Layouts and Coordinates

Functions to compute coordinate layouts for secondary structure plots.

Defines

VRNA_PLOT_TYPE_SIMPLE

#include <ViennaRNA/plotting/layouts.h>

Definition of Plot type simple

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

VRNA_PLOT_TYPE_NAVIEW

#include <ViennaRNA/plotting/layouts.h>

Definition of Plot type Naview

This is the plot type definition for several RNA structure plotting functions telling them to use Naview plotting algorithm [Bruccoleri and Heinrich, 1988] .

VRNA_PLOT_TYPE_CIRCULAR

#include <ViennaRNA/plotting/layouts.h>

Definition of Plot type Circular

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

VRNA_PLOT_TYPE_TURTLE: #include <ViennaRNA/plotting/layouts.h>
Definition of Plot type Turtle [Wiegreffe et al., 2019] .

VRNA_PLOT_TYPE_PUZZLER: #include <ViennaRNA/plotting/layouts.h>
Definition of Plot type RNApuzzler [Wiegreffe et al., 2019] .

VRNA_PLOT_TYPE_DEFAULT: #include <ViennaRNA/plotting/layouts.h>

Typedefs

typedef struct vrna_plot_layout_s vrna_plot_layout_t

#include <ViennaRNA/plotting/layouts.h>

RNA secondary structure figure layout.

Functions

vrna_plot_layout_t *vrna_plot_layout(const char *structure, unsigned int plot_type)

#include <ViennaRNA/plotting/layouts.h>

Create a layout (coordinates, etc.) for a secondary structure plot.

This function can be used to create a secondary structure nucleotide layout that is then further processed by an actual plotting function. The layout algorithm can be specified using the plot_type parameter, and the following algorithms are currently supported:

VRNA_PLOT_TYPE_SIMPLE
VRNA_PLOT_TYPE_NAVIEW
VRNA_PLOT_TYPE_CIRCULAR
VRNA_PLOT_TYPE_TURTLE
VRNA_PLOT_TYPE_PUZZLER

Passing an unsupported selection leads to the default algorithm VRNA_PLOT_TYPE_NAVIEW

See also

vrna_plot_layout_free(), vrna_plot_layout_simple(), vrna_plot_layout_naview(), vrna_plot_layout_circular(), vrna_plot_layout_turtle(), vrna_plot_layout_puzzler(), vrna_plot_coords(), vrna_file_PS_rnaplot_layout()

Note

If only X-Y coordinates of the corresponding structure layout are required, consider using vrna_plot_coords() instead!

Parameters:

structure – The secondary structure in dot-bracket notation
plot_type – The layout algorithm to be used

Returns:

The layout data structure for the provided secondary structure

vrna_plot_layout_t *vrna_plot_layout_simple(const char *structure)

#include <ViennaRNA/plotting/layouts.h>

Create a layout (coordinates, etc.) for a simple secondary structure plot.

This function basically is a wrapper to vrna_plot_layout() that passes the plot_type VRNA_PLOT_TYPE_SIMPLE.

See also

vrna_plot_layout_free(), vrna_plot_layout(), vrna_plot_layout_naview(), vrna_plot_layout_circular(), vrna_plot_layout_turtle(), vrna_plot_layout_puzzler(), vrna_plot_coords_simple(), vrna_file_PS_rnaplot_layout()

Note

If only X-Y coordinates of the corresponding structure layout are required, consider using vrna_plot_coords_simple() instead!

Parameters:

structure – The secondary structure in dot-bracket notation

Returns:

The layout data structure for the provided secondary structure

vrna_plot_layout_t *vrna_plot_layout_circular(const char *structure)

#include <ViennaRNA/plotting/layouts.h>

Create a layout (coordinates, etc.) for a circular secondary structure plot.

This function basically is a wrapper to vrna_plot_layout() that passes the plot_type VRNA_PLOT_TYPE_CIRCULAR.

See also

vrna_plot_layout_free(), vrna_plot_layout(), vrna_plot_layout_naview(), vrna_plot_layout_simple(), vrna_plot_layout_turtle(), vrna_plot_layout_puzzler(), vrna_plot_coords_circular(), vrna_file_PS_rnaplot_layout()

Note

If only X-Y coordinates of the corresponding structure layout are required, consider using vrna_plot_coords_circular() instead!

