galaaz 0.4.1 → 0.4.2

data/examples/sthda_ggplot/all.rb

@@ -20,12 +20,6 @@
 ##########################################################################################
 
 require 'galaaz'
-require 'ggplot'
-
-# install.packages('quantreg')
-# install.packages('hexbin')
-# Library 'quantreg' is needed in misc
-R.install_and_loads('quantreg', 'hexbin')
 
 # Package Hmisc does not yet install on graalvm because of
 # problems with package data.table

data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_hex.rb

@@ -24,7 +24,7 @@
 require 'galaaz'
 require 'ggplot'
 
-Polyglot.eval("R", "library('hexbin')")
+R.install_and_loads('hexbin')
 
 diamonds = ~:diamonds
 

data/examples/sthda_ggplot/two_variables_cont_cont/misc.rb

@@ -24,7 +24,7 @@
 require 'galaaz'
 require 'ggplot'
 
-Polyglot.eval("R", "library('quantreg')")
+R.install_and_loads('quantreg')
 
 R.awt
 

data/examples/sthda_ggplot/two_variables_disc_cont/geom_bar.rb

@@ -30,8 +30,8 @@ df = R.data__frame(dose: R.c("D0.5", "D1", "D2"),
 puts df.head
 
 df2 = R.data__frame(supp: R.rep(R.c("VC", "OJ"), each: 3),
-                   dose: R.rep(R.c("D0.5", "D1", "D2"), 2),
-                   len: R.c(6.8, 15, 33, 4.2, 10, 29.5))
+                    dose: R.rep(R.c("D0.5", "D1", "D2"), 2),
+                    len: R.c(6.8, 15, 33, 4.2, 10, 29.5))
 puts df2.head
 
 f = df.ggplot(E.aes(x: :dose, y: :len))

data/examples/sthda_ggplot/two_variables_disc_disc/geom_jitter.rb

@@ -32,7 +32,6 @@ print diamonds.ggplot(E.aes(:cut, :color)) +
       R.geom_jitter(E.aes(color: :cut), size: 0.5)
 
 sleep(2)
-R.grid__newpage
 
 # a = gets.chomp
 

data/lib/R/eng_ruby.R

@@ -0,0 +1,62 @@
+# define the ruby engine for processing Ruby chunks in
+# rmarkdown
+eng_ruby = function(options) {
+    block_code = paste(options$code, collapse = "\\n");
+    code = paste0("GalaazUtil.exec_ruby(", 
+                  sQuote(block_code), 
+                  ")"
+                  );
+    
+    keep = options$fig.keep
+    keep.idx = NULL
+    if (is.numeric(keep)) {
+        keep.idx = keep
+        keep = "index"
+    }
+    
+    tmp.fig = tempfile(); on.exit(unlink(tmp.fig), add = TRUE)
+    
+                                        # open a device to record plots
+    if (knitr:::chunk_device(options$fig.width[1L], options$fig.height[1L], keep != "none",
+                             options$dev, options$dev.args, options$dpi, options, tmp.fig)) {
+                                        # preserve par() settings from the last code chunk
+        if (keep.pars <- opts_knit$get("global.par"))
+            par2(opts_knit$get("global.pars"))
+        knitr:::showtext(options$fig.showtext)  # showtext support
+        dv = dev.cur()
+        on.exit({
+            if (keep.pars) opts_knit$set(global.pars = par(no.readonly = TRUE))
+            dev.off(dv)
+        }, add = TRUE)
+    }
+    
+                                        # guess plot file type if it is NULL
+    if (keep != "none" && is.null(options$fig.ext))
+        options$fig.ext = knitr:::dev2ext(options$dev)
+    
+    res = eval.polyglot("ruby", code)
+    
+                                        # rearrange locations of figures
+    figs = find_recordedplot(res)
+    if (length(figs) && any(figs)) {
+        if (keep == 'none') {
+            res = res[!figs] # remove all
+        } else {
+            if (options$fig.show == 'hold') res = c(res[!figs], res[figs]) # move to the end
+            figs = find_recordedplot(res)
+            if (length(figs) && sum(figs) > 1) {
+                if (keep %in% c('first', 'last')) {
+                    res = res[-(if (keep == 'last') head else tail)(which(figs), -1L)]
+                } else {
+                                        # keep only selected
+                    if (keep == 'index') res = res[which(figs)[keep.idx]]
+                                        # merge low-level plotting changes
+                    if (keep == 'high') res = merge_low_plot(res, figs)
+                }
+            }
+        }
+    }
+    engine_output(options, block_code, res)
+}
+
+knit_engines$set(ruby = eng_ruby)

