R Graphics Exercise

Do exercises 1-4 and if you have lots of time, exercise 5. In each case, your aim is to create a figure similar to the one shown for the pilot data set.

library(tidyverse)

Registered S3 methods overwritten by 'ggplot2':
  method         from
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1     ✔ purrr   0.3.2
✔ tibble  2.1.2     ✔ dplyr   0.8.1
✔ tidyr   0.8.3     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

options(repr.plot.width=4, repr.plot.height=3)

data <- read_tsv('data/gene_counts_raw.txt')

Parsed with column specification:
cols(
  .default = col_double(),
  Label = col_character(),
  Media = col_character(),
  Strain = col_character()
)
See spec(...) for full column specifications.

0. The Label column has 3 pieces of information Sample, Method andd Person in a single cell. Fix this and save the tidy DataFrame as df.

1. Plot a scatter plot of gene100 against gene 1001. Color points by the method used. Save the image as a PNG file ‘fig1.png’ in the ‘figs’ folder.

2. Make a boxplot plot of gene100 counts by method.

3. Make a jitter plot of gene100 counts by Media and color the points by method. Set the jitter width to be 0.2.

4. Make a grid of histograms of counts for gene100, with rows showing the person and columns showing the method used.

5. Make a row of boxplots of log counts of the top 5 genes where each column shows a different method.

Warning: This involves quite a bit of data processing.