dataviz 2020

This book "Fundamentals of Data Visualization` by Claus Wilke has been made fully reproducible using a Docker container. The compiled book can be read online here. The original repository of the book is in GiHub at this link, and can also be read online here.

The book is great at learning advanced visualization techniques using R without focusing too much on the code but rather on universal, timeless best practices.

The bookdown book structure resides under the folder dataviz-2020. It will be a good exercise on containers, R, Rmarkdown to make effort to compile the book from source.

Details

• R-3.6.3
• RStudio 1.2.5042
• Built using snapshots from MRAN at 2019-06-12

Build and run the image

Build the book with Docker

docker build -t fonzie/wilke:3.6.3 .

Run the book with RStudio

docker run --rm -p 8787:8787 -v /home/msfz751/docker-share/wilke:/home/rstudio/share  -e USERID=$UID -e PASSWORD=wilke  fonzie/wilke:3.6.3

or better:

docker run --rm -p 38787:8787 \
    -v /home/msfz751/docker-share/wilke:/home/rstudio/share  \
    -e USERID=$UID -e PASSWORD=wilke \
     -v ${PWD}/dataviz-2020:/home/rstudio/book \
    fonzie/wilke:3.6.3

Note. There is a script run_docker.sh that simplifies this.

Publishing the book online

Send the publishing folder /dataviz-2020/_book_final to a subtree branch in GitHub gh-pages with:

 git subtree push --prefix dataviz-2020/_book_final origin gh-pages

Packages and dependencies

Build from source

These are the packages that are not in CRAN. The following packages are not in CRAN and need to be cloned to the same folder where the Dockerfile is residing. Later they will be copied to the container and built from source. All these are in the main folder:

• colorblindr
• colorspace
• cowplot
• dviz.supp
• ggtextures
• statebins
• strapgod
• ungeviz

CRAN packages

• bookdown
• egg
• emmeans
• forcats
• foreign
• gapminder
• gganimate
• ggrepel
• ggridges
• ggthemes
• ggforce
• ggmap
• ggplot2movies
• ggspatial
• gridGraphics
• gridExtra
• geofacet
• gtable
• hexbin
• lobstr
• lwgeom
• lubridate
• magick
• maps
• maptools
• mvtnorm
• nycflights13
• nlme
• patchwork
• plot3D
• readr
• rgdal
• rgeos
• rworldmap
• rstanarm
• sf
• statebins
• tidyverse
• tidybayes
• treemapify
• transformr
• units

Other packages

At operating system level these packages need to be installed:

• libmagick++-dev
• libudunits2-dev
• libgdal20
• libgdal-dev
• libgeos-dev
• libproj-dev

These packages work for Debian 10.

Chunks that take longer time to build

In visualizing_uncertainty.Rmd

Common errors

telling_a_story.Rmd

This cannot be fixed yet.

# Error: Error: 'unitType' is not an exported object from 'namespace:grid'
# Fixed by adding eval=FALSE to chunk

figure_titles_captions.Rmd, etc.

Apparently, yhis was fixed with new version of statebins.

# Error: Error: Corrupt `grouped_df` using old (< 0.8.0) format. ℹ Strip off old grouping with `ungroup()`.
# Fixed by adding ungroup(). Disabled.

Dockerfile

FROM rocker/rstudio:3.6.3


RUN apt-get -y update \
 && apt-get -y install  \
    libxml2-dev \
    libz-dev

# Linux: pre-requisites gor GDAL, rgdal, rgeos and units
RUN apt-get install -y \
    libudunits2-dev \
    libgdal20 \
    libgdal-dev \
    libgeos-dev \ 
    libproj-dev     

# Linux: pre-requisites for magick
RUN apt-get install -y \
    libmagick++-dev


# Install R packages
RUN install2.r --error \
    egg \
    forcats \
    foreign \
    magick \
    maps \
    maptools \
    nlme \
    plot3D \
    rgdal \
    rgeos \
    sf \
    units

# Install R packages
RUN install2.r --error \
    gapminder \
    ggrepel \
    ggridges \
    ggthemes \
    ggforce \
    gridGraphics \
    ggplot2movies \
    gridExtra \
    gtable \ 
    hexbin \
    lubridate \
    nycflights13 \ 
    readr \
    treemapify \
    tidyverse \
    bookdown

