RMarkdown demo

In this illustration, the Gapminder package is used for plotting charts. This data set comes with six variables including country, continent, year, life expectancy, population and GDP per capita.

Let’s install the package, load the data and examine the dataset:

install.packages("gapminder", repos = "https://cran.r-project.org")

library(gapminder)

summary(gapminder) # Summary of Gapminder dataset
str(gapminder) # Structure of dataset
gm=gapminder
head(gm)

summary(gm)

Simple Scatterplot:

library(ggplot2)
p <- ggplot(data = gm,
            mapping = aes(x = gdpPercap,
                          y = lifeExp))  # Shows nothing. Why?
p + geom_point()

  theme_bw()

List of 59
 $ line                 :List of 6
  ..$ colour       : chr "black"
  ..$ size         : num 0.5
  ..$ linetype     : num 1
  ..$ lineend      : chr "butt"
  ..$ arrow        : logi FALSE
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_line" "element"
 $ rect                 :List of 5
  ..$ fill         : chr "white"
  ..$ colour       : chr "black"
  ..$ size         : num 0.5
  ..$ linetype     : num 1
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ text                 :List of 11
  ..$ family       : chr ""
  ..$ face         : chr "plain"
  ..$ colour       : chr "black"
  ..$ size         : num 11
  ..$ hjust        : num 0.5
  ..$ vjust        : num 0.5
  ..$ angle        : num 0
  ..$ lineheight   : num 0.9
  ..$ margin       : 'margin' num [1:4] 0pt 0pt 0pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : logi FALSE
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.title.x         :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : num 1
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 2.75pt 0pt 0pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.title.x.top     :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : num 0
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 0pt 0pt 2.75pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.title.y         :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : num 1
  ..$ angle        : num 90
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 0pt 2.75pt 0pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.title.y.right   :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : num 0
  ..$ angle        : num -90
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 0pt 0pt 0pt 2.75pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.text            :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : chr "grey30"
  ..$ size         : 'rel' num 0.8
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.text.x          :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : num 1
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 2.2pt 0pt 0pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.text.x.top      :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : num 0
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 0pt 0pt 2.2pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.text.y          :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : num 1
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 0pt 2.2pt 0pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.text.y.right    :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : num 0
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 0pt 0pt 0pt 2.2pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.ticks           :List of 6
  ..$ colour       : chr "grey20"
  ..$ size         : NULL
  ..$ linetype     : NULL
  ..$ lineend      : NULL
  ..$ arrow        : logi FALSE
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_line" "element"
 $ axis.ticks.length    : 'unit' num 2.75pt
  ..- attr(*, "valid.unit")= int 8
  ..- attr(*, "unit")= chr "pt"
 $ axis.line            : list()
  ..- attr(*, "class")= chr [1:2] "element_blank" "element"
 $ axis.line.x          : NULL
 $ axis.line.y          : NULL
 $ legend.background    :List of 5
  ..$ fill         : NULL
  ..$ colour       : logi NA
  ..$ size         : NULL
  ..$ linetype     : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ legend.margin        : 'margin' num [1:4] 5.5pt 5.5pt 5.5pt 5.5pt
  ..- attr(*, "valid.unit")= int 8
  ..- attr(*, "unit")= chr "pt"
 $ legend.spacing       : 'unit' num 11pt
  ..- attr(*, "valid.unit")= int 8
  ..- attr(*, "unit")= chr "pt"
 $ legend.spacing.x     : NULL
 $ legend.spacing.y     : NULL
 $ legend.key           :List of 5
  ..$ fill         : chr "white"
  ..$ colour       : logi NA
  ..$ size         : NULL
  ..$ linetype     : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ legend.key.size      : 'unit' num 1.2lines
  ..- attr(*, "valid.unit")= int 3
  ..- attr(*, "unit")= chr "lines"
 $ legend.key.height    : NULL
 $ legend.key.width     : NULL
 $ legend.text          :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : 'rel' num 0.8
