RNAlib-2.4.4
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Modules | |
Functions to generate annotations for Secondary Structure Plots, Dot-Plots, and Others | |
Files | |
file | naview.h |
file | plot_aln.h |
Various functions for plotting Sequence / Structure Alignments. | |
file | plot_layouts.h |
Secondary structure plot layout algorithms. | |
file | plot_structure.h |
Various functions for plotting RNA secondary structures. | |
file | plot_utils.h |
Various utilities to assist in plotting secondary structures and consensus structures. | |
file | PS_dot.h |
Various functions for plotting RNA secondary structures, dot-plots and other visualizations. | |
Data Structures | |
struct | COORDINATE |
this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORDINATE More... | |
struct | vrna_dotplot_auxdata_t |
Macros | |
#define | VRNA_PLOT_TYPE_SIMPLE 0 |
Definition of Plot type simple More... | |
#define | VRNA_PLOT_TYPE_NAVIEW 1 |
Definition of Plot type Naview More... | |
#define | VRNA_PLOT_TYPE_CIRCULAR 2 |
Definition of Plot type Circular 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[]) |
int | simple_xy_coordinates (short *pair_table, float *X, float *Y) |
Calculate nucleotide coordinates for secondary structure plot the Simple way More... | |
int | simple_circplot_coordinates (short *pair_table, float *x, float *y) |
Calculate nucleotide coordinates for Circular Plot More... | |
int | PS_dot_plot_list (char *seq, char *filename, plist *pl, plist *mf, char *comment) |
Produce a postscript dot-plot from two pair lists. More... | |
int | PS_dot_plot (char *string, char *file) |
Produce postscript dot-plot. More... | |
Variables | |
int | rna_plot_type |
Switch for changing the secondary structure layout algorithm. More... | |
struct COORDINATE |
this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORDINATE
struct vrna_dotplot_auxdata_t |
#define VRNA_PLOT_TYPE_SIMPLE 0 |
#include <ViennaRNA/plot_layouts.h>
Definition of Plot type simple
This is the plot type definition for several RNA structure plotting functions telling them to use Simple plotting algorithm
#define VRNA_PLOT_TYPE_NAVIEW 1 |
#include <ViennaRNA/plot_layouts.h>
Definition of Plot type Naview
This is the plot type definition for several RNA structure plotting functions telling them to use Naview plotting algorithm
#define VRNA_PLOT_TYPE_CIRCULAR 2 |
#include <ViennaRNA/plot_layouts.h>
Definition of Plot type Circular
This is the plot type definition for several RNA structure plotting functions telling them to produce a Circular plot
int aliPS_color_aln | ( | const char * | structure, |
const char * | filename, | ||
const char * | seqs[], | ||
const char * | names[] | ||
) |
#include <ViennaRNA/plot_aln.h>
PS_color_aln for duplexes
int simple_xy_coordinates | ( | short * | pair_table, |
float * | X, | ||
float * | Y | ||
) |
#include <ViennaRNA/plot_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/plot_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 |
#include <ViennaRNA/PS_dot.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/PS_dot.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
int rna_plot_type |
#include <ViennaRNA/plot_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 [3].