---
title: "Addins"
author:
- Josh DeClercq
- Department of Biostatistics
- Vanderbilt University Medical Center
date: "<small>`r Sys.Date()`</small>"
output:
  bookdown::html_document2: 
    df_print: paged
    toc: true
    toc_depth: 3
    toc_float: true
    number_sections: true
    number_tables: true
  pdf_document: default
header-includes:
- \usepackage{setspace}
- \usepackage{relsize}
---


# Addins
https://rstudio.github.io/rstudioaddins/#overview

RStudio addins are extensions which provide a simple mechanism for executing advanced R functions from within RStudio. 

## colourpicker
https://cran.rstudio.com/web/packages/colourpicker/vignettes/colourpicker.html


  - Write ggplot code as usual
  - rather than specify colors in the `scale_XXX_manual` settings, include the variable `CPCOLS`
  - `CPCOLS` allows the addin to access the colors in the figure
  - run the "Plot Colour Helper" addin to edit colors interactively
  - If you just need to select a color, the addin "Colour Picker" provides menu options

```{r}
require(colourpicker)


CPCOLS <- c("#DB3EE0A8", "#556B2F", "#e31a1c")

ggplot(iris, aes(Sepal.Length, Petal.Length)) +
      geom_point(aes(col = Species)) +
      scale_colour_manual(values = CPCOLS)



```

## ggThemeAssist
https://github.com/calligross/ggthemeassist

  - Allows for extensive interactive editing of ggplot appearance
  - Can make appealing, publication-worthy graphics 


```{r}
install.packages("ggThemeAssist")

require(ggThemeAssist)


ggplot(mtcars, aes(x = hp, y = mpg, colour = factor(cyl)) )+ geom_point()+ scale_colour_manual(values = CPCOLS) + 
  theme(axis.line = element_line(colour = "blue2", 
    linetype = "longdash"), axis.ticks = element_line(colour = "hotpink", 
    size = 3.1, linetype = "twodash"), panel.grid.major = element_line(linetype = "dashed"), 
    panel.grid.minor = element_line(colour = "gray96", 
        linetype = "dotdash"), axis.title = element_text(family = "serif"), 
    axis.text.x = element_text(family = "mono", 
        size = 13, vjust = 0.75, angle = 45), 
    axis.text.y = element_text(family = "mono"), 
    plot.title = element_text(family = "serif", 
        size = 21, hjust = 0.5, vjust = 2), 
    legend.text = element_text(family = "serif"), 
    legend.title = element_text(family = "serif", 
        colour = "brown3"), panel.background = element_rect(fill = "papayawhip", 
        linetype = "dashed"), plot.background = element_rect(colour = "azure", 
        size = 1.9, linetype = "dotted"), 
    legend.key = element_rect(fill = "chartreuse4", 
        linetype = "dotted"), legend.position = c(0.75, 
        0.8378)) +labs(title = "This is the title", x = "Horsey power", 
    y = "gogo", colour = "Cylinders")
```

  - Run plot, then select the "ggplot Theme Assist" addin
  - Select the figure options as you desire
  
```{r}
ggplot(mtcars, aes(x = hp, y = mpg, colour = factor(cyl)) )+ geom_point()+ scale_colour_manual(values = CPCOLS) + theme(axis.ticks = element_line(colour = "lavenderblush", 
    linetype = "dotted"), panel.grid.major = element_line(linetype = "dotdash"), 
    panel.grid.minor = element_line(linetype = "longdash"), 
    axis.text = element_text(hjust = 0, angle = 40), 
    panel.background = element_rect(fill = "lightgray"), 
    plot.background = element_rect(fill = "darkgoldenrod1")) +labs(colour = "cylinder", caption = "This is the caption")
```

## Styler
https://github.com/r-lib/styler

  - provides non-invasive pretty-printing of R source code while adhering to the tidyverse formatting rules
  - styler can be customized to format code according to other style guides too

```{r}
mtcars %>%
  tibble::rownames_to_column() %>%
  separate_rows(., rowname, sep = " ") %>%
  group_by(mpg, wt) %>%
  summarise(across(everything(), first)) %>%
  select(car = rowname, am, mpg) %>%
  ungroup() %>%
  mutate(mpg.am = mpg * am) %>%
  select(1, mpg.am) %>%
  filter(mpg.am > 10) %>%
  group_by(car) %>%
  summarise(mpg.x = sum(mpg.am)) %>%
  pivot_wider(., names_from = car, values_from = mpg.x)
```

## ViewPipeSteps
https://github.com/daranzolin/ViewPipeSteps

  - Having trouble making sense of a lengthy pipe chain? This addin allows you to see each step along the way

```{r}
require(ViewPipeSteps)

mtcars %>%
  tibble::rownames_to_column() %>%
  separate_rows(., rowname, sep = " ") %>%
  group_by(mpg, wt) %>%
  summarise(across(everything(), first)) %>%
  select(car = rowname, am, mpg) %>%
  ungroup() %>%
  mutate(mpg.am = mpg * am) %>%
  select(1, mpg.am) %>%
  filter(mpg.am > 10) %>%
  group_by(car) %>%
  summarise(mpg.x = sum(mpg.am)) %>%
  pivot_wider(., names_from = car, values_from = mpg.x)
```

## RegExplain  
https://www.garrickadenbuie.com/project/regexplain/

  - RegExplain is an RStudio addin slash utility belt for regular expressions. 
    - Interactively build your regexp
    - check the output of common string matching functions
    - consult the interactive help pages
    - use the included resources to learn regular expressions

```{r}
text <- "The quick brown fox jumps over the lazy dog"
pattern <- "[aeiou]" # perl=TRUE
replacement <- "X"

pattern <- "(The)" # perl=TRUE
replacement <- "X"
gsub(pattern, replacement, text)
```

## List of addins

https://github.com/daattali/addinslist#readme

## Very useful blog post

https://statsandr.com/blog/rstudio-addins-or-how-to-make-your-coding-life-easier/



# Open discussion

  - Any volunteers to present
  - Recommendations for presenters
  - Topics of interest
  - What not to do, common pitfalls or aggravating errors
  - Partial presentations: can combine a few presenters into one meeting