R tips and tricks

Import/Export of files

Stop using write.csv, write.table and use the rio library instead. All rio needs is the file extension to figure out what file type you're dealing with. Easy import and export to Excel files for clients.

Parsing in R using Tidyverse

This is a link to a nice tutorial from Ista Zahn from IQSS using stringr and tidyverse for parsing files in R. It is from the Computefest 2017 workshop: http://tutorials-live.iq.harvard.edu:8000/user/zwD2ioESyGbS/notebooks/workshops/R/RProgramming/Rprogramming.ipynb

Better clean default ggplot

install cowplot (https://cran.r-project.org/web/packages/cowplot/index.html)

library(cowplot)

Nice looking log scales

Example for x-axis

library(scales)
   p + scale_x_log10(
         breaks = scales::trans_breaks("log10", function(x) 10^x),
         labels = scales::trans_format("log10", scales::math_format(10^.x))) +
       annotation_logticks(sides='b')

Read a bunch of files into one dataframe

library(purrr)
library(readr)
library(dplyr)
library(tidyr)
read_files = function(files) {
  data_frame(filename = files) %>%
    mutate(contents = map(filename, ~ read_tsv(.))) %>%
    unnest()
}

remove a layer from a ggplot2 object with ggedit

plotGeneSaturation(bcb, interestingGroups=NULL) +
  ggrepel::geom_text_repel(aes(label=description, color=NULL)) 
p %>%
  ggedit::remove_geom('point', 1) +
  geom_point(aes(color=NULL))

Link to information about count normalization methods

The images currently break, but I will update when the course materials are in a more permanent state.