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. More...
int	aliPS_color_aln (const char *structure, const char *filename, const char *seqs[], const char *names[])
	PS_color_aln for duplexes. More...
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	naview_xy_coordinates (short *pair_table, float *X, float *Y)

Variables
int	rna_plot_type
	Switch for changing the secondary structure layout algorithm. More...

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Data Structure Documentation

struct COORDINATE

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

Function Documentation

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!

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!

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_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

Returns

length of sequence on success, 0 otherwise

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 in addition to the actual R² coordinates. the simplest way to do so may be to compute a radius scaling factor in the interval 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 , i.e. and .

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_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

Returns

length of sequence on success, 0 otherwise

int naview_xy_coordinates	(	short *	pair_table,
		float *	X,
		float *	Y
	)

#include <ViennaRNA/plotting/naview.h>

Deprecated:

Consider using vrna_plot_coords_naview_pt() instead!

Variable Documentation

int rna_plot_type

#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 [5].

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