analysis-vignettes's Introduction

Biological analysis vignettes

Jay Hesselberth

Ribosome footprinting

python3 ribo-profiling/rpfs_by_codon.py

Illustrates position of the “ribosome shadow” established by ribosomes stalled at histidine codons in cells starved for histidine and histidinyl-tRNAs.

library(tidyverse)
library(cowplot)

tbl <- read_tsv(
  "ribo-profiling/rpfs.iso.tsv.gz",
  col_names = c("codon", "aa", "offset", "signal")
)

tbl

## # A tibble: 1,324 x 4
##    codon aa    offset signal
##    <chr> <chr>  <dbl>  <dbl>
##  1 TCA   Ser        0  66825
##  2 TCA   Ser       -6  46632
##  3 TCA   Ser       -3  46056
##  4 TCA   Ser       -2  45570
##  5 TCA   Ser       -1  46082
##  6 TCA   Ser        1  58346
##  7 TCA   Ser       -8  33891
##  8 TCA   Ser       -7  42053
##  9 TCA   Ser       -5  35769
## 10 TCA   Ser       -4  44854
## # … with 1,314 more rows

By amino acid

group_by(tbl, aa) %>%
  mutate(prop.signal = signal / sum(signal)) %>%
  ggplot(aes(offset, prop.signal)) +
    geom_col() +
    facet_wrap(~ aa) + 
    theme_minimal_hgrid() +
    labs(
      x = "Codon offset",
      y = "Proportion of reads"
    )

By isodecoder

tbl %>%
  group_by(codon) %>%
  mutate(prop.signal = signal / sum(signal)) %>%
  ggplot(aes(offset, prop.signal)) +
    geom_col() +
    facet_wrap(~ codon) + 
    theme_minimal_hgrid() +
    labs(
      x = "Codon offset",
      y = "Proportion of reads"
    )