galaaz 0.4.5 → 0.4.6

data/blogs/ruby_plot/ruby_plot.md

@@ -143,24 +143,6 @@ following chunk that 'ToothGrowth' is the R  variable and Ruby's '@tooth_growth'
 assigned the value of '~:ToothGrowth'.
 
 
-```ruby
-# Read the R ToothGrowth variable and assign it to the
-# Ruby instance variable @tooth_growth that will be 
-# available to all Ruby chunks in this document.
-@tooth_growth = ~:ToothGrowth
-# print the first few elements of the dataset
-puts @tooth_growth.head
-```
-
-```
-##    len supp dose
-## 1  4.2   VC  0.5
-## 2 11.5   VC  0.5
-## 3  7.3   VC  0.5
-## 4  5.8   VC  0.5
-## 5  6.4   VC  0.5
-## 6 10.0   VC  0.5
-```
 
 Great! We've managed to read the ToothGrowth dataset and take a look at its elements.
 We see here the first 6 rows of the dataset. To access a column, follow the dataset name
@@ -168,15 +150,6 @@ with a dot ('.') and the name of the column. Also use dot notation to chain meth
 in usual Ruby style.
 
 
-```ruby
-# Access the tooth_growth 'len' column and print the first few
-# elements of this column with the 'head' method.
-puts @tooth_growth.len.head
-```
-
-```
-## [1]  4.2 11.5  7.3  5.8  6.4 10.0
-```
  
 The 'dose' column contains a numeric value with either, 0.5, 1 or 2, although the
 first 6 rows as seen above only contain the 0.5 values.  Even though those are
@@ -186,22 +159,11 @@ function from Galaaz the dot ('.') in the function name is substituted by '__' (
 The function 'as.factor' becomes 'R.as__factor' or just 'as__factor' when chaining.
 
 
-```ruby
-# convert the dose to a factor
-@tooth_growth.dose = @tooth_growth.dose.as__factor
-```
 
 Let's explore some more details of this dataset.  In particular, let's look at its dimensions,
 structure and summary statistics.
 
 
-```ruby
-puts @tooth_growth.dim
-```
-
-```
-## [1] 60  3
-```
 
 This dataset has 60 rows, one for each subject and 3 columns, as we have already seen.
 
@@ -210,35 +172,12 @@ functions does not return anything and prints the structure of the dataset
 as a side effect.
 
 
-```ruby
-@tooth_growth.str
-```
-
-```
-## 'data.frame':	60 obs. of  3 variables:
-##  $ len : num  4.2 11.5 7.3 5.8 6.4 10 11.2 11.2 5.2 7 ...
-##  $ supp: Factor w/ 2 levels "OJ","VC": 2 2 2 2 2 2 2 2 2 2 ...
-##  $ dose: Factor w/ 3 levels "0.5","1","2": 1 1 1 1 1 1 1 1 1 1 ...
-```
 Observe that both variables 'supp' and 'dose' are factors.  The system made variable 'supp'
 a factor automatically, since it contais two strings OJ and VC.
 
 Finally, using the summary method, we get the statistical summary for the dataset
 
 
-```ruby
-puts @tooth_growth.summary
-```
-
-```
-##       len        supp     dose   
-##  Min.   : 4.20   OJ:30   0.5:20  
-##  1st Qu.:13.07   VC:30   1  :20  
-##  Median :19.25           2  :20  
-##  Mean   :18.81                   
-##  3rd Qu.:25.27                   
-##  Max.   :33.90
-```
 
 # Doing the Data Analysis
 
@@ -274,23 +213,12 @@ image gets a default name of 'Rplot\<nnn\>' where \<nnn\> is the number of the p
 closes the device and creates the 'png' file. We can
 then include the generated 'png' file in the document by adding an rmarkdown directive.
 
