv
+        samples.flat_map do |sample|
+          sample_presenter.present(times, sample, **options)
+        end
+      end
+
+      def present
+        [ ["Plate #{plate.label}"], *samples_csv ]
       end
     end
   end

data/lib/flex_station_data/presenters/plates_csv.rb

@@ -5,16 +5,23 @@ module FlexStationData
     class PlatesCsv
       include Concerns::Presenter
 
-      attr_reader :file, :plates
+      attr_reader :file, :plates, :plate_presenter, :options
 
-      def initialize(file, plates)
+      def initialize(file, plates, plate_presenter: PlateCsv, **options)
         @file = file
         @plates = plates
+        @plate_presenter = plate_presenter
+        @options = options
       end
 
-      def present(&plate_presenter)
-        plate_presenter ||= PlateCsv
-        [ ["File: #{file.to_path}"], *plates.flat_map(&plate_presenter) ]
+      def plates_csv
+        plates.flat_map do |plate|
+          plate_presenter.present(plate, **options)
+        end
+      end
+
+      def present
+        [ ["File: #{file.to_path}"], *plates_csv ]
       end
     end
   end

data/lib/flex_station_data/presenters/sample_csv.rb

@@ -7,12 +7,13 @@ module FlexStationData
     class SampleCsv
       include Concerns::Presenter
 
-      attr_reader :times, :sample, :quality_control
+      attr_reader :times, :sample, :quality_control, :options
 
-      def initialize(times, sample, quality_control: SampleQuality)
+      def initialize(times, sample, quality_control: SampleQuality, **options)
         @times = times
         @sample = sample
         @quality_control = quality_control
+        @options = options
       end
 
       def readings
@@ -32,7 +33,7 @@ module FlexStationData
       end
 
       def errors
-        @errors ||= quality_control.call(sample).reject(&:good?)
+        @errors ||= quality_control.call(sample, **options).reject(&:good?)
       end
 
       def errors?

data/lib/flex_station_data/services/sample_quality.rb

@@ -4,15 +4,20 @@ module FlexStationData
   class SampleQuality
     include Concerns::Service
 
-    attr_reader :sample, :value_quality_control
+    attr_reader :sample, :value_quality_control, :options
 
-    def initialize(sample, value_quality_control: ValueQuality)
+    def initialize(sample, value_quality_control: ValueQuality, **options)
       @sample = sample
       @value_quality_control = value_quality_control
+      @options = options
+    end
+
+    def value_quality(value)
+      value_quality_control.call(value, **options)
     end
 
     def call
-      sample.readings.flat_map(&:values).map(&value_quality_control).uniq(&:to_s)
+      sample.readings.flat_map(&:values).map(&method(:value_quality)).uniq(&:to_s)
     end
   end
 end

data/lib/flex_station_data/services/value_quality.rb

@@ -35,7 +35,7 @@ module FlexStationData
 
     attr_reader :value, :threshold
 
-    def initialize(value, threshold: nil)
+    def initialize(value, threshold: nil, **_options)
       @value = value
       @threshold = threshold
     end

data/lib/flex_station_data/version.rb

@@ -1,3 +1,3 @@
 module FlexStationData
-  VERSION = "0.2.0"
+  VERSION = "0.3.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: flex-station-data
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.3.0
 platform: ruby
 authors:
 - John Carney
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-08-23 00:00:00.000000000 Z
+date: 2019-08-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -106,6 +106,7 @@ extra_rdoc_files: []
 files:
 - ".gitignore"
 - ".rspec"
+- CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
 - Gemfile.lock
@@ -121,10 +122,14 @@ files:
 - lib/flex_station_data/concerns/service.rb
 - lib/flex_station_data/linear_regression.rb
 - lib/flex_station_data/plate.rb
+- lib/flex_station_data/presenters/linear_regression/plate_hash.rb
+- lib/flex_station_data/presenters/linear_regression/plates_hash.rb
+- lib/flex_station_data/presenters/linear_regression/sample_hash.rb
+- lib/flex_station_data/presenters/linear_regression/sample_regression_hash.rb
+- lib/flex_station_data/presenters/linear_regression/verbose_sample_csv.rb
 - lib/flex_station_data/presenters/plate_csv.rb
 - lib/flex_station_data/presenters/plates_csv.rb
 - lib/flex_station_data/presenters/sample_csv.rb
-- lib/flex_station_data/presenters/sample_linear_regression_csv.rb
 - lib/flex_station_data/readings.rb
 - lib/flex_station_data/sample.rb
 - lib/flex_station_data/services/compute_mean.rb

data/lib/flex_station_data/presenters/sample_linear_regression_csv.rb

@@ -1,29 +0,0 @@
-require "flex_station_data/presenters/sample_csv"
-require "flex_station_data/linear_regression"
-
-module FlexStationData
-  module Presenters
-    class SampleLinearRegressionCsv < SampleCsv
-      include Concerns::Presenter
-
-      def regression_factory
-        LinearRegression.method(:new).curry(2)[times]
-      end
-
-      def regressions
-        [ *sample.readings, sample.mean ].map(&:values).map(&regression_factory)
-      end
-
-      def regressions_csv
-        [
-          [ "slope", *regressions.map(&:slope) ],
-          [ "R²",    *regressions.map(&:r_squared) ]
-        ]
-      end
-
-      def values_csv
-        super + regressions_csv
-      end
-    end
-  end
-end