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ legend.text.align    : NULL
 $ legend.title         :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : num 0
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ legend.title.align   : NULL
 $ legend.position      : chr "right"
 $ legend.direction     : NULL
 $ legend.justification : chr "center"
 $ legend.box           : NULL
 $ legend.box.margin    : 'margin' num [1:4] 0cm 0cm 0cm 0cm
  ..- attr(*, "valid.unit")= int 1
  ..- attr(*, "unit")= chr "cm"
 $ legend.box.background: list()
  ..- attr(*, "class")= chr [1:2] "element_blank" "element"
 $ legend.box.spacing   : 'unit' num 11pt
  ..- attr(*, "valid.unit")= int 8
  ..- attr(*, "unit")= chr "pt"
 $ panel.background     :List of 5
  ..$ fill         : chr "white"
  ..$ colour       : logi NA
  ..$ size         : NULL
  ..$ linetype     : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ panel.border         :List of 5
  ..$ fill         : logi NA
  ..$ colour       : chr "grey20"
  ..$ size         : NULL
  ..$ linetype     : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ panel.spacing        : 'unit' num 5.5pt
  ..- attr(*, "valid.unit")= int 8
  ..- attr(*, "unit")= chr "pt"
 $ panel.spacing.x      : NULL
 $ panel.spacing.y      : NULL
 $ panel.grid           :List of 6
  ..$ colour       : chr "grey92"
  ..$ size         : NULL
  ..$ linetype     : NULL
  ..$ lineend      : NULL
  ..$ arrow        : logi FALSE
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_line" "element"
 $ panel.grid.minor     :List of 6
  ..$ colour       : NULL
  ..$ size         : 'rel' num 0.5
  ..$ linetype     : NULL
  ..$ lineend      : NULL
  ..$ arrow        : logi FALSE
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_line" "element"
 $ panel.ontop          : logi FALSE
 $ plot.background      :List of 5
  ..$ fill         : NULL
  ..$ colour       : chr "white"
  ..$ size         : NULL
  ..$ linetype     : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ plot.title           :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : 'rel' num 1.2
  ..$ hjust        : num 0
  ..$ vjust        : num 1
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 0pt 0pt 5.5pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ plot.subtitle        :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : num 0
  ..$ vjust        : num 1
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 0pt 0pt 5.5pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ plot.caption         :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : 'rel' num 0.8
  ..$ hjust        : num 1
  ..$ vjust        : num 1
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 5.5pt 0pt 0pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ plot.tag             :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : 'rel' num 1.2
  ..$ hjust        : num 0.5
  ..$ vjust        : num 0.5
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ plot.tag.position    : chr "topleft"
 $ plot.margin          : 'margin' num [1:4] 5.5pt 5.5pt 5.5pt 5.5pt
  ..- attr(*, "valid.unit")= int 8
  ..- attr(*, "unit")= chr "pt"
 $ strip.background     :List of 5
  ..$ fill         : chr "grey85"
  ..$ colour       : chr "grey20"
  ..$ size         : NULL
  ..$ linetype     : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ strip.placement      : chr "inside"
 $ strip.text           :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : chr "grey10"
  ..$ size         : 'rel' num 0.8
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 4.4pt 4.4pt 4.4pt 4.4pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ strip.text.x         : NULL
 $ strip.text.y         :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : num -90
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ strip.switch.pad.grid: 'unit' num 2.75pt
  ..- attr(*, "valid.unit")= int 8
  ..- attr(*, "unit")= chr "pt"
 $ strip.switch.pad.wrap: 'unit' num 2.75pt
  ..- attr(*, "valid.unit")= int 8
  ..- attr(*, "unit")= chr "pt"
 - attr(*, "class")= chr [1:2] "theme" "gg"
 - attr(*, "complete")= logi TRUE
 - attr(*, "validate")= logi TRUE

First, we need to start the data component, then add the aesthetic mapping defining the basics (i.e. variables), followed by the geometric objects. Here is an alternative:

# Alternative
p <- ggplot(data=gm, aes(x=gdpPercap, y=lifeExp))

What is still missing?

p + geom_point()

Now, we can add more features to the chart.

# Add some color grouping
p <- ggplot(data = gm,
            mapping = aes(x = gdpPercap,
                          y = lifeExp, color=continent))
p + geom_point()

Now you can knit the Markdown file and publish it to either Rpub or your own github website!— title: “RMarkdown demo” author: “Collin DeVore” date: “March 27, 2019” output: html_document —

0.1 R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

summary(cars)

0.2 Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.