R Graphics Exercise (Solutions)

library(tidyverse)

Warning message:
“package ‘tidyverse’ was built under R version 3.4.2”── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 2.2.1     ✔ purrr   0.2.4
✔ tibble  1.4.2     ✔ dplyr   0.7.4
✔ tidyr   0.8.0     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0
Warning message:
“package ‘tibble’ was built under R version 3.4.3”Warning message:
“package ‘tidyr’ was built under R version 3.4.3”Warning message:
“package ‘purrr’ was built under R version 3.4.2”Warning message:
“package ‘dplyr’ was built under R version 3.4.2”Warning message:
“package ‘forcats’ was built under R version 3.4.3”── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

df <- read_tsv('data/gene_counts.txt')

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

df[1:10, 1:10]

sid	person	method	Label	Media	Strain	gene0	gene1	gene10	gene100
1	J	MA	1_MA_J	YPD	H99	1	0	13	425
1	J	RZ	1_RZ_J	YPD	H99	0	0	14	261
2	C	MA	2_MA_C	YPD	H99	0	0	10	491
2	C	RZ	2_RZ_C	YPD	H99	10	0	18	251
2	C	TOT	2_TOT_C	YPD	H99	1	0	0	14
3	J	MA	3_MA_J	YPD	H99	0	0	8	280
3	J	RZ	3_RZ_J	YPD	H99	0	0	7	168
3	J	TOT	3_TOT_J	YPD	H99	0	0	2	35
4	P	MA	4_MA_P	YPD	H99	1	0	16	571
4	P	RZ	4_RZ_P	YPD	H99	0	0	1	74

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

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.

ggplot(df, aes(x=gene100, y=gene1001, color=method)) +
geom_point()
ggsave('figs/fig1.png')

Data type cannot be displayed:

Saving 7 x 7 in image

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

ggplot(df, aes(x=method, y=gene100)) +
geom_boxplot()
ggsave('figs/fig2.png')

Data type cannot be displayed:

Saving 7 x 7 in image

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

ggplot(df, aes(x=Media, y=gene100, color=method)) +
geom_jitter(width=0.2)
ggsave('figs/fig3.png')

Data type cannot be displayed:

Saving 7 x 7 in image

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

ggplot(df, aes(x=gene100)) +
facet_grid(person ~ method) +
geom_histogram(binwidth=50)
ggsave('figs/fig4.png')

Data type cannot be displayed:

Saving 7 x 7 in image

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

Warning: This is difficult and involves quite a bit of data processing. It involves techniques of data manipulation that will covered later in the course.

genes.top5 <- df %>%
select(starts_with('gene')) %>%
summarize_all(mean) %>%
gather() %>%
arrange(desc(value)) %>%
head(5)

Warning message:
“package ‘bindrcpp’ was built under R version 3.4.4”

genes.top5

key	value
gene1139	884531.49
gene1136	484816.47
gene7418	132744.71
gene363	62325.08
gene7387	45986.86

genes.top5$key

1. 'gene1139'
2. 'gene1136'
3. 'gene7418'
4. 'gene363'
5. 'gene7387'

df %>%
select(c('method', genes.top5$key)) %>%
gather(gene, count, -method) %>%
mutate(logcount = log(count)) %>%
ggplot(aes(x=gene, y=logcount)) +
geom_boxplot() +
facet_wrap(~ method) +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
ggsave('figs/fig5.png')

Data type cannot be displayed:

Saving 7 x 7 in image