gggenomes (version 1.0.1)

pick: Pick bins and seqs by name or position

Description

Pick which bins and seqs to show and in what order. Uses dplyr::select()-like syntax, which means unquoted genome names, positional arguments and selection helpers, such as tidyselect::starts_with() are supported. Renaming is not supported.

Usage

pick(x, ...)
pick_seqs(x, ..., .bins = everything())
pick_seqs_within(x, ..., .bins = everything())
pick_by_tree(x, tree, infer_bin_id = .data$label)

Value

gggenomes object with selected bins and seqs.

gggenomes object with selected seqs.

gggenomes object with selected seqs.

gggenomes object with seqs selected by tree order.

Arguments

x

gggenomes object

...

bins/seqs to pick, select-like expression.

.bins

scope for positional arguments, select-like expression, enclose multiple arguments with c()!

tree

a phylogenetic tree in ggtree::ggtree or ape::ape-package-"phylo" format.

infer_bin_id

an expression to extract bin_ids from the tree data.

Functions

• pick(): pick bins by bin_id, positional argument (start at top) or select-helper.

• pick_seqs(): pick individual seqs seq_id, positional argument (start at top left) or select-helper.

• pick_seqs_within(): pick individual seqs but only modify bins containing those seqs, keep rest as is.

• pick_by_tree(): align bins with the leaves in a given phylogenetic tree.

Details

Use the dots to select bins or sequences (depending on function suffix), and the .bins argument to set the scope for positional arguments. For example, pick_seqs(1) will pick the first sequence from the first bin, while pick_seqs(1, .bins=3) will pick the first sequence from the third bin.

Examples

s0 <- tibble::tibble(
  bin_id = c("A", "B", "B", "B", "C", "C", "C"),
  seq_id = c("a1", "b1", "b2", "b3", "c1", "c2", "c3"),
  length = c(1e4, 6e3, 2e3, 1e3, 3e3, 3e3, 3e3)
)

p <- gggenomes(seqs = s0) + geom_seq(aes(color = bin_id), size = 3) +
  geom_bin_label() + geom_seq_label() +
  expand_limits(color = c("A", "B", "C"))
p

# remove
p %>% pick(-B)

# select and reorder, by ID and position
p %>% pick(C, 1)

# use helper function
p %>% pick(starts_with("B"))

# pick just some seqs
p %>% pick_seqs(1, c3)

# pick with .bin scope
p %>% pick_seqs(3:1, .bins = C)

# change seqs in some bins, but keep rest as is
p %>% pick_seqs_within(3:1, .bins = B)

# same w/o scope, unaffected bins remain as is
p %>% pick_seqs_within(b3, b2, b1)

# Align sequences with and plot next to a phylogenetic tree
library(patchwork) # arrange multiple plots
library(ggtree) # plot phylogenetic trees

# load and plot a phylogenetic tree
emale_mcp_tree <- read.tree(ex("emales/emales-MCP.nwk"))
t <- ggtree(emale_mcp_tree) + geom_tiplab(align = TRUE, size = 3) +
  xlim(0, 0.05) # make room for labels

p <- gggenomes(seqs = emale_seqs, genes = emale_genes) +
  geom_seq() + geom_seq() + geom_bin_label()

# plot next to each other, but with
# different order in tree and genomes
t + p + plot_layout(widths = c(1, 5))

# reorder genomes to match tree order
# with a warning caused by mismatch in y-scale expansions
t + p %>% pick_by_tree(t) + plot_layout(widths = c(1, 5))

# extra genomes are dropped with a notification
emale_seqs_more <- emale_seqs
emale_seqs_more[7, ] <- emale_seqs_more[6, ]
emale_seqs_more$seq_id[7] <- "One more genome"
p <- gggenomes(seqs = emale_seqs_more, genes = emale_genes) +
  geom_seq() + geom_seq() + geom_bin_label()
t + p %>% pick_by_tree(t) + plot_layout(widths = c(1, 5))

try({
  # no shared ids will cause an error
  p <- gggenomes(seqs = tibble::tibble(seq_id = "foo", length = 1)) +
    geom_seq() + geom_seq() + geom_bin_label()
  t + p %>% pick_by_tree(t) + plot_layout(widths = c(1, 5))

  # extra leafs in tree will cause an error
  emale_seqs_fewer <- slice_head(emale_seqs, n = 4)
  p <- gggenomes(seqs = emale_seqs_fewer, genes = emale_genes) +
    geom_seq() + geom_seq() + geom_bin_label()
  t + p %>% pick_by_tree(t) + plot_layout(widths = c(1, 5))
})