mattgalbraith

# Ignore .DS_Store
.DS_Store

# Ignore R image files
rdata/*RData

#####################################
# From Github R .gitignore template #
#####################################
# History files

mattgalbraith

cat download_links.txt | xargs -P 1 wget --content-disposition --trust-server-names -nv -a wget_downloading.log

mattgalbraith

Set up new GitHub repo and push from local

1. Create local repo and create/add/edit required files and dirs
   eg README.md, Dockerfile, .gitignore, .github/workflows/docker-image.yml

2. On GitHub select "New repository" from the "+" menu and set name to match local repo.
   Do not add any template files.

3. Initialize up local repo and push to GitHub:
   (assumes currently in local repo root dir)

mattgalbraith

# get standard ggplot colors
gg_color_hue <- function(n) {
  hues = seq(15, 375, length = n + 1)
  hcl(h = hues, l = 65, c = 100)[1:n]
}

mattgalbraith

obj_size <- function(x) object.size(x) %>% print(units = "auto")

mattgalbraith

mem_used <- function() lobstr::mem_used() %>% as.numeric() %>% R.utils::hsize()

mattgalbraith

## Excel export function
export_excel <- function(named_list, filename = "") {
  wb <- openxlsx::createWorkbook()
  ## Loop through the list of split tables as well as their names
  ## and add each one as a sheet to the workbook
  Map(function(data, name){
    openxlsx::addWorksheet(wb, name)
    openxlsx::writeData(wb, name, data)
  }, named_list, names(named_list))
  ## Save workbook to working directory

mattgalbraith

## Density color function
# usage:
# tbl |> 
#     mutate(density = getDenCols(x, y, transform = TRUE)) |> # transformation here must match aes()
#     arrange(density) |> # ensures highest desity points on top
#     ggplot(aes(log2(x), log2(y), color = density)) +
#     geom_point() +
#     scale_color_vididis_c() # works best with viridis
getDenCols <- function(x, y, transform = TRUE) { # set to TRUE if using log2 transformation of data
  if(transform) {

mattgalbraith

# See https://usethis.r-lib.org/articles/git-credentials.html
# Need to periodically add/update personal access token (PAT) for Github

# check token status and git details
usethis::gh_token_help()
usethis::git_sitrep()

# To generate a new PAT (takes you to a pre-filled form to create a new PAT)
usethis::create_github_token() 

mattgalbraith

## Setting and modifying default theme for plots
theme_set(theme_gray(base_size=12, base_family="Arial") +
            theme(
              panel.border=element_rect(colour="black", fill="transparent"), 
              plot.title=element_text(face="bold", hjust=0),
              axis.text=element_text(color="black", size=14), 
              axis.text.x=element_text(angle=0, hjust=0.5),
              axis.ticks = element_line(color = "black"), # make sure tick marks are black
              panel.background=element_blank(),
              panel.grid=element_blank(),