improved resolution and automation of 3D plotly figures in pdf

Closes #330

Author: ttimbers

build_html.sh

@@ -1,2 +1,2 @@
 # Script to generate HTML book
-docker run --rm -m 5g -v $(pwd):/home/rstudio/introduction-to-datascience ubcdsci/intro-to-ds:v0.15.0 /bin/bash -c "cd /home/rstudio/introduction-to-datascience; Rscript _build_html.r"
+docker run --rm -m 5g -v $(pwd):/home/rstudio/introduction-to-datascience ubcdsci/intro-to-ds:v0.16.0 /bin/bash -c "cd /home/rstudio/introduction-to-datascience; Rscript _build_html.r"

build_pdf.sh

@@ -22,7 +22,7 @@ cp -r data/ pdf/data
 cp -r img/ pdf/img
 
 # Build the book with bookdown
-docker run --rm -m 5g -v $(pwd):/home/rstudio/introduction-to-datascience ubcdsci/intro-to-ds:v0.15.0 /bin/bash -c "cd /home/rstudio/introduction-to-datascience/pdf; Rscript _build_pdf.r"
+docker run --rm -m 5g -v $(pwd):/home/rstudio/introduction-to-datascience ubcdsci/intro-to-ds:v0.16.0 /bin/bash -c "cd /home/rstudio/introduction-to-datascience/pdf; Rscript _build_pdf.r"
 
 # clean files in pdf dir
 rm -rf pdf/references.bib

classification1.Rmd

@@ -10,6 +10,7 @@ knitr::opts_chunk$set(echo = TRUE,
 options(knitr.table.format = function() {
   if (knitr::is_latex_output()) 'latex' else 'pandoc'
 })
+reticulate::use_miniconda('r-reticulate')
 ```
 
 ## Overview 
@@ -598,7 +599,7 @@ plot_3d <- scaled_cancer_3 |>
             z = ~Symmetry,
             color = ~Class,
             opacity = 0.4,
-            size = 150,
+            size = 5,
             colors = c("orange2", "steelblue2", "red"), 
             symbol = ~Class, symbols = c('circle','circle','diamond'))
 
@@ -637,6 +638,9 @@ plot_3d <- plot_3d  %>%
 if(!is_latex_output()){  
   plot_3d
 } else {
+  scene = list(camera = list(eye = list(x=2, y=2, z = 1.5)))
+  plot_3d <- plot_3d  %>% layout(scene = scene)
+  save_image(plot_3d, "img/plot3d_knn_classification.png", scale = 10)
   knitr::include_graphics("img/plot3d_knn_classification.png")
 }
 ```

docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   book-env:
-    image: ubcdsci/intro-to-ds:v0.12.0
+    image: ubcdsci/intro-to-ds:v0.16.0
     ports:
       - "8787:8787"
     volumes:
@@ -10,5 +10,5 @@ services:
     deploy:
       resources:
         limits:
-          memory: 4G
+          memory: 5G
 

regression1.Rmd

@@ -5,6 +5,7 @@ library(knitr)
 library(plotly)
 
 knitr::opts_chunk$set(fig.align = "center")
+reticulate::use_miniconda('r-reticulate')
 ```
 
 ## Overview 
@@ -797,6 +798,9 @@ plot_3d <- plot_ly() |>
 if(!is_latex_output()){  
   plot_3d
 } else {
+  scene = list(camera = list(eye = list(x=2, y=2, z = 1.5)))
+  plot_3d <- plot_3d  %>% layout(scene = scene)
+  save_image(plot_3d, "img/plot3d_knn_regression.png", scale = 10)
   knitr::include_graphics("img/plot3d_knn_regression.png")
 }
 ```

regression2.Rmd

@@ -5,6 +5,7 @@ library(knitr)
 library(plotly)
 
 knitr::opts_chunk$set(fig.align = "center")
+reticulate::use_miniconda('r-reticulate')
 ```
 
 ## Overview 
@@ -491,6 +492,9 @@ plot_3d <- plot_ly() |>
 if(!is_latex_output()){  
   plot_3d
 } else {
+  scene = list(camera = list(eye = list(x=2, y=2, z = 1.5)))
+  plot_3d <- plot_3d  %>% layout(scene = scene)
+  save_image(plot_3d, "img/plot3d_linear_regression.png", scale = 10)
   knitr::include_graphics("img/plot3d_linear_regression.png")
 }
 ```