# mvtnorm required by ungeviz
# rstanarm required by dviz.supp
# install statebins from source
RUN install2.r --error \
  rworldmap \
  lwgeom \
  mvtnorm \
  rstanarm

RUN install2.r --error \
  ggmap \
  geofacet \
  ggspatial
  
RUN install2.r --error \  
  emmeans \
  lobstr \
  gganimate \
  transformr


COPY colorspace /home/rstudio/pkg/colorspace
COPY strapgod /home/rstudio/pkg/strapgod
COPY ungeviz /home/rstudio/pkg/ungeviz
COPY cowplot /home/rstudio/pkg/cowplot
COPY colorblindr /home/rstudio/pkg/colorblindr
COPY dviz.supp /home/rstudio/pkg/dviz.supp
COPY ggtextures /home/rstudio/pkg/ggtextures
COPY statebins /home/rstudio/pkg/statebins

RUN Rscript -e "install.packages(c(\
  '/home/rstudio/pkg/colorspace', \
  '/home/rstudio/pkg/strapgod', \
  '/home/rstudio/pkg/ungeviz', \
  '/home/rstudio/pkg/cowplot', \
  '/home/rstudio/pkg/colorblindr', \
  '/home/rstudio/pkg/dviz.supp', \
  '/home/rstudio/pkg/ggtextures', \
  '/home/rstudio/pkg/statebins' \
  ), repos = NULL, type='source')"


RUN install2.r --error \  
  patchwork \
  tidybayes

COPY dataviz-2020 /home/rstudio/book
RUN chmod a+rwx -R /home/rstudio/book

Scripts

Build book script

#!/bin/sh

rm -rf ./_book_final/
Rscript -e "bookdown::render_book(input = 'index.Rmd', output_format = 'bookdown::gitbook', config_file = '_bookdown_final.yml')"

# copy the book to the shared folder in the host
cp -r _book_final/ ../share/

bookdown.yaml

delete_merged_file: true
new_session: yes
output_dir: "_book_final"

rmd_files: [
  "index.Rmd",

  "preface.Rmd",
  "introduction.Rmd",

  # Part I
  "aesthetic_mapping.Rmd", # completed
  "coordinate_systems_axes.Rmd", # completed
  "color_basics.Rmd", # completed
  "directory_of_visualizations.Rmd",
  "visualizing_amounts.Rmd", # completed
  "visualizing_distributions_I.Rmd", # completed
  "visualizing_distributions_II.Rmd", # completed
  "boxplots_violins.Rmd", # completed
  "visualizing_proportions.Rmd", # completed
  "nested_proportions.Rmd", # completed
  "visualizing_associations.Rmd", # completed
  "time_series.Rmd", # completed
  "visualizing_trends.Rmd", # completed
  "geospatial_data.Rmd", # completed
  "visualizing_uncertainty.Rmd", # completed

  # Part II

  "proportional_ink.Rmd", # completed
  "overlapping_points.Rmd", # completed
  "pitfalls_of_color_use.Rmd", # completed
  "redundant_coding.Rmd", # completed
  "multi-panel_figures.Rmd", # completed
  "figure_titles_captions.Rmd", # completed
  "balance_data_context.Rmd", # completed
  "small_axis_labels.Rmd", # completed
  "avoid_line_drawings.Rmd", # completed
  "no_3d.Rmd", # completed

  # Part III
  "image_file_formats.Rmd", # completed
  "choosing_visualization_software.Rmd", # completed
  "telling_a_story.Rmd", # completed
  "annotated_bibliography.Rmd",

  "technical_notes.Rmd",

  "references.Rmd"
]

common.R

set.seed(7654)
options(digits = 3)

knitr::opts_chunk$set(
  echo = FALSE,
  message = FALSE,
  warning = FALSE,
  cache = FALSE,
  #dpi = 105, # not sure why, but need to divide this by 2 to get 210 at 6in, which is 300 at 4.2in
  fig.align = 'center',
  fig.width = 6,
  fig.asp = 0.618,  # 1 / phi
  fig.show = "hold"
)

options(dplyr.print_min = 6, dplyr.print_max = 6)

library(dviz.supp)