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Plot the domain composition of a set of TALE arrays

Source: R/tales_plot.R
plot.tales.Rd

A compact, information-rich view of the arrays in a tales object: one point per part, positioned by its place in the array, outlined by domain type and filled by part type and amino-acid length. Each repeat carries its RVD, each terminus the short name of its code (N-, -C, or ?? for a terminus that does not match its TALE domain profile; see tales_anchor_codes). Arrays are listed from the top in alphabetical order of array_id.

The fill colours follow the role of each part. The canonical 34-aa repeat and the 20-aa half-repeat that ends every array get calm colours, so a repeat of any other length (an aberrant repeat, for instance) stands out. N-termini are shades of wine and C-termini shades of teal, lighter when shorter, which makes a truncated terminus visible. The legend gives the length of each colour, its keys outlined like the parts they stand for. All colours are chosen to stay distinct for colour-blind readers.

A tales_msa dispatches to plot.tales_msa instead, being the more specific class.

Usage

# S3 method for class 'tales'
plot(x, position = c("array", "alignment"), facet_by = "seqnames", ...)

Arguments

x

A tales object, as returned by tales_from_telltales or in the tales element of tales_compare_distal's output. A data frame of parts is accepted and converted with tales.

position

Which coordinate to lay the parts out on. "array" (default) uses position_in_array, so each array starts at 1 and runs contiguously. "alignment" uses alignment_position, which requires an aligned object (or one demoted from a tales_msa, which keeps the column): gaps then appear as empty columns and shared features line up. Aberrant repeats, for instance, are visible as a column in the aligned layout and scattered in the unaligned one.

facet_by

Names of the columns whose values split the plot into panels, stacked in rows whose height follows the number of arrays. Each column must hold one value per array: "seqnames" (the default, one panel per source sequence) or "strain" for a set of genomes, for instance, and c("strain", "seqnames") for both. NULL draws a single panel, as does the default when x has no seqnames column.

...

Unused, present for compatibility with the plot generic.

Value

A ggplot object. Like any ggplot, it is drawn when printed, which happens automatically at the console; inside a loop or a function, call print() on it.

See also

Other TALE plots: plot.tales_msa(), plot_target_preds(), talomes_heatmap()

Examples

x <- tales_from_telltales(system.file("extdata", "tellTaleExampleOutput",
                                      package = "tantale"))
plot(x)

plot(x, facet_by = NULL)