outline.md

Lesson 0

• Philosophy behind these instructional materials
• Why R?
• Introduction to R
• Getting settled in RStudio
• Setting up a project

Lesson 1

• Determine when a scatter plot is an appropriate data visualization tool
• Manipulate plotting symbols and colors to plot metadata
• Adapt existing code to achieve a goal
• Install R packages and libraries
• Axis labels
• Getting help

Lesson 2

• Data frames
• Input from and output to files
• Exploring data frames
• Clean up data frames
• Adding and modifying columns in a data frame
• Bar plots

Lesson 3

• Merging data frames
• Selecting columns from data frames
• Selecting rows from data frames
• Connecting steps in data processing with pipes
• Boolean operations

Lesson 4

• Aggregating and summarizing data by a categorical variable
• Adding columns to data frames
• Sorting data frames
• If/else statements
• Creating customized functions
• The importance of keeping code DRY

Lesson 5

• Problems with bar plots to represent mean/median values
• Strip charts
• Box plots
• Violin plots
• Factors

Lesson 6

• Scripting analysis
• Making data "tidy"
• Generating line plots
• Rarefaction curves
• Adding lines to annotate plots
• Working with text

Lesson 7

• More complex aggregation approach
• Transforming data to make them normally distributed
• Extracting columns from a data frame
• Parsing output from complex variables
• Formula notation
• Simple statistical tests
• Overlaying models on scatter plots

Lesson 8

• Complex string manipulations
• Regular expressions
• Representing taxonomic data
• Developing multistep workflow to answer a problem
• Customizing axes

To do...

• Build in project organization from the beginning
• Incorporate comments to code
• Pull out as bookdown book

Lesson 9

• Faceting
• Multiple panels
• Themes

Lesson 10

• Rmarkdown
• kable
• xtable
• citations
• paste / format / round

Lesson 11

• Putting it together: Machine learning

Lesson 12

• Putting it together:

Not covered

• Base R stuff

  • read.xxxx / write.xxxx
  • plotting options

• Non-tabular data

  • Lists
  • HTML/XML
  • JSON

• Other plot types

  • Heat maps
  • Network
  • Trees
    • rgl
    • googleViz
    • Polygons ~ back to back plot?
    • Drawing - making a mouse model
  • Text annotation of figures

• Putting it together

  • Simulations in R
    • rentrez - Pulling down web data
    • Cleveland dot plots
    • Bi-plots

• Unit tests

• Shiny app

• Building a package