codon-example.rmd

```{r echo=FALSE, results='hide', warning=FALSE}
library = function (name)
    suppressMessages(base::library(as.character(substitute(name)),
                                   character.only = TRUE,
                                   quietly = TRUE, warn.conflicts = FALSE))
library(dplyr)
library(pander)
library(knitr)

options(stringsAsFactors = FALSE)

transform_counts = function (counts, ...)
    mutate_each_(counts, funs_(lazyeval::lazy_dots(...)), col_data$Sample)

summarize_each = summarise_each

panderOptions('table.split.table', Inf)
panderOptions('table.alignment.default',
              function (df) ifelse(sapply(df, is.numeric), 'right', 'left'))
panderOptions('table.alignment.rownames', 'left')

# Enable automatic table reformatting.
opts_chunk$set(render = function (object, ...) {
    if (pander_supported(object))
        pander(object, style = 'rmarkdown')
    else if (isS4(object))
        show(object)
    else
        print(object)
})

pander_supported = function (object)
    UseMethod('pander_supported')

pander_supported.default = function (object)
    any(class(object) %in% sub('^pander\\.', '', methods('pander')))

pander.table = function (x, ...)
    pander(`rownames<-`(rbind(x), NULL), ...)

# Helpers for dplyr tables

is.tbl_df = function (x)
    inherits(x, 'tbl_df')

pander.tbl_df = function (x, ...)
    pander(trunc_mat(x), ...)

# Copied from dplyr:::print.trunc_mat
pander.trunc_mat = function (x, ...) {
    if (! is.null(x$table))
        pander(x$table, ...)

    if (length(x$extra) > 0) {
        var_types = paste0(names(x$extra), ' (', x$extra, ')', collapse = ', ')
        pander(dplyr:::wrap('Variables not shown: ', var_types))
    }
}

# Disable code re-formatting, set caching and adjust figure output
opts_chunk$set(tidy = FALSE,
               cache = TRUE,
               dev = c('png', 'pdf'),
               fig.path = 'knitr/codon/figure/',
               cache.path = 'knitr/codon/cache/')
```

The data.

```{r}
data = c(𝐴 = 'AUG GAU UAC AAA GAC AAA GAC GAC AAA UAC AUG AAG GAC UGA',
         𝐵 = 'AUG AAA UAC GAU AUG AAG GAU UAC AUG AAG UAC UAC UAC AAG UAC GAU UAC UGA')

data = strsplit(data, ' ')
# No stop codon!
levels = sort(setdiff(unique(unlist(data)), 'UGA'))
```

Codon usage.

```{r}
x = as.data.frame(sapply(sapply(data, factor, levels), table)) %>%
    add_rownames('Codon') %>%
    tbl_df()
(x = mutate(x, `𝐴 + 𝐵` = 𝐴 + 𝐵, µ = `𝐴 + 𝐵` / 2))
```

Codon usage with gene expression counts.

```{r}
(counts = list(𝐴 = 10, 𝐵 = 20))

xp = x %>% mutate_each(funs(. * counts$.), 2, 3) %>%
    mutate(`𝐴 + 𝐵` = 𝐴 + 𝐵, µ = `𝐴 + 𝐵` / 2)

xp
```

Relative codon usage.

```{r}
genetic_code = data.frame(Codon = levels,
                          AA = c('Lys', 'Lys', 'Met', 'Asp', 'Asp', 'Tyr'))

m = inner_join(genetic_code, x, by = 'Codon') %>%
    group_by(AA) %>%
    mutate_each(funs(. / sum(.)), -Codon, -AA) %>%
    ungroup()

m
```

Relative codon usage using expression counts.

```{r}
mp = inner_join(genetic_code, xp, by = 'Codon') %>%
    group_by(AA) %>%
    mutate_each(funs(. / sum(.)), -Codon, -AA) %>%
    ungroup()

mp
```