---
title: 'Adding glyphs on scatterplot'
author: "Wayne Oldford and Zehao Xu"
date: "`r Sys.Date()`"
bibliography: references.bib
fontsize: 12pt
link-citations: yes
linkcolor: blue
output:
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  %\VignetteIndexEntry{Adding glyphs on scatterplot}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
header-includes:
- \usepackage{graphicx}
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---


```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(echo = TRUE, 
                      warning = FALSE,
                      message = FALSE,
                      fig.align = "center", 
                      fig.width = 7, 
                      fig.height = 6,
                      out.width = "60%", 
                      collapse = TRUE,
                      comment = "#>",
                      tidy.opts = list(width.cutoff = 65),
                      tidy = FALSE)
library(knitr)
set.seed(12314159)
imageDirectory <- "./images/glyph"
dataDirectory <- "./data/glyph"
path_concat <- function(path1, ..., sep="/") {
  # The "/" is standard unix directory separator and so will
  # work on Macs and Linux.
  # In windows the separator might have to be sep = "\" or 
  # even sep = "\\" or possibly something else. 
  paste(path1, ..., sep = sep)
}
library(ggplot2, quietly = TRUE)
library(dplyr, quietly = TRUE)
```

Glyphs can be used as point symbols in a scatterplot to convey more information on each point.  This information could range from providing a more evocative picture for each point (e.g., an airplane for flight data  or a team's logo for sports data) to incorporating quantitative information (e.g., the values of other variables in a serial axes or star glyph or as a Chernoff face).

In `ggmulti` we provide "glyph" layers to help add this information as point symbols on a plot [@loon].

## Polygon glyphs

Consider, for example, the lower 48 USA destinations  of "nyc" flights in 2013. Each destination could be marked as a "airplane" polygon symbol and New York city is highlighted by a blue star.

```{r glyph_ggplot, fig.width=10}
library(ggmulti)
library(nycflights13)
library(maps)

# Flight destinations
destinations <- nycflights13::airports %>% 
  dplyr::rename(dest = faa) %>% 
  dplyr::semi_join(nycflights13::flights, by = "dest") %>% 
  dplyr::mutate(tzone = gsub("America/", "", tzone)) %>% 
  dplyr::filter(lon > -151, 
                lat < 55)

# New York City coordinates
NY <- data.frame(
  lon = -73.935242,
  lat = 40.730610
)
US <- map_data("state")  %>% 
  ggplot(aes(long, lat)) +
  geom_polygon(mapping = aes(group = group), 
               color="black", fill="cornsilk") 
NYflightDestinationMap <- US + 
  geom_polygon_glyph(data = destinations,
                     mapping = aes(x = lon, y = lat),
                     fill = "pink",
                     # negate x to have each plane face west
                     polygon_x = -x_airplane, 
                     polygon_y = y_airplane,
                     alpha = 0.75) + 
  geom_polygon_glyph(data = NY,
                     mapping = aes(x = lon, y = lat),
                     polygon_x = x_star,
                     polygon_y = y_star, 
                     alpha = 0.75, 
                     fill = "blue")
NYflightDestinationMap
```

Package "ggmulti" provides several polygon coordinates that can be used in `geom_polygon_glyph`, check `help("polygon_glyph", "ggmulti")`.

## Image glyphs

We can also load image files (png, jpeg, etc) and set each image as a point glyph. Let's draw a chart of two 2020 Final NBA Teams.

```{r download images}
library(png)
img_path <- list.files(file.path(find.package(package = 'ggmulti'),
                                 "images"),
                       full.names = TRUE)
Raptors <- png::readPNG(img_path[grepl("Raptors", img_path)])
Warriors <- png::readPNG(img_path[grepl("Warriors", img_path)])
```

```{r image glyph NBA 2020}
# Golden State Coordinate
GoldenState <- data.frame(
  lon = -119.4179,
  lat = 36.7783
)

Toronto <- data.frame(
  lon = -79.3832,
  lat = 43.6532
)

# Get the Canada lakes
cdn.lakes <-  maps::map("lakes",
                        plot=FALSE,
                        fill=TRUE)$names[c(7,8,27,22, 25,
                                           68:73, 82, 85
                        )]

US + 
  geom_polygon(
    data = maps::map("world",  "Canada", fill=TRUE, plot=FALSE),
    mapping = aes(long, lat, group = group), 
    fill="#ffcccb", colour = "black"
  ) + 
  geom_polygon(
    # lakes in Canada
    data =  maps::map("lakes", cdn.lakes, plot=FALSE, fill=TRUE),
    mapping = aes(long, lat, group = group), 
    fill="lightblue", colour = "black"
  ) + 
  geom_image_glyph(data = GoldenState,
                   mapping = aes(x = lon, y = lat), 
                   images = Warriors,
                   imagewidth = 1, 
                   imageheight = 1, 
                   colour = NA) + 
  geom_image_glyph(data = Toronto,
                   mapping = aes(x = lon, y = lat), 
                   imagewidth = 1, 
                   imageheight = 1, 
                   colour = NA,
                   images = Raptors) + 
  ggtitle("2019 NBA Finals")
```

## Serialaxes glyphs

Additionally, 'serial axes' can also be drawn as glyphs. 

```{r serialaxes glyph}
ggplot(iris) +
  geom_serialaxes_glyph(
    mapping = aes(Sepal.Length, Sepal.Width, colour = Species),
     # set serial axes data set (could be different from the original data)
    serialaxes.data = iris,
    # parallel or radial axes
    axes.layout = "radial", 
     # sequence of serial axes
    axes.sequence = colnames(iris)[-5]
  )
```

In this figure, we can tell the specie 'setosa' lays on the left top corner and the glyph shape is like a triangle that is very distinguishable from the rest two species.

## Reference
