Process index annotations and rasterise to a x/y/layer dataframe (generic ggDNAvis helper)
Source: R/dna_tools.R
rasterise_index_annotations.Rdrasterize_index_annotations() is an alias for rasterise_index_annotations().
This function is called by
visualise_many_sequences(), visualise_methylation(), and visualise_single_sequence()
to create the x/y position data for placing the index annotations on the graph.
Its arguments are either intermediate variables produced by the visualisation functions,
or arguments of the visualisation functions directly passed through.
Returns a dataframe with x_position, y_position, and value columns, where the
values are the index annotations.
Usage
rasterise_index_annotations(
new_sequences_vector,
original_sequences_vector,
index_annotation_lines,
index_annotation_interval = 15,
index_annotation_full_line = TRUE,
index_annotations_above = TRUE,
index_annotation_vertical_position = 1/3,
index_annotation_always_first_base = FALSE,
sum_indices = FALSE,
spacing = NA,
offset_start = 0
)Arguments
- new_sequences_vector
vector. The output ofinsert_at_indices()when used with identical arguments. Should beoriginal_sequences_vectorwith some additional blank lines inserted.- original_sequences_vector
vector. The vector of sequences used for plotting, that was originally given tovisualise_many_sequences()/visualise_methylation()or split from the input sequence tovisualise_single_sequence(). Must also have been used as input toinsert_at_indices()to createnew_sequences_vector.- index_annotation_lines
integer vector. The lines (i.e. elements ofsequences_vector) that should have their base incides annotated. 1-indexed e.g.c(1, 10)would annotate the first and tenth elements ofsequences_vector.
Extra lines are inserted above or below (depending onindex_annotations_above) the selected lines - note that the line numbers come fromsequences_vector, so are unaffected by these insertions.
Setting toNAdisables index annotations (and prevents adding additional blank lines). Defaults toc(1)i.e. first sequence is annotated.- index_annotation_interval
integer. The frequency at which numbers should be placed underneath indicating base index, starting counting from the leftmost base. Defaults to15(every 15 bases along each row).
Setting to0disables index annotations (and prevents adding additional blank lines).- index_annotation_full_line
logical. Whether index annotations should continue to the end of the longest sequence (TRUE, default) or should only continue as far as each selected line does (FALSE).- index_annotations_above
logical. Whether index annotations should go above (TRUE, default) or below (FALSE) each line of sequence.- index_annotation_vertical_position
numeric. How far annotation numbers should be rendered above (ifindex_annotations_above = TRUE) or below (ifindex_annotations_above = FALSE) each base. Defaults to1/3.
Not recommended to change at all. Strongly discouraged to set below 0 or above 1.- index_annotation_always_first_base
logical. Whether to force the first base in each line to always be annotated regardless of whether it occurs at theindex_annotation_interval. Defaults toFALSE.- sum_indices
logical. Whether indices should be counted separately along each line (FALSE, default) or summed along all annotated lines (TRUE). May behave unexpectedly ifTRUEwhenannotate_full_linesis alsoTRUE.- spacing
integer. The number of blank lines inserted for each index annotation. Set toNA(default) to infer fromannotation_vertical_position.- offset_start
integer. The number of blank lines not present at the start, that otherwise would be expected based onspacingorannotation_vertical_position. Defaults to0.
Value
dataframe. A dataframe with columns x, y, and value, with one observation per annotation number that needs to be drawn onto the ggplot.
