galaaz 0.4.1 → 0.4.2

data/specs/tmp.rb

@@ -22,8 +22,262 @@
 ##########################################################################################
 
 require 'galaaz'
+#require 'ggplot'
+
+# Read the R ToothGrowth variable and assign it to the
+# Ruby tooth_growth variable
+tooth_growth = ~:ToothGrowth
+# convert the dose to a factor
+tooth_growth.dose = tooth_growth.dose.as__factor
+
+# print the first few elements of the dataset
+puts tooth_growth.head
+puts tooth_growth.dim
+puts tooth_growth.str
+puts tooth_growth.summary
+
+
+=begin
+module CorpTheme
+
+  # face can be  (1=plain, 2=bold, 3=italic, 4=bold-italic)
+  def self.text_element(size, face = "plain")
+    E.element_text(color: "#000080", 
+                   face: face,
+                   size: size,
+                   hjust: 1)
+  end
+  
+  #---------------------------------------------------------------------------------
+  # Defines the plot theme (visualization).  In this theme we remove major and minor
+  # grids, borders and background.  We also turn-off scientific notation.
+  #---------------------------------------------------------------------------------
+  
+  def self.global_theme(faceted = false)
+    
+    R.options(scipen: 999)  # turn-off scientific notation like 1e+48
+    
+    # remove major grids
+    gb = R.theme(panel__grid__major: E.element_blank())
+    # remove minor grids
+    gb = gb + R.theme(panel__grid__minor: E.element_blank)
+    # gb = R.theme(panel__grid__minor: E.element_blank)
+    # remove border
+    gb = gb + R.theme(panel__border: E.element_blank)
+    # remove background. When working with faceted graphs, the background makes
+    # it easier to see each facet, so leave it
+    gb = gb + R.theme(panel__background: E.element_blank) if !faceted
+    # Change axis font
+    gb = gb + R.theme(axis__text: text_element(8))
+    # change axis title font
+    gb = gb + R.theme(axis__title: text_element(10, "plain"))
+    # change font of title
+    gb = gb + R.theme(title: text_element(12, "bold"))
+    # change font of captions
+    gb = gb + R.theme(plot__caption: text_element(8))
+    
+  end
+   
+end
+
+#R.png("final.png")
+R.awt
+
+# Read the R ToothGrowth variable and assign it to the
+# Ruby tooth_growth variable
+tooth_growth = ~:ToothGrowth
+# convert the dose to a factor
+tooth_growth.dose = tooth_growth.dose.as__factor
+
+# print the first few elements of the dataset
+puts tooth_growth.head
+
+# Create the basic plot
+bp = tooth_growth.ggplot(E.aes(x: :dose, y: :len, group: :dose)) + 
+     R.geom_boxplot(E.aes(fill: :dose)) + R.geom_point
+
+caption = <<-EOT
+Length of odontoblasts in 60 guinea pigs. 
+Each animal received one of three dose levels of vitamin C.
