Convert a vector of sequences to a dataframe for plotting sequence contents and index annotations (visualise_single_sequence() helper) — convert_sequences_to

Takes the sequence list output from convert_input_seq_to_sequence_list() and creates a dataframe specifying x and y coordinates and the character to plot at each coordinate. This applies to both the sequence itself (e.g. determining where on the plot to place an "A") and the periodicit annotations of index number (e.g. determining where on the plot to annotate base number 15).

Usage

convert_sequences_to_annotations(
  sequences,
  line_length,
  interval = 15,
  annotations_above = TRUE,
  annotation_vertical_position = 1/3
)

Arguments

sequences: character vector. Sequence to be plotted, split into lines and optionally including blank spacer lines. Output of convert_input_seq_to_sequence_list().
line_length: integer. How long each line should be.
interval: integer. How frequently bases should be annotated with their index. Defaults to 15.
annotations_above: logical. Whether annotations should go above (TRUE, default) or below (FALSE) each line of sequence.
annotation_vertical_position: numeric. How far annotation numbers should be rendered above (if index_annotations_above = TRUE) or below (if index_annotations_above = FALSE) each base. Defaults to 1/3. Not recommended to change at all. Strongly discouraged to set below 0 or above 1.

Value

dataframe Dataframe of coordinates and labels (e.g. "A" or "15), readable by geom_text.

Examples

convert_sequences_to_annotations(
    c("GGCGGC", "", "ATCG", ""),
    line_length = 6,
    interval = 3,
    annotations_above = TRUE,
    annotation_vertical_position = 1/3
)
#>    x_position y_position annotation     type
#> 1  0.08333333  0.8750000          G Sequence
#> 2  0.25000000  0.8750000          G Sequence
#> 3  0.41666667  0.8750000          C Sequence
#> 4  0.41666667  1.0833333          3   Number
#> 5  0.58333333  0.8750000          G Sequence
#> 6  0.75000000  0.8750000          G Sequence
#> 7  0.91666667  0.8750000          C Sequence
#> 8  0.91666667  1.0833333          6   Number
#> 9  0.08333333  0.3750000          A Sequence
#> 10 0.25000000  0.3750000          T Sequence
#> 11 0.41666667  0.3750000          C Sequence
#> 12 0.41666667  0.5833333          9   Number
#> 13 0.58333333  0.3750000          G Sequence

convert_sequences_to_annotations(
    c("GGCGGC", "", "ATCG", ""),
    line_length = 6,
    interval = 0
)
#>    x_position y_position annotation     type
#> 1  0.08333333      0.875          G Sequence
#> 2  0.25000000      0.875          G Sequence
#> 3  0.41666667      0.875          C Sequence
#> 4  0.58333333      0.875          G Sequence
#> 5  0.75000000      0.875          G Sequence
#> 6  0.91666667      0.875          C Sequence
#> 7  0.08333333      0.375          A Sequence
#> 8  0.25000000      0.375          T Sequence
#> 9  0.41666667      0.375          C Sequence
#> 10 0.58333333      0.375          G Sequence