RNAlib-2.6.3
 
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Deprecated Interface for Plotting Utilities

Detailed Description

+ Collaboration diagram for Deprecated Interface for Plotting Utilities:

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.
 

Data Structure Documentation

◆ COORDINATE

struct COORDINATE

this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORDINATE

Function Documentation

◆ PS_color_aln()

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.

Deprecated:
Use vrna_file_PS_aln() instead!

◆ aliPS_color_aln()

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.

Deprecated:
Use vrna_file_PS_aln() instead!

◆ simple_xy_coordinates()

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

See also
make_pair_table(), rna_plot_type, simple_circplot_coordinates(), naview_xy_coordinates(), vrna_file_PS_rnaplot_a(), vrna_file_PS_rnaplot, svg_rna_plot()
Deprecated:
Consider switching to vrna_plot_coords_simple_pt() instead!
Parameters
pair_tableThe pair table of the secondary structure
Xa pointer to an array with enough allocated space to hold the x coordinates
Ya pointer to an array with enough allocated space to hold the y coordinates
Returns
length of sequence on success, 0 otherwise

◆ simple_circplot_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.

Note
In order to draw nice arcs using quadratic bezier curves that connect base pairs one may calculate a second tangential point $P^t$ in addition to the actual R2 coordinates. the simplest way to do so may be to compute a radius scaling factor $rs$ in the interval $[0,1]$ that weights the proportion of base pair span to the actual length of the sequence. This scaling factor can then be used to calculate the coordinates for $P^t$, i.e. $ P^{t}_x[i] = X[i] * rs$ and $P^{t}_y[i] = Y[i] * rs$.
See also
make_pair_table(), rna_plot_type, simple_xy_coordinates(), naview_xy_coordinates(), vrna_file_PS_rnaplot_a(), vrna_file_PS_rnaplot, svg_rna_plot()
Deprecated:
Consider switching to vrna_plot_coords_circular_pt() instead!
Parameters
pair_tableThe pair table of the secondary structure
xa pointer to an array with enough allocated space to hold the x coordinates
ya pointer to an array with enough allocated space to hold the y coordinates
Returns
length of sequence on success, 0 otherwise

◆ PS_dot_plot_list()

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.

See also
assign_plist_from_pr(), assign_plist_from_db()
Parameters
seqThe RNA sequence
filenameA filename for the postscript output
plThe base pair probability pairlist
mfThe mfe secondary structure pairlist
commentA comment
Returns
1 if postscript was successfully written, 0 otherwise

◆ PS_dot_plot()

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

Note
DO NOT USE THIS FUNCTION ANYMORE SINCE IT IS NOT THREADSAFE
Deprecated:
This function is deprecated and will be removed soon! Use PS_dot_plot_list() instead!

Variable Documentation

◆ rna_plot_type

int rna_plot_type
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].

Note
To provide thread safety please do not rely on this global variable in future implementations but pass a plot type flag directly to the function that decides which layout algorithm it may use!
See also
VRNA_PLOT_TYPE_SIMPLE, VRNA_PLOT_TYPE_NAVIEW, VRNA_PLOT_TYPE_CIRCULAR