data/lib/R/eng_ruby.R~

@@ -0,0 +1,63 @@
+# define the ruby engine for processing Ruby chunks in
+# rmarkdown
+eng_ruby = function(options) {
+  block_code = paste(options$code, collapse = "\\n");
+  code = paste0("GalaazUtil.exec_ruby(", 
+                   shQuote(block_code), 
+                  ")
+                ");
+
+  # png(paste0("gknit_files/figure-html/", options$label, ".png"));
+
+  keep = options$fig.keep
+  keep.idx = NULL
+  if (is.numeric(keep)) {
+    keep.idx = keep
+    keep = "index"
+  }
+
+  tmp.fig = tempfile(); on.exit(unlink(tmp.fig), add = TRUE)
+
+  # open a device to record plots
+  if (chunk_device(options$fig.width[1L], options$fig.height[1L], keep != "none",
+                   options$dev, options$dev.args, options$dpi, options, tmp.fig)) {
+    # preserve par() settings from the last code chunk
+    if (keep.pars <- opts_knit$get("global.par"))
+      par2(opts_knit$get("global.pars"))
+    showtext(options$fig.showtext)  # showtext support
+    dv = dev.cur()
+    on.exit({
+      if (keep.pars) opts_knit$set(global.pars = par(no.readonly = TRUE))
+      dev.off(dv)
+    }, add = TRUE)
+   }
+
+  # guess plot file type if it is NULL
+  if (keep != "none" && is.null(options$fig.ext))
+    options$fig.ext = dev2ext(options$dev)
+
+  # out = eval.polyglot("ruby", code);
+  res = eval.polyglot("ruby", code);
+
+# rearrange locations of figures
+  figs = find_recordedplot(res)
+  if (length(figs) && any(figs)) {
+    if (keep == 'none') {
+      res = res[!figs] # remove all
+    } else {
+      if (options$fig.show == 'hold') res = c(res[!figs], res[figs]) # move to the end
+      figs = find_recordedplot(res)
+      if (length(figs) && sum(figs) > 1) {
+        if (keep %in% c('first', 'last')) {
+          res = res[-(if (keep == 'last') head else tail)(which(figs), -1L)]
+        } else {
+          # keep only selected
+          if (keep == 'index') res = res[which(figs)[keep.idx]]
+          # merge low-level plotting changes
+          if (keep == 'high') res = merge_low_plot(res, figs)
+        }
+      }
+    }
+}
+  engine_output(options, block_code, res)
+}

data/lib/R_interface/capture_plot.rb~

@@ -0,0 +1,23 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+

data/lib/{R → R_interface}/r.rb

@@ -29,7 +29,8 @@ module R
   RCONSTANTS = ["LETTERS", "letters", "month.abb", "month.name", "pi"]
 
   #----------------------------------------------------------------------------------------
-  #
+  # Executes a missing method. If a block is given, then the method needs to be executed
+  # in the scope of the block.  @bug: Not ready yeat
   #----------------------------------------------------------------------------------------
 
   def self.method_missing(symbol, *args, &block)
@@ -117,3 +118,11 @@ require_relative 'ruby_extensions'
 # Class to allow R calling back into Ruby
 require_relative 'ruby_callback'
 
+# R packages and functions needed
+# Requires ggplot for plotting graphics
+# require 'ggplot'
+# require 'knitr'
+
+# Methods to capture a plot sent to a device
+require_relative 'rdevices'
+

data/lib/{R → R_interface}/r_methods.rb

@@ -30,19 +30,35 @@ module R
     #--------------------------------------------------------------------------------------
     
     def self.capture
-      
       Polyglot.eval("R", <<-R)
         function(obj, ...) {
-          sink(tt <- textConnection("results","w"), split=FALSE);
+          sink(tt <- textConnection("results","w"), split=FALSE, type = c("output", "message"));
           print(obj, ...);
           sink();
           close(tt);
           results
         }
       R
-      
-    end 
-    
+    end
+
+    def self.start_capture
+      Polyglot.eval("R", <<-R)
+        function(cap_variable) {
+          sink(con <- textConnection(cap_variable,"w"), split=FALSE, type = c("output"));
+          con
+        }
+      R
+    end
+
+    def self.stop_capture
+      Polyglot.eval("R", <<-R)
+        function(con) {
+          sink();
+          close(con);
+        }
+      R
+    end
+
     #--------------------------------------------------------------------------------------
     # multi-dimensional indexing
     #--------------------------------------------------------------------------------------

data/lib/{R → R_interface}/rbinary_operators.rb

@@ -60,6 +60,7 @@ module R
   #--------------------------------------------------------------------------------------
 
   module FormulaBinOp
+    
     #--------------------------------------------------------------------------------------
     #
     #--------------------------------------------------------------------------------------
@@ -93,6 +94,10 @@ module R
       
     end
 
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
   end
 
   #--------------------------------------------------------------------------------------
@@ -220,7 +225,7 @@ module R
     def coerce(numeric)
       [R.c(numeric), self]
     end
-    
+
   end
 
 end

data/lib/R_interface/rclosure.rb

@@ -0,0 +1,38 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+module R
+
+  class Closure < Object
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def call(*args)
+      R::Support.exec_function(@r_interop, *args)
+    end
+
+  end
+
+end