+EOT
+
+# Facet the plot by the s
+bp = bp + R.facet_grid(+:all =~ +:supp) +
+     R.labs(title: "Tooth Growth:  Length by Dose",
+            subtitle: "Faceted by delivery method, Orange Juince (OJ) or Ascorbic Acid (VC)",
+            x: "Dose (mg)", y: "Teeth length",
+            caption: caption) +
+     CorpTheme.global_theme(faceted: true)
+
+puts bp
+
+# CorpTheme.layout("Plot of length by dose", "subtitle", bp)
+
+a = gets.chomp
+sleep(20)
+
+R.dev__off
+=end
+
+=begin
+
+awt1 = R::Device.new('awt')
+awt1.open
+
+awt2 = R::Device.new('awt')
+awt2.open
+
+puts R.dev__list
+
+sleep(10)
+
+awt1.close
+
+puts R.dev__list
+
+# puts R::Devices.list
+=end
+
+=begin
+#awt1 = R::Device.new('awt')
+#awt1.open
+
+b = R.ggplot(:mpg, E.aes(:fl))
+
+# Basic plot
+print b + R.geom_bar
+
+awt2 = R::Device.new('awt')
+awt2.open
+
+# Change fill color
+print b + R.geom_bar(fill: "steelblue", color: "steelblue") +
+      R.theme_minimal
+
+sleep(5)
+
+awt1.close
+
+sleep(5)
+=end
+
+
+
+=begin
+R.theme_set R.theme_bw
+
+# Data Prep
+mtcars = ~:mtcars
+mtcars.car_name = R.rownames(:mtcars)
+# compute normalized mpg 
+mtcars.mpg_z = ((mtcars.mpg - mtcars.mpg.mean)/mtcars.mpg.sd).round 2
+mtcars.mpg_type = mtcars.mpg_z < 0 ? "below" : "above"
+mtcars = mtcars[mtcars.mpg_z.order, :all]
+# convert to factor to retain sorted order in plot
+mtcars.car_name = mtcars.car_name.factor levels: mtcars.car_name
+
+# Diverging Barcharts
+gg = mtcars.ggplot(E.aes(x: :car_name, y: :mpg_z, label: :mpg_z)) + 
+     R.geom_bar(E.aes(fill: :mpg_type), stat: 'identity',  width: 0.5) +
+     R.scale_fill_manual(name: "Mileage", 
+                         labels: R.c("Above Average", "Below Average"), 
+                         values: R.c("above": "#00ba38", "below": "#f8766d")) + 
+     R.labs(subtitle: "Normalised mileage from 'mtcars'", 
+            title: "Diverging Bars") + 
+     R.coord_flip()
+
+p gg
+puts gg.rclass
+gg.rclass = "list"
+puts gg
+=end
+
+#lst = gg.as__list
+#lst.rclass = "list"
+#puts lst.rclass
+#puts lst
+
+=begin
+R::Support.eval(<<-R)
+
+library(ggplot2)
+library(ggcorrplot)
+
+# Correlation matrix
+data(mtcars)
+corr <- round(cor(mtcars), 1)
+
+# Plot
+gg = ggcorrplot(corr, hc.order = TRUE, 
+           type = "lower", 
+           lab = TRUE, 
+           lab_size = 3, 
+           method="circle", 
+           colors = c("tomato2", "white", "springgreen3"), 
+           title="Correlogram of mtcars", 
+           ggtheme=theme_bw)
+
+lst = as.list(gg)
+print(lst[[1]])
+R
+=end
+=begin
+# mtcars$`car name` <- rownames(mtcars)  # create new column for car names
+# mtcars$mpg_z <- round((mtcars$mpg - mean(mtcars$mpg))/sd(mtcars$mpg), 2)  # compute normalized mpg
+# mtcars$mpg_type <- ifelse(mtcars$mpg_z < 0, "below", "above")  # above / below avg flag
+# mtcars <- mtcars[order(mtcars$mpg_z), ]  # sort
+mtcars$`car name` <- factor(mtcars$`car name`, levels = mtcars$`car name`)  # convert to factor to retain sorted order in plot.
