Convert vector of sequences to character matrix (generic ggDNAvis helper)

This function takes a vector of sequences (e.g. input to visualise_many_sequences() or visualise_methylation(), or vector split from input to visualise_single_sequence()). It converts it into a matrix e.g. c("GGCGGC", "", "ACGT", "") would become:

G  G  C  G  G  C
NA NA NA NA NA NA
A  C  G  T  NA NA
NA NA NA NA NA NA

The resulting matrix can then be rasterised into a coordinate-value dataframe via rasterise_matrix().

Usage

convert_sequences_to_matrix(sequences, line_length = NA, blank_value = NA)

Arguments

sequences: character vector. The sequences to transform into a matrix
line_length: integer. The width of the matrix. Set to NA (default) to automatically use the length of the longest sequence in sequences.
blank_value: value. The value that should be used to fill in blank/missing points of the matrix.

Value

matrix. A matrix of the sequences with one line per sequence, ready for rasterisation via rasterise_matrix().

Examples

convert_sequences_to_matrix(
    sequences = c("GGCGGC", "", "ACGT", "")
)
#>      [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,] "G"  "G"  "C"  "G"  "G"  "C" 
#> [2,] NA   NA   NA   NA   NA   NA  
#> [3,] "A"  "C"  "G"  "T"  NA   NA  
#> [4,] NA   NA   NA   NA   NA   NA  

convert_sequences_to_matrix(
    sequences = c("GGCGGC", "", "ACGT", ""),
    line_length = 10,
    blank_value = "X"
)
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] "G"  "G"  "C"  "G"  "G"  "C"  "X"  "X"  "X"  "X"  
#> [2,] "X"  "X"  "X"  "X"  "X"  "X"  "X"  "X"  "X"  "X"  
#> [3,] "A"  "C"  "G"  "T"  "X"  "X"  "X"  "X"  "X"  "X"  
#> [4,] "X"  "X"  "X"  "X"  "X"  "X"  "X"  "X"  "X"  "X"