write a brief informative commit message

howework#12.Rmd

@@ -1,65 +1,222 @@
 ---
-title: "Vignette Title"
-author: "Vignette Author"
-date: "`r Sys.Date()`"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{Vignette Title}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
+title: "Homework #12"
+mainfont: DejaVu Sans
+output:
+  html_document: default
+  pdf_document:
+    latex_engine: xelatex
+  word_document: default
+font-family: Times New Roman
 ---
 
-```{r setup, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-```
-
-Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The `html_vignette` output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The `html_vignette` format:
+## Pckages
 
-- Never uses retina figures
-- Has a smaller default figure size
-- Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style
+```{r echo=FALSE, message=FALSE, warning=FALSE}
+library(ggstatsplot)
+library(palmerpenguins)
+library(tidyverse)
+library(patchwork)
+library(plotly)
 
-## Vignette Info
+```
 
-Note the various macros within the `vignette` section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the `title` field and the `\VignetteIndexEntry` to match the title of your vignette.
 
-## Styles
+## Experimenting with rendering
+
+```{r echo=FALSE, message=FALSE, warning=FALSE}
+data("penguins", package = "palmerpenguins")
+penguins <- drop_na(penguins)
+```
 
-The `html_vignette` template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:
+## Histogram
+```{r echo=FALSE, message=FALSE, warning=FALSE}
+
+hist <- ggplot(data = penguins, aes(x = flipper_length_mm)) +
+  geom_histogram(aes(fill = species), 
+                 color = "black",            # Add black outline to bars
+                 alpha = 0.5, 
+                 position = "identity",
+                 binwidth = 5) +            # Adjust bin width as needed
+  scale_fill_manual(values = c("darkblue", "red", "cyan4")) +
+  labs(x = "Flipper length (mm)",
+       y = "Frequency",
+       title = "Flipper") +
+  theme(panel.background = element_rect(fill = "lightgray"),  # Add background color
+        panel.grid.major = element_line(color = "white", size = 0.5),  # Add grid lines
+        panel.grid.minor = element_line(color = "white", size = 0.25))
+
+hist
+
+# # Convert ggplot to interactive plot
+# hist_interactive  <- ggplotly(hist)
+# 
+# hist_interactive 
 
-    output: 
-      rmarkdown::html_vignette:
-        css: mystyles.css
+```
 
-## Figures
+## Interactive plot
+```{r echo=FALSE, message=FALSE, warning=FALSE}
+# Initial bin width
+initial_binwidth <- 5
+
+# Function to create histogram
+create_histogram <- function(binwidth) {
+  ggplot(data = penguins, aes(x = flipper_length_mm)) +
+    geom_histogram(aes(fill = species), 
+                   color = "black",
+                   alpha = 0.5, 
+                   position = "identity",
+                   binwidth = binwidth) +
+    scale_fill_manual(values = c("darkblue", "red", "cyan4")) +
+    labs(x = "Flipper length (mm)",
+         y = "Frequency",
+         title = "Flipper ") +
+    theme(panel.background = element_rect(fill = "lightgray"),
+          panel.grid.major = element_line(color = "white", size = 0.5),
+          panel.grid.minor = element_line(color = "white", size = 0.25))
+}
+
+# Create initial plot
+histogram <- create_histogram(initial_binwidth)
+
+# Convert ggplot to plotly
+histogram_plotly <- ggplotly(histogram)
+
+# Add slider for bin width
+histogram_plotly <- histogram_plotly %>%
+  layout(
+    updatemenus = list(
+      list(
+        active = 0,
+        buttons = list(
+          list(
+            label = "Bin Width",
+            method = "update",
+            args = list(list(visible = c(TRUE, FALSE)),
+                        list(title = "Bin Width",
+                             xaxis = list(title = "Flipper length (mm)"),
+                             yaxis = list(title = "Frequency")))),
+          list(
+            label = "5",
+            method = "update",
+            args = list(list(visible = c(TRUE, FALSE)),
+                        list(title = "Bin Width",
+                             xaxis = list(title = "Flipper length (mm)"),
+                             yaxis = list(title = "Frequency")),
+                        list(binwidth = 5))),
+          list(
+            label = "10",
+            method = "update",
+            args = list(list(visible = c(TRUE, FALSE)),
+                        list(title = "Bin Width",
+                             xaxis = list(title = "Flipper length (mm)"),
+                             yaxis = list(title = "Frequency")),
+                        list(binwidth = 10)))
+        )
+      )
+    )
+  )
+
+# Show plot
+histogram_plotly
+```
+## Scatter plot
+```{r echo=FALSE, message=FALSE, warning=FALSE}
+point <- ggplot(data = penguins, 
+                       aes(x = flipper_length_mm,
+                           y = body_mass_g)) +
+  geom_point(aes(color = species, 
+                 shape = species),
+             size = 6,
+             alpha = 0.8) +
+  geom_smooth(method = "lm", se = FALSE, color = "black", linetype = "dashed") +  # Add a trend line
+  scale_color_manual(values = c("darkblue","red","cyan4")) +
+  scale_shape_manual(values = c(16, 17, 15)) +  # Modify point shapes
+  labs(title = "Penguin size",
+       subtitle = "Flipper length and body mass",
+       x = "Flipper length (mm)",
+       y = "Body mass (g)",
+       color = "Penguin species",
+       shape = "Penguin species") +
+  theme(legend.position = "right",  # Adjust legend position
+        plot.title.position = "plot",
+        plot.caption = element_text(hjust = 0, face= "italic"),
+        plot.caption.position = "plot")
+
+point
+
+ggplotly(point)
 
