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 parametersstart,end, andoffsetbefore thecolumnsargument. Thus, it resembles thevrna_file_PS_aln_slice()function. The last four arguments may be omitted, indicating the default ofstart= 0,end= 0,offset= 0, andcolumns= 60. See, e.g.RNA.file_PS_aln()in the Python API.
See also
- 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
startandendposition. The additionaloffsetparameter 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, indicatingstart= 0,end= 0,offset= 0, andcolumns= 60. See, e.g.RNA.file_PS_aln()in the Python API.
See also
- 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)
-
int vrna_file_PS_aln(const char *filename, const char **seqs, const char **names, const char *structure, unsigned int columns)