Alignment Plots

Functions to generate Alignment plots with annotated consensus structure. More...

Detailed Description

Functions to generate Alignment plots with annotated consensus structure.

Collaboration diagram for Alignment Plots:

Functions
int	vrna_file_PS_aln (const char *filename, const char **seqs, const char **names, const char *structure, unsigned int columns)
	Create an annotated PostScript alignment plot. More...
int	vrna_file_PS_aln_slice (const char *filename, const char **seqs, const char **names, const char *structure, unsigned int start, unsigned int end, int offset, unsigned int columns)
	Create an annotated PostScript alignment plot. More...

Function Documentation

int vrna_file_PS_aln	(	const char *	filename,
		const char **	seqs,
		const char **	names,
		const char *	structure,
		unsigned int	columns
	)

#include <ViennaRNA/plotting/alignments.h>

Create an annotated PostScript alignment plot.

See also

vrna_file_PS_aln_slice()

Parameters

filename	The output file name
seqs	The aligned sequences
names	The names of the sequences
structure	The consensus structure in dot-bracket notation
columns	The number of columns before the alignment is wrapped as a new block (a value of 0 indicates no wrapping)

SWIG Wrapper Notes:

This function is available as overloaded function file_PS_aln() with three additional parameters start, end, and offset before the columns argument. Thus, it resembles the vrna_file_PS_aln_slice() function. The last four arguments may be omitted, indicating the default of start = 0, end = 0, offset = 0, and columns = 60.

int vrna_file_PS_aln_slice	(	const char *	filename,
		const char **	seqs,
		const char **	names,
		const char *	structure,
		unsigned int	start,
		unsigned int	end,
		int	offset,
		unsigned int	columns
	)

#include <ViennaRNA/plotting/alignments.h>

Create an annotated PostScript alignment plot.

Similar to vrna_file_PS_aln() but allows the user to print a particular slice of the alignment by specifying a start and end position. The additional offset parameter allows for adjusting the alignment position ruler value.

See also

vrna_file_PS_aln_slice()

Parameters

filename	The output file name
seqs	The aligned sequences
names	The names of the sequences
structure	The consensus structure in dot-bracket notation
start	The start of the alignment slice (a value of 0 indicates the first position of the alignment, i.e. no slicing at 5' side)
end	The end of the alignment slice (a value of 0 indicates the last position of the alignment, i.e. no slicing at 3' side)
offset	The alignment coordinate offset for the position ruler.
columns	The number of columns before the alignment is wrapped as a new block (a value of 0 indicates no wrapping)

SWIG Wrapper Notes:

This function is available as overloaded function file_PS_aln() where the last four parameter may be omitted, indicating start = 0, end = 0, offset = 0, and columns = 60.