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.
	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	naview.h
	Implementation of the Naview RNA secondary structure layout algorithm [5].
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 [23].
file	RNAturtle.h
	Implementation of the RNAturtle RNA secondary structure layout algorithm [23].

Data Structures
struct	vrna_dotplot_auxdata_t

Functions
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...
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'. More...
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'. More...
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. More...
int	ssv_rna_plot (char *string, char *structure, char *ssfile)
	Produce a secondary structure graph in SStructView format. More...
int	svg_rna_plot (char *string, char *structure, char *ssfile)
	Produce a secondary structure plot in SVG format and write it to a file. More...
int	xrna_plot (char *string, char *structure, char *ssfile)
	Produce a secondary structure plot for further editing in XRNA. More...
int	PS_rna_plot (char *string, char *structure, char *file)
	Produce a secondary structure graph in PostScript and write it to 'filename'. More...
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'. More...
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) More...

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Data Structure Documentation

struct vrna_dotplot_auxdata_t

Collaboration diagram for vrna_dotplot_auxdata_t:

Function Documentation

int PS_dot_plot_list	(	char *	seq,
		char *	filename,
		plist *	pl,
		plist *	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

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

Returns

1 if postscript was successfully written, 0 otherwise

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!

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

seq	The RNA sequence
structure	The secondary structure in dot-bracket notation
file	The filename of the postscript output
md_p	Model parameters used to generate a commandline option string in the output (Maybe NULL)

Returns

1 on success, 0 otherwise

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

seq	The RNA sequence
structure	The secondary structure in dot-bracket notation
file	The filename of the postscript output
pre	PostScript code to appear before the secondary structure plot
post	PostScript code to appear after the secondary structure plot
md_p	Model parameters used to generate a commandline option string in the output (Maybe NULL)

Returns

1 on success, 0 otherwise

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

string	The RNA sequence
structure	The secondary structure in dot-bracket notation
ssfile	The filename of the gml output
option	The option flag

Returns

1 on success, 0 otherwise

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

string	The RNA sequence
structure	The secondary structure in dot-bracket notation
ssfile	The filename of the ssv output

Returns

1 on success, 0 otherwise

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

string	The RNA sequence
structure	The secondary structure in dot-bracket notation
ssfile	The filename of the svg output

Returns

1 on success, 0 otherwise

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

string	The RNA sequence
structure	The secondary structure in dot-bracket notation
ssfile	The filename of the xrna output

Returns

1 on success, 0 otherwise

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!

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!

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!