RNAlib-2.6.3
 
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Plotting

Functions for Creating Secondary Structure Plots, Dot-Plots, and More. More...

Detailed Description

Functions for Creating Secondary Structure Plots, Dot-Plots, and More.

+ Collaboration diagram for Plotting:

Modules

 Layouts and Coordinates
 Functions to compute coordinate layouts for secondary structure plots.
 
 Annotation
 Functions to generate annotations for Secondary Structure Plots, Dot-Plots, and Others.
 
 Probabilities
 Functions related to plotting of probabilities, such as dot-plots.
 
 Alignment Plots
 Functions to generate Alignment plots with annotated consensus structure.
 
 Deprecated Interface for Plotting Utilities
 

Files

file  alignments.h
 Various functions for plotting Sequence / Structure Alignments.
 
file  layouts.h
 Secondary structure plot layout algorithms.
 
file  probabilities.h
 Various functions for plotting RNA secondary structures, dot-plots and other visualizations.
 
file  structures.h
 Various functions for plotting RNA secondary structures.
 
file  utils.h
 Various utilities to assist in plotting secondary structures and consensus structures.
 
file  RNApuzzler.h
 Implementation of the RNApuzzler RNA secondary structure layout algorithm [29].
 
file  RNAturtle.h
 Implementation of the RNAturtle RNA secondary structure layout algorithm [29].
 

Functions

int vrna_file_PS_rnaplot (const char *seq, const char *structure, const char *file, vrna_md_t *md_p)
 Produce a secondary structure graph in PostScript and write it to 'filename'.
 
int vrna_file_PS_rnaplot_a (const char *seq, const char *structure, const char *file, const char *pre, const char *post, vrna_md_t *md_p)
 Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'.
 
int gmlRNA (char *string, char *structure, char *ssfile, char option)
 Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file.
 
int ssv_rna_plot (char *string, char *structure, char *ssfile)
 Produce a secondary structure graph in SStructView format.
 
int svg_rna_plot (char *string, char *structure, char *ssfile)
 Produce a secondary structure plot in SVG format and write it to a file.
 
int xrna_plot (char *string, char *structure, char *ssfile)
 Produce a secondary structure plot for further editing in XRNA.
 
int PS_rna_plot (char *string, char *structure, char *file)
 Produce a secondary structure graph in PostScript and write it to 'filename'.
 
int PS_rna_plot_a (char *string, char *structure, char *file, char *pre, char *post)
 Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'.
 
int PS_rna_plot_a_gquad (char *string, char *structure, char *ssfile, char *pre, char *post)
 Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename' (detect and draw g-quadruplexes)
 

Function Documentation

◆ vrna_file_PS_rnaplot()

int vrna_file_PS_rnaplot ( const char *  seq,
const char *  structure,
const char *  file,
vrna_md_t md_p 
)

#include <ViennaRNA/plotting/structures.h>

Produce a secondary structure graph in PostScript and write it to 'filename'.

Note that this function has changed from previous versions and now expects the structure to be plotted in dot-bracket notation as an argument. It does not make use of the global base_pair array anymore.

Parameters
seqThe RNA sequence
structureThe secondary structure in dot-bracket notation
fileThe filename of the postscript output
md_pModel parameters used to generate a commandline option string in the output (Maybe NULL)
Returns
1 on success, 0 otherwise

◆ vrna_file_PS_rnaplot_a()

int vrna_file_PS_rnaplot_a ( const char *  seq,
const char *  structure,
const char *  file,
const char *  pre,
const char *  post,
vrna_md_t md_p 
)

#include <ViennaRNA/plotting/structures.h>

Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'.

Same as vrna_file_PS_rnaplot() but adds extra PostScript macros for various annotations (see generated PS code). The 'pre' and 'post' variables contain PostScript code that is verbatim copied in the resulting PS file just before and after the structure plot. If both arguments ('pre' and 'post') are NULL, no additional macros will be printed into the PostScript.

Parameters
seqThe RNA sequence
structureThe secondary structure in dot-bracket notation
fileThe filename of the postscript output
prePostScript code to appear before the secondary structure plot
postPostScript code to appear after the secondary structure plot
md_pModel parameters used to generate a commandline option string in the output (Maybe NULL)
Returns
1 on success, 0 otherwise

◆ gmlRNA()

int gmlRNA ( char *  string,
char *  structure,
char *  ssfile,
char  option 
)

#include <ViennaRNA/plotting/structures.h>

Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file.

If 'option' is an uppercase letter the RNA sequence is used to label nodes, if 'option' equals 'X' or 'x' the resulting file will coordinates for an initial layout of the graph.

Parameters
stringThe RNA sequence
structureThe secondary structure in dot-bracket notation
ssfileThe filename of the gml output
optionThe option flag
Returns
1 on success, 0 otherwise

◆ ssv_rna_plot()

int ssv_rna_plot ( char *  string,
char *  structure,
char *  ssfile 
)

#include <ViennaRNA/plotting/structures.h>

Produce a secondary structure graph in SStructView format.

Write coord file for SStructView

Parameters
stringThe RNA sequence
structureThe secondary structure in dot-bracket notation
ssfileThe filename of the ssv output
Returns
1 on success, 0 otherwise

◆ svg_rna_plot()

int svg_rna_plot ( char *  string,
char *  structure,
char *  ssfile 
)

#include <ViennaRNA/plotting/structures.h>

Produce a secondary structure plot in SVG format and write it to a file.

Parameters
stringThe RNA sequence
structureThe secondary structure in dot-bracket notation
ssfileThe filename of the svg output
Returns
1 on success, 0 otherwise

◆ xrna_plot()

int xrna_plot ( char *  string,
char *  structure,
char *  ssfile 
)

#include <ViennaRNA/plotting/structures.h>

Produce a secondary structure plot for further editing in XRNA.

Parameters
stringThe RNA sequence
structureThe secondary structure in dot-bracket notation
ssfileThe filename of the xrna output
Returns
1 on success, 0 otherwise

◆ PS_rna_plot()

int PS_rna_plot ( char *  string,
char *  structure,
char *  file 
)

#include <ViennaRNA/plotting/structures.h>

Produce a secondary structure graph in PostScript and write it to 'filename'.

Deprecated:
Use vrna_file_PS_rnaplot() instead!

◆ PS_rna_plot_a()

int PS_rna_plot_a ( char *  string,
char *  structure,
char *  file,
char *  pre,
char *  post 
)

#include <ViennaRNA/plotting/structures.h>

Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'.

Deprecated:
Use vrna_file_PS_rnaplot_a() instead!

◆ PS_rna_plot_a_gquad()

int PS_rna_plot_a_gquad ( char *  string,
char *  structure,
char *  ssfile,
char *  pre,
char *  post 
)

#include <ViennaRNA/plotting/structures.h>

Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename' (detect and draw g-quadruplexes)

Deprecated:
Use vrna_file_PS_rnaplot_a() instead!