sqprint {tidysq}

Print sq object

Description

Prints input sq object in a human-friendly form.

Arguments

x

[sq]
An object this function is applied to.

max_sequences

[integer(1)]
How many sequences should be printed.

use_color

[logical(1)]
Should sequences be colored?

letters_sep

[character(1)]
How the letters should be separated.

NA_letter

[character(1)]
A string that is used to interpret and display NA value in the context of sq class. Default value equals to "!".

...

further arguments to be passed from or to other methods.

Details

print method is often called implicitly by calling variable name. Only explicit calling of this method allows its parameters to be changed.

Printed information consists of three parts:

• First line is always a header that contains info about the type of sequences contained.

• The next part is the content. Each sequence has its own line, but not all sequences are printed. The number of printed sequences is limited by parameter max_sequences, defaulting to 10. These sequences are printed with:

  • left-aligned index of sequence in square brackets (e.g. [3]),

  • left-aligned sequence data (more about it in paragraph below),

  • right-aligned sequence length in angle brackets (e.g. <27>).

• Finally, if number of sequences is greater than max_sequences, then a footer is displayed with how many sequences are there and how many were printed.

Each sequence data is printed as letters. If sequence is too long to fit in one line, then only a subsequence is displayed - a subsequence that begins from the first letter. Sequence printing is controlled by letters_sep and NA_letter parameters. The first one specifies a string that should be inserted between any two letters. By default it's empty when all letters are one character in length; and a space otherwise. NA_letter dictates how NA values are displayed, by default it's an exclamation mark ("!").

Most consoles support color printing, but when any of these do not, then the user might use use_color parameter set to FALSE - or better yet, change related option value, where said option is called "tidysq_print_use_color".

Value

An object that was passed as the first argument to the function. It is returned invisibly (equivalent of invisible(x))

See Also

Functions that display sequence info: get_tidysq_options()

Examples

# Creating objects to work on:
sq_ami <- sq(c("MIAANYTWIL","TIAALGNIIYRAIE", "NYERTGHLI", "MAYXXXIALN"),
             alphabet = "ami_ext")
sq_dna <- sq(c("ATGCAGGA", "GACCGNBAACGAN", "TGACGAGCTTA"),
             alphabet = "dna_bsc")
sq_unt <- sq(c("ATGCAGGA?", "TGACGAGCTTA", "", "TIAALGNIIYRAIE"))

# Printing without explicit function calling with default parameters:
sq_ami
sq_dna
sq_unt

# Printing with explicit function calling and specific parameters:
print(sq_ami)
print(sq_dna, max_sequences = 1, use_color = FALSE)
print(sq_unt, letters_sep = ":")