Data Structures | |
struct | COORDINATE |
this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORDINATE More... | |
Functions | |
int | PS_color_aln (const char *structure, const char *filename, const char *seqs[], const char *names[]) |
Produce PostScript sequence alignment color-annotated by consensus structure. | |
int | aliPS_color_aln (const char *structure, const char *filename, const char *seqs[], const char *names[]) |
PS_color_aln for duplexes. | |
int | simple_xy_coordinates (short *pair_table, float *X, float *Y) |
Calculate nucleotide coordinates for secondary structure plot the Simple way | |
int | simple_circplot_coordinates (short *pair_table, float *x, float *y) |
Calculate nucleotide coordinates for Circular Plot | |
int | PS_dot_plot_list (char *seq, char *filename, vrna_ep_t *pl, vrna_ep_t *mf, char *comment) |
Produce a postscript dot-plot from two pair lists. | |
int | PS_dot_plot (char *string, char *file) |
Produce postscript dot-plot. | |
Variables | |
int | rna_plot_type |
Switch for changing the secondary structure layout algorithm. | |
struct COORDINATE |
this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORDINATE
int PS_color_aln | ( | const char * | structure, |
const char * | filename, | ||
const char * | seqs[], | ||
const char * | names[] | ||
) |
#include <ViennaRNA/plotting/alignments.h>
Produce PostScript sequence alignment color-annotated by consensus structure.
int aliPS_color_aln | ( | const char * | structure, |
const char * | filename, | ||
const char * | seqs[], | ||
const char * | names[] | ||
) |
#include <ViennaRNA/plotting/alignments.h>
PS_color_aln for duplexes.
int simple_xy_coordinates | ( | short * | pair_table, |
float * | X, | ||
float * | Y | ||
) |
#include <ViennaRNA/plotting/layouts.h>
Calculate nucleotide coordinates for secondary structure plot the Simple way
pair_table | The pair table of the secondary structure |
X | a pointer to an array with enough allocated space to hold the x coordinates |
Y | a pointer to an array with enough allocated space to hold the y coordinates |
int simple_circplot_coordinates | ( | short * | pair_table, |
float * | x, | ||
float * | y | ||
) |
#include <ViennaRNA/plotting/layouts.h>
Calculate nucleotide coordinates for Circular Plot
This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.
pair_table | The pair table of the secondary structure |
x | a pointer to an array with enough allocated space to hold the x coordinates |
y | a pointer to an array with enough allocated space to hold the y coordinates |
int PS_dot_plot_list | ( | char * | seq, |
char * | filename, | ||
vrna_ep_t * | pl, | ||
vrna_ep_t * | mf, | ||
char * | comment | ||
) |
#include <ViennaRNA/plotting/probabilities.h>
Produce a postscript dot-plot from two pair lists.
This function reads two plist structures (e.g. base pair probabilities and a secondary structure) as produced by assign_plist_from_pr() and assign_plist_from_db() and produces a postscript "dot plot" that is written to 'filename'.
Using base pair probabilities in the first and mfe structure in the second plist, the resulting "dot plot" represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy structure.
seq | The RNA sequence |
filename | A filename for the postscript output |
pl | The base pair probability pairlist |
mf | The mfe secondary structure pairlist |
comment | A comment |
int PS_dot_plot | ( | char * | string, |
char * | file | ||
) |
#include <ViennaRNA/plotting/probabilities.h>
Produce postscript dot-plot.
Wrapper to PS_dot_plot_list
Reads base pair probabilities produced by pf_fold() from the global array pr and the pair list base_pair produced by fold() and produces a postscript "dot plot" that is written to 'filename'. The "dot plot" represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy
|
extern |
#include <ViennaRNA/plotting/layouts.h>
Switch for changing the secondary structure layout algorithm.
Current possibility are 0 for a simple radial drawing or 1 for the modified radial drawing taken from the naview program of [6].