-
-```ruby
-require 'ggplot'
-
-R.png("figures/dose_len.png")
-
-e = @tooth_growth.ggplot(E.aes(x: :dose, y: :len))
-print e + R.geom_boxplot
-
-R.dev__off
-```
+<img src="/home/rbotafogo/desenv/galaaz/blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.svg" width="50%" />
 
 [//]: # (Including the 'png' file generated above.  In future releases)
 [//]: # (of gKnit, the figures should be automatically saved and the name)
 [//]: # (taken from the chunk 'label' and possibly chunk parameters)
 
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/96db2729e02ced0f9336216d87d14af141c1e81b/dose_len.png)
 
 Great! We've just managed to create and save our first plot in Ruby with only
 four lines of code. We can now easily see with this plot a clear trend: as the
@@ -329,21 +257,6 @@ facet the plot based on the ```supp``` variable and split the plot vertically.
 the formula to ```+:supp =~ +:all``` would split the plot horizontally.
 
 
-```ruby
-R.png("figures/facet_by_delivery.png")
-
-@base_tooth = @tooth_growth.ggplot(E.aes(x: :dose, y: :len, group: :dose))
-
-@bp = @base_tooth + R.geom_boxplot +
-      # Split in vertical direction
-      R.facet_grid(+:all =~ +:supp)
-      
-puts @bp
-
-R.dev__off
-```
-
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/96db2729e02ced0f9336216d87d14af141c1e81b/facet_by_delivery.png)
 
 It now becomes clear that although both methods of delivery have a direct
 impact on tooth growth, method (OJ) is non-linear having a higher impact with smaller
@@ -360,16 +273,6 @@ enough to add ```fill: :dose``` to the aesthetic of boxplot.  With this command
 factor gets its own color.
 
 
-```ruby
-R.png("figures/facets_by_delivery_color.png")
-
-@bp = @bp + R.geom_boxplot(E.aes(fill: :dose))
-puts @bp
-
-R.dev__off
-```
-
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/96db2729e02ced0f9336216d87d14af141c1e81b/facets_by_delivery_color.png)
 
 Facetting helps us compare the general trends for each delivery method.
 Adding color allow us to compare specifically how each dosage impacts the tooth growth.
@@ -401,18 +304,6 @@ each of the 60 pigs in the experiment.  For that, add the function 'R.geom_point
 plot.
 
 
-```ruby
-R.png("figures/facets_with_points.png")
-
-# Split in vertical direction
-@bp = @bp + R.geom_point
-
-puts @bp
-
-R.dev__off
-```
-
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/96db2729e02ced0f9336216d87d14af141c1e81b/facets_with_points.png)
 
 Now we can see the actual distribution of all the 60 subjects.  Actually, this is not
 totally true.  We have a hard time seing all 60 subjects. It seems that some points
@@ -426,16 +317,6 @@ prevents data hiding.  We also add
 color and change the shape of the points, making them even easier to see.
 
 
-```ruby
-R.png("figures/facets_with_jitter.png")
-
-# Split in vertical direction
-puts @bp + R.geom_jitter(shape: 23, color: "cyan3", size: 1)
-
-R.dev__off
-```
-
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/96db2729e02ced0f9336216d87d14af141c1e81b/facets_with_jitter.png)
 
 Now we can see all 60 points in the graph. We have here a much higher information density
 and we can see outliers and subjects distribution.
@@ -471,20 +352,6 @@ This ordering seems more natural and
 matches with the actual order of the colors in the plot.
 
 
-```ruby
-R.png("figures/facets_by_delivery_color2.png")
-
-@bp = @bp +
-      R.scale_fill_manual(values: R.c("cyan", "deepskyblue", "deepskyblue4"),
-                          breaks: R.c("2","1","0.5"))
-
-puts @bp
-
-R.dev__off
-```
-
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/96db2729e02ced0f9336216d87d14af141c1e81b/facets_by_delivery_color2.png)
-
 
 ## Violin Plot and Jitter
 
@@ -504,21 +371,6 @@ a boxplot known as a _violin plot_ with jittered data.
 > The central dot represents the median average value. 
 
 
-```ruby
-R.png("figures/violin_with_jitter.png")
-
-@violin = @base_tooth + R.geom_violin(E.aes(fill: :dose)) + 
-   R.facet_grid(+:all =~ +:supp) +
-   R.geom_jitter(shape: 23, color: "cyan3", size: 1) +
-   R.scale_fill_manual(values: R.c("cyan", "deepskyblue", "deepskyblue4"),
-                       breaks: R.c("2","1","0.5"))
-
-puts @violin
-
-R.dev__off
-```
-
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/96db2729e02ced0f9336216d87d14af141c1e81b/violin_with_jitter.png)
 
 This plot is an alternative to the original boxplot.  For the final presentation, it is
 important to think which graphics will be best understood by our audience. A violin plot
@@ -539,26 +391,6 @@ for information about the plot (for clarity, we defined a caption variable using
 Here Doc style).
 