+
+# Diverging Barcharts
+ggplot(mtcars, aes(x=`car name`, y=mpg_z, label=mpg_z)) + 
+  geom_bar(stat='identity', aes(fill=mpg_type), width=.5)  +
+  scale_fill_manual(name="Mileage", 
+                    labels = c("Above Average", "Below Average"), 
+                    values = c("above"="#00ba38", "below"="#f8766d")) + 
+  labs(subtitle="Normalised mileage from 'mtcars'", 
+       title= "Diverging Bars") + 
+  coord_flip()
+
+=end
+
+# dir = File.dirname(File.expand_path('.', __FILE__))
+# GalaazUtil.inline_file("awsome_print", "require ")
+
+
+
+
+
+=begin
+R::Support.eval(<<-R)
+  old_dispatch = UseMethod;
+  print(old_dispatch);
+
+  print(typeof(UseMethod));
+
+  UseMethod = function(x, ...) {
+    print("in local UseMethod");
+    print(x);
+    print(...);
+    old_dispatch(x, ...);
+  }
+
+  vec = c(1, 2, 3);
+  print(vec);
+  print(mean(vec));
+  # UseMethod("mean", vec);
+
+R
+=end
+
+
+
+
+
+
+
+
+
 
-# puts GalaazUtil.exec_ruby("puts 1 + 1")
 
 =begin
 R::Support.eval(<<-R)

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "galaaz"
-$version="0.4.1"
+$version="0.4.2"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: galaaz
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.4.2
 platform: ruby
 authors:
 - Rodrigo Botafogo
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-10-18 00:00:00.000000000 Z
+date: 2018-11-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: pry
@@ -66,20 +66,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '5.0'
-- !ruby/object:Gem::Dependency
-  name: rake
-  prerelease: false
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '12.0'
-  type: :development
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '12.0'
 description: "Galaaz brings the power of R to the Ruby community. Galaaz \nis based
   on TruffleRuby and FastR, GraalVM-based interpreters for Ruby and the R language
   \nfor statistical computing respectively.\n\nOver the past two decades, the R language
@@ -106,16 +92,62 @@ files:
 - Rakefile
 - bin/galaaz
 - bin/gknit
+- bin/gknit2
+- bin/gknit2~
 - bin/gstudio
 - bin/gstudio.rb
 - bin/ogk~
+- bin/prepareR.rb
+- bin/prepareR.rb~
+- bin/tmp.py
+- blogs/dev/dev.Rmd
+- blogs/dev/dev.Rmd~
+- blogs/dev/dev.html
+- blogs/dev/dev.md
+- blogs/dev/dev_files/figure-html/bubble-1.png
+- blogs/dev/model.rb
 - blogs/galaaz_ggplot/galaaz_ggplot.Rmd
+- blogs/galaaz_ggplot/galaaz_ggplot.aux
+- blogs/galaaz_ggplot/galaaz_ggplot.dvi
 - blogs/galaaz_ggplot/galaaz_ggplot.html
 - blogs/galaaz_ggplot/galaaz_ggplot.md
+- blogs/galaaz_ggplot/galaaz_ggplot.out
+- blogs/galaaz_ggplot/galaaz_ggplot.pdf
+- blogs/galaaz_ggplot/galaaz_ggplot.tex
 - blogs/galaaz_ggplot/midwest.Rmd
 - blogs/galaaz_ggplot/midwest.html
 - blogs/galaaz_ggplot/midwest.png
+- blogs/galaaz_ggplot/midwest_external_png
+- blogs/galaaz_ggplot/midwest_external_png~
 - blogs/galaaz_ggplot/scatter_plot.png
+- blogs/gknit/gknit.Rmd
+- blogs/gknit/gknit.Rmd~
+- blogs/gknit/gknit.Rnd~
+- blogs/gknit/gknit.html
+- blogs/gknit/gknit.md
+- blogs/gknit/gknit.pdf
+- blogs/gknit/gknit.tex
+- blogs/gknit/gknit_files/figure-html/bubble-1.png
+- blogs/gknit/gknit_files/figure-html/diverging_bar.png
+- blogs/gknit/model.rb
+- blogs/gknit/model.rb~