-The figure sizes have been customised so that you can easily put two images side-by-side. 
+```
 
-```{r, fig.show='hold'}
-plot(1:10)
-plot(10:1)
+## Statistical plot
+```{r echo=FALSE, message=FALSE, warning=FALSE}
+stat_plot <- ggbetweenstats(
+  data = penguins,
+  x = species,
+  y = bill_length_mm
+)
+stat_plot  <- stat_plot  + 
+  # Add labels and title
+  labs(
+    x = "Penguins Species",
+    y = "Bill Length",
+    title = "Distribution of bill length across penguins species"
+  ) + 
+  # Customizations
+  theme(
+    # This is the new default font in the plot
+    text = element_text(family = "Roboto", size = 8, color = "black"),
+    plot.title = element_text(
+      family = "Lobster Two", 
+      size = 20,
+      face = "bold",
+      color = "#2a475e"
+    ),
+    # Statistical annotations below the main title
+    plot.subtitle = element_text(
+      family = "Roboto", 
+      size = 15, 
+      face = "bold",
+      color="#1b2838"
+    ),
+    plot.title.position = "plot", # slightly different from default
+    axis.text = element_text(size = 10, color = "black"),
+    axis.title = element_text(size = 12)
+  )
+# stat_plot 
+
+stat_plot  <- stat_plot   +
+  theme(
+    axis.ticks = element_blank(),
+    axis.line = element_line(colour = "grey50"),
+    panel.grid = element_line(color = "#b4aea9"),
+    panel.grid.minor = element_blank(),
+    panel.grid.major.x = element_blank(),
+    panel.grid.major.y = element_line(linetype = "dashed"),
+    panel.background = element_rect(fill = "#fbf9f4", color = "#fbf9f4"),
+    plot.background = element_rect(fill = "#fbf9f4", color = "#fbf9f4")
+  )
+stat_plot + facet_wrap(~species, scales = "free_y")
 ```
 
-You can enable figure captions by `fig_caption: yes` in YAML:
 
-    output:
-      rmarkdown::html_vignette:
-        fig_caption: yes
+## Multiple plots in ggplot2 with patchwork
+
+```{r echo=FALSE, message=FALSE, warning=FALSE}
+point + hist + stat_plot + plot_layout(ncol = 1, nrow = 3)
 
-Then you can use the chunk option `fig.cap = "Your figure caption."` in **knitr**.
+stat_plot + {
+  hist + 
+    point + 
+    plot_layout(ncol = 1)
+} +
+  plot_layout(ncol = 1, heights = c(2,1,1))
 
-## More Examples
+(stat_plot / hist) | point
 
-You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using `knitr::kable()`.
 
-```{r, echo=FALSE, results='asis'}
-knitr::kable(head(mtcars, 10))
+(stat_plot | hist) / point
 ```
 
-Also a quote using `>`:
 
-> "He who gives up [code] safety for [code] speed deserves neither."
-([via](https://twitter.com/hadleywickham/status/504368538874703872))