Examples
## Set up arguments (e.g. from visualise_many_sequences() call)
sequences_data <- example_many_sequences
index_annotation_lines <- c(1, 23, 37)
index_annotation_interval <- 10
index_annotations_above <- TRUE
index_annotation_full_line <- FALSE
index_annotation_vertical_position <- 1/3
## Create sequences vector
sequences <- extract_and_sort_sequences(
example_many_sequences,
grouping_levels = c("family" = 8, "individual" = 2)
)
sequences
#> [1] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [2] "GGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [3] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [4] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [5] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [6] ""
#> [7] ""
#> [8] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGAGGCGGCGGAGGAGGAGGCGGCGGA"
#> [9] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGAGGCGGCGGAGGAGGAGGCGGCGGA"
#> [10] ""
#> [11] ""
#> [12] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [13] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGA"
#> [14] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGCGGA"
#> [15] ""
#> [16] ""
#> [17] ""
#> [18] ""
#> [19] ""
#> [20] ""
#> [21] ""
#> [22] ""
#> [23] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA"
#> [24] ""
#> [25] ""
#> [26] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA"
#> [27] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA"
#> [28] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA"
#> [29] ""
#> [30] ""
#> [31] ""
#> [32] ""
#> [33] ""
#> [34] ""
#> [35] ""
#> [36] ""
#> [37] "GGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [38] "GGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [39] ""
#> [40] ""
#> [41] "GGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [42] "GGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGA"
#> [43] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGCGGCGGA"
#> [44] ""
#> [45] ""
#> [46] "GGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [47] ""
#> [48] ""
#> [49] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [50] "GGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGCGGA"
#> [51] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGCGGCGGA"
## Insert blank rows as needed
new_sequences <- insert_at_indices(
sequences,
insertion_indices = index_annotation_lines,
insert_before = index_annotations_above,
insert = "",
vert = index_annotation_vertical_position
)
new_sequences
#> [1] ""
#> [2] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [3] "GGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [4] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [5] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [6] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [7] ""
#> [8] ""
#> [9] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGAGGCGGCGGAGGAGGAGGCGGCGGA"
#> [10] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGAGGCGGCGGAGGAGGAGGCGGCGGA"
#> [11] ""
#> [12] ""
#> [13] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA"
#> [14] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGA"
#> [15] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGCGGA"
#> [16] ""
#> [17] ""
#> [18] ""
#> [19] ""
#> [20] ""
#> [21] ""
#> [22] ""
#> [23] ""
#> [24] ""
#> [25] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA"
#> [26] ""
#> [27] ""
#> [28] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA"
#> [29] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA"
#> [30] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA"
#> [31] ""
#> [32] ""
#> [33] ""
#> [34] ""
#> [35] ""
#> [36] ""
#> [37] ""
#> [38] ""
#> [39] ""
#> [40] "GGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [41] "GGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [42] ""
#> [43] ""
#> [44] "GGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [45] "GGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGA"
#> [46] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGCGGCGGA"
#> [47] ""
#> [48] ""
#> [49] "GGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [50] ""
#> [51] ""
#> [52] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA"
#> [53] "GGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGCGGA"
#> [54] "GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGCGGCGGA"
## Create annnotation dataframe
rasterise_index_annotations(
new_sequences_vector = new_sequences,
original_sequences_vector = sequences,
index_annotation_lines = index_annotation_lines,
index_annotation_interval = 10,
index_annotation_full_line = index_annotation_full_line,
index_annotations_above = index_annotations_above,
index_annotation_vertical_position = index_annotation_vertical_position,
sum_indices = FALSE,
spacing = NA, ## infer from vertical position
offset_start = 0
)
#> x y value
#> 1 0.09313725 0.9876543 10
#> 2 0.19117647 0.9876543 20
#> 3 0.28921569 0.9876543 30
#> 4 0.38725490 0.9876543 40
#> 5 0.48529412 0.9876543 50
#> 6 0.58333333 0.9876543 60
#> 7 0.68137255 0.9876543 70
#> 8 0.77941176 0.9876543 80
#> 9 0.87745098 0.9876543 90
#> 10 0.97549020 0.9876543 100
#> 11 0.09313725 0.5617284 10
#> 12 0.19117647 0.5617284 20
#> 13 0.28921569 0.5617284 30
#> 14 0.38725490 0.5617284 40
#> 15 0.48529412 0.5617284 50
#> 16 0.58333333 0.5617284 60
#> 17 0.68137255 0.5617284 70
#> 18 0.77941176 0.5617284 80
#> 19 0.87745098 0.5617284 90
#> 20 0.09313725 0.2839506 10
#> 21 0.19117647 0.2839506 20
#> 22 0.28921569 0.2839506 30
#> 23 0.38725490 0.2839506 40
#> 24 0.48529412 0.2839506 50
#> 25 0.58333333 0.2839506 60
#> 26 0.68137255 0.2839506 70
#> 27 0.77941176 0.2839506 80
#> 28 0.87745098 0.2839506 90