Merge pull request #50 from reconhub/slide_bag

Slide bag

content/post/lecture-bag-of-slides.Rmd

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+---
+title: A bag of slides
+author: Thibaut Jombart
+authors: ["Thibaut Jombart"]
+categories: ["lectures"]
+topics: ["rmarkdown", "data science", "reproducibility", "ggplot2"]
+date: 2018-11-15
+image: img/highres/suitcase.jpg
+slug: bag_of_slides
+showonlyimage: true
+css: css/custom.css
+licenses: CC-BY
+---
+
+
+```{r options, include = FALSE}
+library(knitr)
+opts_chunk$set(collapse = TRUE)
+```
+
+
+# Collection of miscellaneous slides
+
+This is a collection of short slide decks on various topics, too short to form a
+lecture, but useful every now and then.
+
+
+
+## Importing data into R
+
+**Click on the image below to access the slides:**
+
+<center>
+<a href="../../slides/slides_bag/import_data.html"><img class="gateway" src="../../img/highres/old_photographs.jpg" width="50%" alt="click there for slides" align="middle"></a>
+</center>
+
+
+
+
+## Graphics using *ggplot2*
+
+**Click on the image below to access the slides:**
+
+<center>
+<a href="../../slides/slides_bag/ggplot2.html"><img class="gateway" src="../../img/highres/old_photographs.jpg" width="50%" alt="click there for slides" align="middle"></a>
+</center>
+
+
+
+
+
+# About this document
+
+## Contributors
+
+- Thibaut Jombart: initial version
+
+Contributions are welcome via [pull requests](https://github.com/reconhub/learn/pulls). The source files include:
+
+- [**import data slides**](https://raw.githubusercontent.com/reconhub/learn/master/static/slides/slides_bag/import_data.Rmd)
+
+- [**this post**](https://raw.githubusercontent.com/reconhub/learn/master/content/post/bag_of_slides.Rmd)
+
+
+
+## Legal stuff
+
+**License**: [CC-BY](https://creativecommons.org/licenses/by/3.0/)
+**Copyright**: Thibaut Jombart, 2017 

content/post/lecture-bag-of-slides.md

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+---
+title: A bag of slides
+author: Thibaut Jombart
+authors: ["Thibaut Jombart"]
+categories: ["lectures"]
+topics: ["rmarkdown", "data science", "reproducibility", "ggplot2"]
+date: 2018-11-15
+image: img/highres/suitcase.jpg
+slug: bag_of_slides
+showonlyimage: true
+css: css/custom.css
+licenses: CC-BY
+---
+
+Collection of miscellaneous slides
+==================================
+
+This is a collection of short slide decks on various topics, too short to form a lecture, but useful every now and then.
+
+Importing data into R
+---------------------
+
+**Click on the image below to access the slides:**
+
+<center>
+<a href="../../slides/slides_bag/import_data.html"><img class="gateway" src="../../img/highres/old_photographs.jpg" width="50%" alt="click there for slides" align="middle"></a>
+</center>
+Graphics using *ggplot2*
+------------------------
+
+**Click on the image below to access the slides:**
+
+<center>
+<a href="../../slides/slides_bag/ggplot2.html"><img class="gateway" src="../../img/highres/old_photographs.jpg" width="50%" alt="click there for slides" align="middle"></a>
+</center>
+About this document
+===================
+
+Contributors
+------------
+
+-   Thibaut Jombart: initial version
+
+Contributions are welcome via [pull requests](https://github.com/reconhub/learn/pulls). The source files include:
+
+-   [**import data slides**](https://raw.githubusercontent.com/reconhub/learn/master/static/slides/slides_bag/import_data.Rmd)
+
+-   [**this post**](https://raw.githubusercontent.com/reconhub/learn/master/content/post/bag_of_slides.Rmd)
+
+Legal stuff
+-----------
+
+**License**: [CC-BY](https://creativecommons.org/licenses/by/3.0/) **Copyright**: Thibaut Jombart, 2017

