Add exon number

add_exon_number() adds the exon number (the order the exons are transcribed within each transcript) as a column in exons. This can be useful when visualizing long, complex transcript structures, in order to keep track of specific exons of interest.

Usage

add_exon_number(exons, group_var = NULL)

Arguments

exons

data.frame() contains exons which can originate from multiple transcripts differentiated by group_var.

group_var

character() if input data originates from more than 1 transcript, group_var must specify the column that differentiates transcripts (e.g. "transcript_id").

Value

data.frame() equivalent to input exons, with the additional column "exon_number".

Details

To note, a "strand" column must be present within exons. The strand is used to differentiate whether exon numbers should be calculated according to ascending ("+") or descending ("-") genomic co-ordinates. For ambiguous strands ("*"), add_exon_number() will be assume the strand be "+".

Examples

library(magrittr)
library(ggplot2)

# to illustrate the package's functionality
# ggtranscript includes example transcript annotation
sod1_annotation %>% head()
#> # A tibble: 6 × 8
#>   seqnames  start    end strand type  gene_name transcript_name transcript_biot…
#>   <fct>     <int>  <int> <fct>  <fct> <chr>     <chr>           <chr>           
#> 1 21       3.17e7 3.17e7 +      gene  SOD1      NA              NA              
#> 2 21       3.17e7 3.17e7 +      tran… SOD1      SOD1-202        protein_coding  
#> 3 21       3.17e7 3.17e7 +      exon  SOD1      SOD1-202        protein_coding  
#> 4 21       3.17e7 3.17e7 +      CDS   SOD1      SOD1-202        protein_coding  
#> 5 21       3.17e7 3.17e7 +      star… SOD1      SOD1-202        protein_coding  
#> 6 21       3.17e7 3.17e7 +      exon  SOD1      SOD1-202        protein_coding  

# extract exons
sod1_exons <- sod1_annotation %>% dplyr::filter(type == "exon")
sod1_exons %>% head()
#> # A tibble: 6 × 8
#>   seqnames  start    end strand type  gene_name transcript_name transcript_biot…
#>   <fct>     <int>  <int> <fct>  <fct> <chr>     <chr>           <chr>           
#> 1 21       3.17e7 3.17e7 +      exon  SOD1      SOD1-202        protein_coding  
#> 2 21       3.17e7 3.17e7 +      exon  SOD1      SOD1-202        protein_coding  
#> 3 21       3.17e7 3.17e7 +      exon  SOD1      SOD1-202        protein_coding  
#> 4 21       3.17e7 3.17e7 +      exon  SOD1      SOD1-202        protein_coding  
#> 5 21       3.17e7 3.17e7 +      exon  SOD1      SOD1-202        protein_coding  
#> 6 21       3.17e7 3.17e7 +      exon  SOD1      SOD1-204        processed_trans…

# add the exon number for each transcript
sod1_exons <- sod1_exons %>% add_exon_number(group_var = "transcript_name")

base <- sod1_exons %>%
    ggplot(aes(
        xstart = start,
        xend = end,
        y = transcript_name
    )) +
    geom_range() +
    geom_intron(
        data = to_intron(sod1_exons, "transcript_name"),
        strand = "+"
    )

# it can be useful to annotate exons with their exon number
# using ggplot2::geom_text()
base +
    geom_text(aes(
        x = (start + end) / 2, # plot label at midpoint of exon
        label = exon_number
    ),
    size = 3.5,
    nudge_y = 0.4
    )


# Or alternatively, using ggrepel::geom_label_repel()
# to separate labels from exons
base +
    ggrepel::geom_label_repel(ggplot2::aes(
        x = (start + end) / 2,
        label = exon_number
    ),
    size = 3.5,
    min.segment.length = 0
    )