| Type: | Package |
| Title: | Render an ASCII Ruler |
| Version: | 0.2 |
| Date: | 2018-01-29 |
| Author: | Jeremy Leipzig <leipzig@gmail.com> |
| Maintainer: | Jeremy Leipzig <leipzig@gmail.com> |
| Description: | An ASCII ruler is for measuring text and is especially useful for sequence analysis. Included in this package are methods to create ASCII rulers and associated GenBank sequence blocks, multi-column text displays that make it easy for viewers to locate nucleotides by position. |
| License: | GPL-3 | file LICENSE |
| Depends: | R (≥ 2.14) |
| Imports: | stringr |
| Collate: | 'asciiruler.R' |
| RoxygenNote: | 6.0.1 |
| Suggests: | testthat |
| NeedsCompilation: | no |
| Packaged: | 2018-01-30 15:15:42 UTC; leipzig |
| Repository: | CRAN |
| Date/Publication: | 2018-01-30 16:53:24 UTC |
Generate an ascii ruler
Description
'
' v borders ' +-----------------------------------------------------------------+<-borders ' |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||<-dense_ticks ' | | | | | | | | | | | | | | |<-sparse_ticks ' |-30 -20 -10 0 10 20 30 | ' +-----------------------------------------------------------------+<-borders '
Usage
asciiruler(low = 0L, high = 50L, sparse_ticks = 5L, dense_ticks = TRUE,
block_space = 0L, borders = FALSE, numbers_down = TRUE,
line_break = "\n", strict_width = FALSE)
default.asciiruler(x)
Arguments
low |
the range start, can be negative |
high |
the range end, can be negative |
sparse_ticks |
intermittent ticks appear every sparse_ticks, set to 0 to hide row |
dense_ticks |
display a row of ticks at every position |
block_space |
break up the ruler with a space every block_space blocks encountered, a multiple of sparse_ticks, set to 0 to disable |
borders |
display borders |
numbers_down |
display the ruler so the numbers are below the ticks |
line_break |
the line break character(s) |
strict_width |
hide numbers whose display would force the ruler to be wider than width(high-low) |
x |
the asciiruler |
Value
asciiruler object with the following slots:
- output
delimited ruler string ready to cat
- content
vector of lines comprising the ruler
- width
width of ruler
- leftmargin
position of the first tick relative to the left edge of the ruler
References
Inspired by http://codegolf.stackexchange.com/questions/4910/ascii-ruler-generation
Examples
asciiruler(low=-30,high=30,borders=TRUE)
Generate a GenBank sequence block
Description
'
' 1 6 11 16 21 26 31 36 41 46 51 56 ' | | | | | | | | | | | | ' |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ' 1 GATCACAGGT CTATCACCCT ATTAACCACT CACGGGAGCT CTCCATGCAT TTGGTATTTT ' 61 CGTCTGGGGG GTGTGCACGC GATAGCATTG CGAGACGCTG GAGCCGGAGC ACCCTATGTC ' 121 GCAGTATCTG TCTTTGATTC CTGCCCCATC CTATTATTTA TCGCACCTAC GTTCAATATT ' 181 ACAGGCGAAC ATACTTACTA AAGTGTGTTA ATTAATTAAT GCTTGTAGGA CATAATAATA ' 241 ACAATTGAAT GTCTGCACAG CCGCTTTCCA CACAGACATC ATAACAAAAA ATTTCCACCA ' 301 AACCCCCCCT CCCCCGCTTC TGGCCACAGC ACTTAAACAC ATCTCTGC '
Usage
genbank_seqblock(string, start = 1L, end = 0L, blocksize = 10L,
width = 60L, sep = " ", line_break = "\n", ruler = TRUE, ...)
Arguments
string |
the sequence string to display |
start |
the substring start, should be 1 or greater |
end |
substring end, should be >start, negative to trim |
blocksize |
number of characters in each block |
width |
width of the sequence block |
sep |
space character between blocks |
line_break |
the line break character(s) |
ruler |
display an ascii ruler |
... |
additional arguments passed to asciiruler |
Value
delimited GenBank block string ready to cat
Examples
my_sequence<-'GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG
GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA
ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC'
my_seqblock<-genbank_seqblock(my_sequence)
cat(my_seqblock)
Print an asciiruler
Description
Print an asciiruler
Usage
## S3 method for class 'asciiruler'
print(x, ...)
Arguments
x |
the asciiruler |
... |
additional arguments |
Get the total width of an ascii ruler
Description
Get the total width of an ascii ruler
Usage
width(x, ...)
Arguments
x |
the asciiruler |
... |
additional arguments |