Plot genomes, features and synteny maps

Source: R/gggenomes.R

gggenomes() initializes a gggenomes-flavored ggplot object. It is used to declare the input data for gggenomes' track system.

(See for more details on the track system, gggenomes vignette or the Details/Arguments section)

gggenomes(
  genes = NULL,
  seqs = NULL,
  feats = NULL,
  links = NULL,
  .id = "file_id",
  spacing = 0.05,
  wrap = NULL,
  adjacent_only = TRUE,
  infer_bin_id = seq_id,
  infer_start = min(start, end),
  infer_end = max(start, end),
  infer_length = max(start, end),
  theme = c("clean", NULL),
  .layout = NULL,
  ...
)

Arguments

genes, feats

A data.frame, a list of data.frames, or a character vector with paths to files containing gene data. Each item is added as feature track.

For a single data.frame the track_id will be "genes" and "feats", respectively. For a list, track_ids are parsed from the list names, or if names are missing from the name of the variable containing each data.frame. Data columns:

  • required: seq_id,start,end

  • recognized: strand,bin_id,feat_id,introns

seqs

A data.frame or a character vector with paths to files containing sequence data. Data columns:

  • required: seq_id,length

  • recognized: bin_id,start,end,strand

links

A data.frame or a character vector with paths to files containing link data. Each item is added as links track. Data columns:

  • required: seq_id,seq_id2

  • recognized: start,end,bin_id,start2,end2,bin_id2,strand

.id

The name of the column for file labels that are created when reading directly from files. Defaults to "file_id". Set to "bin_id" if every file represents a different bin.

spacing

between sequences in bases (>1) or relative to longest bin (<1)

wrap

wrap bins into multiple lines with at most this many nucleotides per lin.

adjacent_only

Indicates whether links should be created between adjacent sequences/chromosomes only. By default it is set to adjacent_only = TRUE. If FALSE, links will be created between all sequences

(not recommended for large data sets)

infer_length, infer_start, infer_end, infer_bin_id

used to infer pseudo seqs if only feats or links are provided, or if no bin_id column was provided. The expressions are evaluated in the context of the first feat or link track.

By default subregions of sequences from the first to the last feat/link are generated. Set infer_start to 0 to show all sequences from their true beginning.

theme

choose a gggenomes default theme, NULL to omit.

.layout

a pre-computed layout from layout_genomes(). Useful for developmental purposes.

Value

gggenomes-flavored ggplot object

Details

gggenomes::gggenomes() resembles the functionality of ggplot2::ggplot(). It is used to construct the initial plot object, and is often followed by "+" to add components to the plot (e.g. "+ geom_gene()").

A big difference between the two is that gggenomes has a multi-track setup ('seqs', 'feats', 'genes' and 'links'). gggenomes() pre-computes a layout and adds coordinates (y,x,xend) to each data frame prior to the actual plot construction. This has some implications for the usage of gggenomes:

  • Data frames for tracks have required variables. These predefined variables are used during import to compute x/y coordinates (see arguments).

  • gggenomes' geoms can often be used without explicit aes() mappings This works because we always know the names of the plot variables ahead of time: they originate from the pre-computed layout, and we can use that information to set sensible default aesthetic mappings for most cases.

Examples

# Compare the genomic organization of three viral elements
# EMALEs: endogenous mavirus-like elements (example data shipped with gggenomes)
gggenomes(emale_genes, emale_seqs, emale_tirs, emale_ava) +
  geom_seq() + geom_bin_label() +                  # chromosomes and labels
  geom_feat(size=8) +                              # terminal inverted repeats
  geom_gene(aes(fill=strand), position="strand") + # genes
  geom_link(offset = 0.15)                         # synteny-blocks
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.


