<style type="text/css">
div#TOC li {
    list-style:none;
    background-image:none;
    background-repeat:none;
    background-position:0;
}

h1.title {
  font-size: 20px;
  color: DarkRed;
  text-align: center;
}
h4.author { /* Header 4 - and the author and data headers use this too  */
    font-size: 18px;
  font-family: "Times New Roman", Times, serif;
  color: DarkRed;
  text-align: center;
}
h4.date { /* Header 4 - and the author and data headers use this too  */
  font-size: 18px;
  font-family: "Times New Roman", Times, serif;
  color: DarkBlue;
  text-align: center;
}
h1 { /* Header 3 - and the author and data headers use this too  */
    font-size: 22px;
    font-family: "Times New Roman", Times, serif;
    color: darkred;
    text-align: center;
}
h2 { /* Header 3 - and the author and data headers use this too  */
    font-size: 18px;
    font-family: "Times New Roman", Times, serif;
    color: navy;
    text-align: left;
}

h3 { /* Header 3 - and the author and data headers use this too  */
    font-size: 15px;
    font-family: "Times New Roman", Times, serif;
    color: navy;
    text-align: left;
}

h4 { /* Header 4 - and the author and data headers use this too  */
    font-size: 18px;
    font-family: "Times New Roman", Times, serif;
    color: darkred;
    text-align: left;
}
</style>

```{r setup, include=FALSE}
if (!require("knitr")) {
   install.packages("knitr")
   library(knitr)
}
if (!require("shiny")) {
   install.packages("shiny")
   library(shiny)
}
if (!require("ggplot2")) {
   install.packages("ggplot2")
   library(ggplot2)
}
if (!require("tidyverse")) {
   install.packages("tidyverse")
   library(tidyverse)
}
if (!require("dplyr")) {
   install.packages("dplyr")
   library(dplyr)
}
if (!require("flexdashboard")) {
   install.packages("flexdashboard")
   library(flexdashboard)
}
if (!require("leaflet")) {
   install.packages("leaflet")
   library(leaflet)
}
if (!require("beanplot")) {
   install.packages("beanplot")
   library(beanplot)
}


knitr::opts_chunk$set(echo = FALSE,       
                      warning = FALSE,   
                      result = TRUE,   
                      message = FALSE,
                      fig.align='center', 
                      fig.pos = 'ht')
```


### **WCU Applied Statistics** 



```{r}
wcuicon <- makeIcon(
  iconUrl = "https://github.com/pengdsci/sta553/blob/main/image/goldenRamLogo.png?raw=true", 
  iconWidth = 60, iconHeight = 60)
# define a leaflet map 
  leaflet() %>% setView(lng=-75.5978, lat=39.9522, zoom = 20) %>%
     addTiles() %>%   # Add default OpenStreetMap map tiles
     addMarkers(lng=-75.5978, lat=39.9522,  icon = wcuicon)
```

***

https://www.wcupa.edu/sciences-mathematics/mathematics/gradstat/

- WCU Applied Statistics Program offers the Master of Science Degree and Certificate in Applied Statistics.

- The programs bring together statistics, computer science, scientific research, and communication skills using the latest state-of-the-art technologies. 

- The Programs prepare students for immediate employment in a variety of high-paying industry positions or doctoral study in applied statistics or a related field.





### Iris Flowers

```{r}
include_graphics("https://raw.githubusercontent.com/pengdsci/sta553/main/shiny/iris-dataset.png")
```


***

This well-known data set has been used frequently in statistics and machine learning to illustrate 
various classification models and algorithms. We use this data set to create various descriptive plots 
to demonstrate to create visual storytelling presentation using `storyline` in **flexdashboard**.


### Distribution of Numerical Variables

```{r}
library(beanplot)
xiris <- iris
xiris$Species <- NULL
beanplot(xiris, main = "Iris flowers",col=c('#ff8080','#0000FF','#0000FF','#FF00FF'), border = "#000000")
```

***

Some stories about the distribution of width and length of sepal and petal of iris flowers......



