# H/plot_layouts.h File Reference

Secondary structure plot layout algorithms. More...

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## Defines

#define | VRNA_PLOT_TYPE_SIMPLE 0
| Definition of Plot type simple
#define | VRNA_PLOT_TYPE_NAVIEW 1
| Definition of Plot type Naview
#define | VRNA_PLOT_TYPE_CIRCULAR 2
| Definition of Plot type Circular

## Functions

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

## Variables

int | rna_plot_type
| Switch for changing the secondary structure layout algorithm.

## Detailed Description

Secondary structure plot layout algorithms.

c Ronny Lorenz The ViennaRNA Package

## Define Documentation

#define VRNA_PLOT_TYPE_SIMPLE 0

Definition of Plot type simple

This is the plot type definition for several RNA structure plotting functions telling them to use Simple plotting algorithm

See also:
  rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()

#define VRNA_PLOT_TYPE_NAVIEW 1

Definition of Plot type Naview

This is the plot type definition for several RNA structure plotting functions telling them to use Naview plotting algorithm

See also:
  rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()

#define VRNA_PLOT_TYPE_CIRCULAR 2

Definition of Plot type Circular

This is the plot type definition for several RNA structure plotting functions telling them to produce a Circular plot

See also:
  rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()

## Function Documentation

int simple_xy_coordinates | ( | short * | pair_table,
|  | float * | X,
|  | float * | Y |
| ) |  |  |

Calculate nucleotide coordinates for secondary structure plot the Simple way

See also:
  make_pair_table(), rna_plot_type, simple_circplot_coordinates(), naview_xy_coordinates(), PS_rna_plot_a(), PS_rna_plot, svg_rna_plot()

Parameters:

  pair_table

  The pair table of the secondary structure
  Parameters:

    X

    a pointer to an array with enough allocated space to hold the x coordinates
    Parameters:

      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 |
| ) |  |  |

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(), PS_rna_plot_a(), PS_rna_plot, svg_rna_plot()

Parameters:

  pair_table

  The pair table of the secondary structure
  Parameters:

    x

    a pointer to an array with enough allocated space to hold the x coordinates
    Parameters:

      y

      a pointer to an array with enough allocated space to hold the y coordinates
      Returns:
        length of sequence on success, 0 otherwise

## Variable Documentation

int rna_plot_type

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 Bruccoleri & Heinrich (1988).

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