static/slides/slides_bag/ggplot2.Rmd

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+---
+title: "Making graphics using *ggplot2*"
+author: "Thibaut Jombart"
+date: "2018-11-15"
+output:
+  ioslides_presentation:
+    incremental: false
+---
+
+<style>
+img {
+    border-radius: 8px;
+	box-shadow: 5px 5px 5px #999;
+}
+</style>
+
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(collapse = TRUE, out.width = "60%",
+                      warning = FALSE, message = FALSE,
+                      tidy = FALSE, fig.align = "center")
+```
+
+
+## A simple example: Fisher's Iris
+
+<center>
+<img src="../../img/slides/iris.jpg" width="35%"></a>
+</center>
+
+<br>
+
+```{r fisher}
+head(iris)
+```
+
+
+## The basic graphics system
+
+Functions create graphics, example with Fisher's Iris:
+
+```{r basic-plot}
+hist(iris$Petal.Length, col = "grey", border = "white",
+     main = "Example of a histogram", xlab = "Fisher's Iris: petal length")
+```
+
+
+
+## *ggplot2*: treating graphics as objects
+
+Functions create a graphical object:
+
+```{r ggplot2-plot, echo = -1}
+library(ggplot2)
+my_plot <- ggplot(iris) + geom_histogram(aes(Petal.Length)) +
+  labs(title = "Example of a histogram",
+       x = "Fisher's Iris: petal length")
+my_plot
+```
+
+
+
+## A grammar for graphics
+
+*ggplot2* builds graphics one component at a time. The grammar includes:
+
+- `ggplot()`: to provide the data
+- `geom_...`: to define the type of graph
+- `aes()`: to map features of data into *aesthetic* properties (e.g. shapes, colors)
+
+
+```{r eval = FALSE}
+my_plot <- ggplot(iris) + # use 'iris' data.frame
+  geom_histogram(aes(Petal.Length)) + # hist using petal length
+  labs(title = "Example of a histogram", # add title
+       x = "Fisher's Iris: petal length") # add x label
+```
+
+
+
+## Making customisation easy
+
+For instance, to color histograms by species:
+
+```{r iris_colors}
+my_plot + aes(fill = Species)
+```
+
+
+
+
+## Making customisation easy: scatterplot
+
+
+```{r iris_scatterplot}
+my_plot <- ggplot(iris, aes(x = Petal.Length, y = Sepal.Length)) +
+  geom_point(aes(color = Species, shape = Species),
+             size = 5, alpha = .75) +
+  geom_smooth() +
+  labs(title = "Example of a scatterplot")
+my_plot
+```
+
+
+
+## Going further
+
+<center>
+<img src="../../img/slides/palette.jpg" width="35%"></a>
+</center>
+
+<br>
+
+Learn more about *ggplot2*:
+
+- check the package's [website](https://ggplot2.tidyverse.org/)
+- a list of [all available `geoms_`](https://ggplot2.tidyverse.org/reference/index.html#section-layer-geoms) (types of plot)
+- a list of [`aes()` specifications](https://ggplot2.tidyverse.org/articles/ggplot2-specs.html) (colors / shapes / etc.)
+- a [gallery of extensions](http://www.ggplot2-exts.org/gallery/) to *ggplot2*
+
+
+
+
+## Useful tips: specifying your colors
+
+- select your favourite colors, e.g. using a [color picker](https://www.w3schools.com/colors/colors_picker.asp)
+- make a named vector storing these colors as `character`
+- specify your colors using e.g.:
+
+```{r custom_colors}
+col <- c(setosa = "#666699", versicolor = "#99cc00", virginica = "#b30059")
+my_plot + scale_color_manual(values = col)
+```
+
+Note that you will need to use `scale_fill_manual` for colors specified through `fill = ...`. 
+
+
+
+
+## Useful tips: using panels
+
+You can use `facet_grid(rows ~ columns)` to specify panels:
+```{r ggplot2_panels}
+new_plot <- ggplot(iris) +
+  geom_histogram(aes(x = Petal.Length, fill = Species)) +
+  scale_fill_manual(values = col) + facet_grid(Species ~  .)
+new_plot
+```
+
+
+
+## Useful tips: moving the legend
+
+Use `theme(legend.position = c(x_coord, y_coord))` to move the legend:
+
+```{r ggplot2_legend_position}
+new_plot + theme(legend.position = c(.9, .8))
+```
+
+
+
+## Useful tips: changing the theme
+
+Other *themes* are available and can be customised:
+
+```{r ggplot2_themes}
+new_plot + theme_light(base_family = "Times", base_size = 20)
+```

static/slides/slides_bag/import_data.Rmd

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+---
+title: "Importing data into R"
+author: "Thibaut Jombart"
+date: "2018-11-15"
+output:
+  ioslides_presentation:
+    incremental: false
+---
+
+<style>
+img {
+    border-radius: 8px;
+	box-shadow: 5px 5px 5px #999;
+}
+</style>
+
+
+## What data usually look like
+
+<center> 
+<img src="../../img/slides/shot_spreadsheet.png" width="75%">
+</center> 
+
+<br>
+Typical spreadsheet:
+
+- <font color="#99004d">rows</font>: observations (typically individuals)
+- <font color="#99004d">columns</font>: variables
+
+
+## What data look like in R
+
+<center> 
+<img src="../../img/slides/shot_imported_data.png" width="70%">
+</center> 
+
+<br>
+A <font color="#99004d">`data.frame`</font> is the R equivalent of a
+spreadsheet.
+
+
+## How does the magic happen
+
+<center> 
+<img src="../../img/slides/magic.png" width="35%">
+</center> 
+
+> <font color="#99004d">Basic R:</font>
+
+- `read.table("some_data.txt")` for general text files
+- `read.csv("some_data.csv")` for csv files
+
+> <font color="#99004d">In packages:</font>
+
+- `readr::read_csv("some_data.csv")` for csv files
+- `readxl::read_xlsx("some_data.xlsx")` for Excel format
+- `haven::read_dta("some_data.dta")` for Stata 
+- ...
+