 
-```ruby
-R.png("figures/facets_with_decorations.png", width: 540, height: 560)
-
-caption = <<-EOT
-Length of odontoblasts in 60 guinea pigs. 
-Each animal received one of three dose levels of vitamin C.
-EOT
-
-@decorations =
-  R.labs(title: "Tooth Growth:  Length vs Vitamin C Dose",
-         subtitle: "Faceted by delivery method, OJ or VC",
-         x: "Dose (mg)", y: "Teeth length",
-         caption: caption)
-
-puts @bp + @decorations
-
-R.dev__off
-```
-
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/225058450f4e69e5e82a01e22f69725554746893/facets_with_decorations.png)
 
 ## The Corp Theme
 
@@ -576,57 +408,6 @@ a shade o blue (color: '#00080').  Axis labels are moved near the end of the axi
 written in 'bold'.
 
 
-```ruby
-module CorpTheme
-
-  R.install_and_loads 'RColorBrewer'
-  
-  #---------------------------------------------------------------------------------
-  # face can be  (1=plain, 2=bold, 3=italic, 4=bold-italic)
-  #---------------------------------------------------------------------------------
-  
-  def self.text_element(size, face: "plain", hjust: nil)
-    E.element_text(color: "#000080", 
-                   face: face,
-                   size: size,
-		   hjust: hjust)
-  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
-    #    R.theme_set(R.theme_bw)
-    
-    # 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, face: "bold", hjust: 1))
-    # change font of title
-    gb = gb + R.theme(title: text_element(12, face: "bold"))
-    # change font of subtitle
-    gb = gb + R.theme(plot__subtitle: text_element(9))
-    # change font of captions
-    gb = gb + R.theme(plot__caption: text_element(8))
-
-  end
-   
-end
-```
 
 ## Final Box Plot
 
@@ -640,30 +421,11 @@ the decorations (@decorations), plus the corporate theme.
 Here is our final boxplot, without jitter.
 
 
-```ruby
-R.png("figures/final_box_plot.png", width: 540, height: 560)
-
-puts @bp + @decorations + CorpTheme.global_theme(faceted: true)
-
-R.dev__off
-```
-
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/225058450f4e69e5e82a01e22f69725554746893/final_box_plot.png)
 
 And here is the final violin plot, with jitter and the same look and feel of the corporate
 boxplot.
 
 
-```ruby
-R.png("figures/final_violin_plot.png", width: 540, height: 560)
-
-puts @violin + @decorations + CorpTheme.global_theme(faceted: true)
-
-R.dev__off
-```
-
-
-![]https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/225058450f4e69e5e82a01e22f69725554746893/final_violin_plot.png
 
 ## Another View
 
@@ -672,28 +434,6 @@ dose and not by supplement.  This shows how easy it is to create new plots by ju
 changing small statement on the _grammar of graphics_.
 
 
-```ruby
-R.png("figures/facet_by_dose.png", width: 540, height: 560)
-
-caption = <<-EOT
-Length of odontoblasts in 60 guinea pigs. 
-Each animal received one of three dose levels of vitamin C.
-EOT
-
-@bp = @tooth_growth.ggplot(E.aes(x: :supp, y: :len, group: :supp)) + 
-      R.geom_boxplot(E.aes(fill: :supp)) + R.facet_grid(+:all =~ +:dose) +
-      R.scale_fill_manual(values: R.c("cyan", "deepskyblue4")) +
-      R.labs(title: "Tooth Growth:  Length by Dose",
-             subtitle: "Faceted by dose",
-             x: "Delivery method", y: "Teeth length",
-             caption: caption) +
-      CorpTheme.global_theme(faceted: true)
-puts @bp
-
-R.dev__off
-```
-
-![](https://gist.githubusercontent.com/rbotafogo/5538d6c679a59f4d56179b2c030e8d28/raw/96db2729e02ced0f9336216d87d14af141c1e81b/facet_by_dose.png)
 
 # Conclusion
 

data/blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.svg

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