data/lib/R_interface/rdevices.R

@@ -0,0 +1,31 @@
+#" Capture snapshot of current device.
+#"
+#" There's currently no way to capture when a graphics device changes,
+#" except to check its contents after the evaluation of every expression.
+#" This means that only the last plot of a series will be captured.
+#"
+#" @return \code{NULL} if plot is blank or unchanged, otherwise the output of
+#"   \code{\link[grDevices]{recordPlot}}.
+_plot_snapshot = function() {
+    evaluate:::plot_snapshot()
+}
+
+# Function accessible from Galaaz to call non-exported knitr:::chunk_device function
+_ck_dv = function(width, height, record = TRUE, dev, dev.args, dpi, options, 
+                  tmp = tempfile()) {
+    knitr:::chunk_device(width, height, record, dev, dev.args, dpi, options, tmp)
+}
+
+# Function to guess the extension name of a file based on the device type
+knitr_dev2ext = function(x) {
+    knitr:::dev2ext(x)
+}
+
+knitr_save_plot = function(plot, name, dev, width, height, ext, dpi, options) {
+    print(options)
+    knitr:::save_plot(plot, name, dev, width, height, ext, dpi, options)
+}
+
+knitr_opts_chunk = function() {
+    knitr:::opts_chunk
+}

data/lib/R_interface/rdevices.rb

@@ -0,0 +1,225 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'singleton'
+
+dir = File.dirname(File.expand_path('.', __FILE__))
+src = "#{dir}/rdevices.R"
+
+R.source(src)
+
+module R
+
+  class Device
+
+    attr_reader :dev_type, :filename, :width, :height, :dpi, :record,
+                :args, :options, :tmp_file, 
+                :dev_number
+    attr_accessor :file_dir
+
+    
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+
+    def self.list
+      R.dev__list
+    end
+    
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+    
+    def initialize(dev_type, filename: nil, file_dir: '.', width: nil, height: nil,
+                   dpi: nil, record: false, args: nil, options: nil, tmp_file: nil)
+
+      @dev_type = dev_type
+      @filename = filename
+      @width = width
+      @height = height
+      @dpi = dpi
+      # TODO: Needs to allow false, but truffle is crashing when false. When it is
+      # fixed, just change to @record = record
+      @record = true
+      
+      @args = args
+      @options = options
+      @tmp_file = tmp_file
+      
+    end
+
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+
+    def open
+      
+      case @dev_type
+           
+      when 'svg'
+      when 'awt'
+        R.awt(width: @width, height: @height)
+        @record ? R.dev__control(displaylist: 'enable') :
+          R.dev__control(displaylist: 'inhibit')
+        @dev_number = R.dev__cur
+      when 'png'
+        R.png(filename: @filename, width: @width, height: @height, units: 'in', res: dpi)
+      when 'jpg'
+      when 'bmp'
+      else
+        raise "Device type #{@dev_type} not allowed"
+      end
+      
+    end
+    
+    #--------------------------------------------------------------------------------------
+    # Opens the device, evaluates the given graphics block expressions and closes the
+    # device at the end of execution
+    #--------------------------------------------------------------------------------------
+    
+    def eval(&block)
+        
+      if block_given?
+        begin
+          open
+          yield
+        ensure
+          close
+        end
+      end
+      
+    end
+    
+    #--------------------------------------------------------------------------------------
+    # copies the temporary file to the definitive location
+    #--------------------------------------------------------------------------------------
+    
+    def copy
+      file = "#{@file_dir}/#{@file_name}.#{ext}"
+      puts file
+      FileUtils.cp(@tmp_file << 0, file)
+    end
+        
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+    
+    def close
+      R.dev__off(which: @dev_number)
+      # copy if @record
+    end
+
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+
+    def newpage
+      R.grid__newpage
+    end
+    
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+
+    def plot_snapshot
+      R.knitr_plot_snapshot
+    end
+
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+
+    def ext
+      R.knitr_dev2ext(@dev) << 0
+    end
+
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+
+    def save_plot(plot, name, dev, width, height, ext, dpi, options = R.list())
+      R.knitr_save_plot(plot, name, dev, width, height, ext, dpi, options)
+    end
+    
+  end
+
+
+  #--------------------------------------------------------------------------------------
+  # 
+  #--------------------------------------------------------------------------------------
+  
+  class Panel <  Device
+    include Singleton
+
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+    
+    def initialize
+      super('awg', width: nil, height: nil, dpi: nil, record: false, args: nil,
+            options: nil)
+    end
+
+    def exec(&block)
+      yield
+    end
+    
+  end
+  
+end
+
+=begin
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+    
+    def open2
+      
+      case @dev
+      when 'svg'
+        R.svg(@tmp_file)
+      when 'awt'
+        @record = false
+        R.awt
+      when 'png'
+        # for 'png' @record needs to be true, otherwise the device is not
+        # opened.  Don't know why, yet!
+        @record = true
+        # opens a device for plot recording. 
+        if (R._ck_dv(@width, @height, @dev, @args, @dpi, tmp: @tmp_file,
+                     record: @record) << 0)
+          @dv = R.dev__cur
+        else
+          raise "Problem opening the device"
+        end
+      else
+        if (R._ck_dv(@width, @height, @dev, @args, @dpi, tmp: @tmp_file,
+                     record: @record) << 0)
+          @dv = R.dev__cur
+        else
+          raise "Problem opening the device"
+        end
+      end
+      
+    end
+=end