### Plotly plots of regression related to iris data.

```{r}
myplot.theme_new <- function() {
  theme(
    #ggplot margins
     plot.margin = margin(t = 50,  # Top margin
                          r = 30,  # Right margin
                          b = 30,  # Bottom margin
                          l = 30), # Left margin
    ## ggplot titles
    plot.title = element_text(face = "bold", 
                              size = 12,
                              family = "sans", 
                              color = "navy",
                              hjust = 0.5,
                              margin=margin(0,0,30,0)), # left(0),right(1)
    # add border 1)
    panel.border = element_rect(colour = NA, 
                                fill = NA, 
                                linetype = 2),
    # color background 2)
    panel.background = element_rect(fill = "#f6f6f6"),
    # modify grid 3)
    panel.grid.major.x = element_line(colour = 'white', 
                                      linetype = 3, 
                                      size = 0.5),
    panel.grid.minor.x = element_blank(),
    panel.grid.major.y =  element_line(colour = 'white', 
                                       linetype = 3, 
                                       size = 0.5),
    panel.grid.minor.y = element_blank(),
    # modify text, axis and colour 4) and 5)
    axis.text = element_text(colour = "navy", 
                             #face = "italic", 
                             size = 7,
                             #family = "Times New Roman"
                             ),
    axis.title = element_text(colour = "navy", 
                              size = 7,
                              #family = "Times New Roman"
                              ),
    axis.ticks = element_line(colour = "navy"),
    # legend at the bottom 6)
    legend.position = "bottom",
    legend.key.size = unit(0.6, 'cm'), #change legend key size
    legend.key.height = unit(0.6, 'cm'), #change legend key height
    legend.key.width = unit(0.6, 'cm'), #change legend key width
    #legend.title = element_text(size=8), #change legend title font size
    legend.title=element_blank(),  # remove all legend titles
    legend.key = element_rect(fill = "white"),
    #####
    legend.text = element_text(size=8)) #change legend text font size
}
```




```{r}
library(plotly)
p <- ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width,
                              color = factor(Species)), linetype = Species) +
             geom_point(size = 2, alpha = 0.7) +
             stat_smooth(method = lm, se=FALSE, size = 0.3) +
             scale_color_manual(values=c("dodgerblue4", "darkolivegreen4", "darkorchid3")) +
             labs(
                 x = "Sepal Length",
                 y = "Sepal Width",
                 title = "Association between Sepal Length and Width") +
             myplot.theme_new() + 
              annotate(geom="text" , 
                       x=6.8, 
                       y=2,
                       label=paste("The Pearson correlation coefficient r = ",                          
                                   round(cor(iris$Sepal.Length, iris$Sepal.Width),3)), 
                          size = 2,
                          color = "navy") + 
               coord_fixed(1)    ## This changes the aspect ratio of the graph
ggplotly(p)
```

***

https://plot.ly/ggplot2/

If you use ggplot2, `ggplotly()` converts your plots to an interactive, web-based version! It also provides sensible tooltips, which assists decoding of values encoded as visual properties in the plot.

plotly supports some chart types that ggplot2 doesn't (such as 3D surface, point, and line plots). You can create these (or any other plotly) charts using `plot_ly()`.


### MetricsGraphics enables easy creation of D3 scatterplots, line charts, and histograms.

```{r}
library(metricsgraphics)
mjs_plot(mtcars, x=wt, y=mpg) %>%
  mjs_point(color_accessor=carb, size_accessor=carb) %>%
  mjs_labs(x="Weight of Car", y="Miles per Gallon")
```

***

https://hrbrmstr.github.io/metricsgraphics/

Building metricsgraphics charts follows the “piping” idiom made popular through the magrittr, ggvis and dplyr packages. This makes it possible to avoid one giant function with a ton of parameters and facilitates breaking out the chart building into logical steps. 

While MetricsGraphics.js charts may not have the flexibility of ggplot2, you can build functional, interactive [multi-]line, scatterplot, bar charts & histograms and + even link charts together.