# with some more information
gggenomes(emale_genes, emale_seqs, emale_tirs, emale_ava) %>%
  add_feats(emale_ngaros, emale_gc) %>%
  add_clusters(emale_cogs) %>%
  flip_by_links() +
  geom_link(offset = 0.15, color="white") +                        # synteny-blocks
  geom_seq() + geom_bin_label() +                                  # chromosomes and labels
  # thistle4, salmon4, burlywood4
  geom_feat(size=6, position="identity") +                         # terminal inverted repeats
  geom_feat(data=feats(emale_ngaros), color="turquoise4", alpha=.3,
            position="strand", size=16) +
  geom_feat_note(aes(label=type), data=feats(emale_ngaros),
                 position="strand", nudge_y = .3) +
  geom_gene(aes(fill=cluster_id), position="strand") + # genes
  scale_fill_brewer("Conserved genes", palette="Dark2", na.value = "cornsilk3") +
  #scale_fill_viridis_b() +
  geom_ribbon(aes(x=(x+xend)/2, ymax=y+.24, ymin=y+.38-(.4*score),
                  group=seq_id, linetype="GC-content"), feats(emale_gc),
              fill="lavenderblush4", position=position_nudge(y=-.1))
#> Joining with `by = join_by(feat_id)`
#> Flipping: 2,3,4


# initialize plot directly from files
gggenomes(
  ex("emales/emales.gff"),
  ex("emales/emales.gff"),
  ex("emales/emales-tirs.gff"),
  ex("emales/emales.paf")
) + geom_seq() + geom_gene() + geom_feat() + geom_link()
#> Reading 'gff3' with `read_gff3()`:
#> * file_id: emales [/home/runner/work/_temp/Library/gggenomes/extdata/emales/emales.gff]
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
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#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
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#> Warning: 'length(x) = 4 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 4 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 4 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 5 > 1' in coercion to 'logical(1)'
#> Harmonizing attribute names
#> • ID -> feat_id
#> • Name -> name
#> • Note -> note
#> Features read
#> # A tibble: 1 × 3
#>   source type      n
#>   <chr>  <chr> <int>
#> 1 MFG    CDS     143
#> Reading 'gff3' with `read_gff3()`:
#> * file_id: emales-tirs [/home/runner/work/_temp/Library/gggenomes/extdata/emales/emales-tirs.gff]
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> Harmonizing attribute names
#> • ID -> feat_id
#> • Name -> name
#> Features read
#> # A tibble: 1 × 3
#>   source type              n
#>   <chr>  <chr>         <int>
#> 1 MFG    repeat_region    12
#> Reading 'paf' with `read_paf()`:
#> * file_id: emales [/home/runner/work/_temp/Library/gggenomes/extdata/emales/emales.paf]
#> Warning: Found tags in max_tags column, you should increase max_tags to
#> Read and tidied up a .paf file with 10 optional tag fields:
#> NM, ms, AS, nn, tp, cm, s1, de, rl, cg
#> Note: warnings about fewer than expected columns are expected for this format.
#> Note: .paf files use 0-based coordinate starts - transforming to 1-based
#> Reading 'gff3' with `read_seq_len()`:
#> * file_id: emales [/home/runner/work/_temp/Library/gggenomes/extdata/emales/emales.gff]


# multi-contig genomes wrap to fixed width
s0 <- read_seqs(list.files(ex("cafeteria"), "Cr.*\\.fa", full.names = TRUE))
#> Reading 'fasta' with `read_seq_len()`:
#> * file_id: CrBVI [/home/runner/work/_temp/Library/gggenomes/extdata/cafeteria/CrBVI.fa]
#> * file_id: CrCflag [/home/runner/work/_temp/Library/gggenomes/extdata/cafeteria/CrCflag.fa]
#> * file_id: CrE410P [/home/runner/work/_temp/Library/gggenomes/extdata/cafeteria/CrE410P.fa]
#> * file_id: CrRCC970 [/home/runner/work/_temp/Library/gggenomes/extdata/cafeteria/CrRCC970.fa]
s1 <- s0 %>% filter(length > 5e5)
gggenomes(seqs=s1, infer_bin_id=file_id, wrap=5e6) +
  geom_seq() + geom_bin_label() + geom_seq_label()