Alignment Plots

Functions to generate Alignment plots with annotated consensus structure.

Functions

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.

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. See, e.g. RNA.file_PS_aln() in the Python API.

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)

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.

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. See, e.g. RNA.file_PS_aln() in the Python API.

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)