+- blogs/ruby_plot/figures/dose_len.png
+- blogs/ruby_plot/figures/facet_by_delivery.png
+- blogs/ruby_plot/figures/facet_by_dose.png
+- blogs/ruby_plot/figures/facets_by_delivery_color.png
+- blogs/ruby_plot/figures/facets_by_delivery_color2.png
+- blogs/ruby_plot/figures/facets_with_decorations.png
+- blogs/ruby_plot/figures/facets_with_jitter.png
+- blogs/ruby_plot/figures/facets_with_points.png
+- blogs/ruby_plot/figures/final_box_plot.png
+- blogs/ruby_plot/figures/final_violin_plot.png
+- blogs/ruby_plot/figures/violin_with_jitter.png
+- blogs/ruby_plot/ruby_plot.Rmd
+- blogs/ruby_plot/ruby_plot.Rmd~
+- blogs/ruby_plot/ruby_plot.html
+- blogs/ruby_plot/ruby_plot.md
+- blogs/ruby_plot/ruby_plot.pdf
+- blogs/ruby_plot/ruby_plot.tex
 - examples/50Plots_MasterList/Images/midwest-scatterplot.PNG
 - examples/50Plots_MasterList/ScatterPlot.rb
 - examples/50Plots_MasterList/scatter_plot.rb
@@ -164,32 +196,48 @@ files:
 - examples/sthda_ggplot/two_variables_disc_cont/geom_violin.rb
 - examples/sthda_ggplot/two_variables_disc_disc/geom_jitter.rb
 - examples/sthda_ggplot/two_variables_error/geom_crossbar.rb
-- lib/R/expression.rb
-- lib/R/r.rb
-- lib/R/r.rb~
-- lib/R/r_methods.rb
-- lib/R/rbinary_operators.rb
-- lib/R/rclosure.rb
-- lib/R/rdata_frame.rb
-- lib/R/renvironment.rb
-- lib/R/rexpression.rb
-- lib/R/rindexed_object.rb
-- lib/R/rlanguage.rb
-- lib/R/rlist.rb
-- lib/R/rmatrix.rb
-- lib/R/rmd_indexed_object.rb
-- lib/R/robject.rb
-- lib/R/rpkg.rb
-- lib/R/rsupport.rb
-- lib/R/rsupport_scope.rb
-- lib/R/rsymbol.rb
-- lib/R/ruby_callback.rb
-- lib/R/ruby_extensions.rb
-- lib/R/runary_operators.rb
-- lib/R/rvector.rb
+- lib/R/eng_ruby.R
+- lib/R/eng_ruby.R~
+- lib/R_interface/capture_plot.rb~
+- lib/R_interface/expression.rb
+- lib/R_interface/r.rb
+- lib/R_interface/r.rb~
+- lib/R_interface/r_methods.rb
+- lib/R_interface/rbinary_operators.rb
+- lib/R_interface/rclosure.rb
+- lib/R_interface/rdata_frame.rb
+- lib/R_interface/rdevices.R
+- lib/R_interface/rdevices.rb
+- lib/R_interface/rdevices.rb~
+- lib/R_interface/renvironment.rb
+- lib/R_interface/rexpression.rb
+- lib/R_interface/rindexed_object.rb
+- lib/R_interface/rlanguage.rb
+- lib/R_interface/rlist.rb
+- lib/R_interface/rmatrix.rb
+- lib/R_interface/rmd_indexed_object.rb
+- lib/R_interface/robject.rb
+- lib/R_interface/rpkg.rb
+- lib/R_interface/rsupport.rb
+- lib/R_interface/rsupport_scope.rb
+- lib/R_interface/rsymbol.rb
+- lib/R_interface/ruby_callback.rb
+- lib/R_interface/ruby_extensions.rb
+- lib/R_interface/runary_operators.rb
+- lib/R_interface/rvector.rb
 - lib/galaaz.rb
+- lib/gknit.rb
+- lib/gknit.rb~
+- lib/gknit/knitr_engine.rb
+- lib/gknit/knitr_engine.rb~
+- lib/gknit/ruby_engine.rb
+- lib/gknit/ruby_engine.rb~
 - lib/util/exec_ruby.rb
+- lib/util/inline_file.rb
+- lib/util/inline_file.rb~
 - r_requires/ggplot.rb
+- r_requires/knitr.rb
+- r_requires/knitr.rb~
 - specs/all.rb
 - specs/r_dataframe.spec.rb
 - specs/r_eval.spec.rb
@@ -198,6 +246,8 @@ files:
 - specs/r_list.spec.rb
 - specs/r_list_apply.spec.rb
 - specs/r_matrix.spec.rb
+- specs/r_plots.spec.rb
+- specs/r_plots.spec.rb~
 - specs/r_vector_creation.spec.rb
 - specs/r_vector_functions.spec.rb
 - specs/r_vector_object.spec.rb