Parameters:

structure – The secondary structure in dot-bracket notation

Returns:

The layout data structure for the provided secondary structure

vrna_plot_layout_t *vrna_plot_layout_turtle(const char *structure)

#include <ViennaRNA/plotting/layouts.h>

Create a layout (coordinates, etc.) for a secondary structure plot using the Turtle Algorithm [Wiegreffe et al., 2019] .

This function basically is a wrapper to vrna_plot_layout() that passes the plot_type VRNA_PLOT_TYPE_TURTLE.

See also

vrna_plot_layout_free(), vrna_plot_layout(), vrna_plot_layout_simple(), vrna_plot_layout_circular(), vrna_plot_layout_naview(), vrna_plot_layout_puzzler(), vrna_plot_coords_turtle(), vrna_file_PS_rnaplot_layout()

Note

If only X-Y coordinates of the corresponding structure layout are required, consider using vrna_plot_coords_turtle() instead!

Parameters:

structure – The secondary structure in dot-bracket notation

Returns:

The layout data structure for the provided secondary structure

vrna_plot_layout_t *vrna_plot_layout_puzzler(const char *structure, vrna_plot_options_puzzler_t *options)

#include <ViennaRNA/plotting/layouts.h>

Create a layout (coordinates, etc.) for a secondary structure plot using the RNApuzzler Algorithm [Wiegreffe et al., 2019] .

This function basically is a wrapper to vrna_plot_layout() that passes the plot_type VRNA_PLOT_TYPE_PUZZLER.

See also

vrna_plot_layout_free(), vrna_plot_layout(), vrna_plot_layout_simple(), vrna_plot_layout_circular(), vrna_plot_layout_naview(), vrna_plot_layout_turtle(), vrna_plot_coords_puzzler(), vrna_file_PS_rnaplot_layout()

Note

If only X-Y coordinates of the corresponding structure layout are required, consider using vrna_plot_coords_puzzler() instead!

Parameters:

structure – The secondary structure in dot-bracket notation

Returns:

The layout data structure for the provided secondary structure

void vrna_plot_layout_free(vrna_plot_layout_t *layout)

#include <ViennaRNA/plotting/layouts.h>

Free memory occupied by a figure layout data structure.

See also

vrna_plot_layout_t, vrna_plot_layout(), vrna_plot_layout_simple(), vrna_plot_layout_circular(), vrna_plot_layout_naview(), vrna_plot_layout_turtle(), vrna_plot_layout_puzzler(), vrna_file_PS_rnaplot_layout()

Parameters:

layout – The layout data structure to free

int vrna_plot_coords(const char *structure, float **x, float **y, int plot_type)

#include <ViennaRNA/plotting/layouts.h>

Compute nucleotide coordinates for secondary structure plot.

This function takes a secondary structure and computes X-Y coordinates for each nucleotide that then can be used to create a structure plot. The parameter plot_type is used to select the underlying layout algorithm. Currently, the following selections are provided:

VRNA_PLOT_TYPE_SIMPLE
VRNA_PLOT_TYPE_NAVIEW
VRNA_PLOT_TYPE_CIRCULAR
VRNA_PLOT_TYPE_TURTLE
VRNA_PLOT_TYPE_PUZZLER

Passing an unsupported selection leads to the default algorithm VRNA_PLOT_TYPE_NAVIEW

Here is a simple example how to use this function, assuming variable structure contains a valid dot-bracket string:

float *x, *y;

if (vrna_plot_coords(structure, &x, &y)) {
  printf("all fine");
} else {
  printf("some failure occured!");
}

free(x);
free(y);

Note

On success, this function allocates memory for X and Y coordinates and assigns the pointers at addressess x and y to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

structure – The secondary structure in dot-bracket notation
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)
plot_type – The layout algorithm to be used

Returns:

The length of the structure on success, 0 otherwise

int vrna_plot_coords_pt(const short *pt, float **x, float **y, int plot_type)

#include <ViennaRNA/plotting/layouts.h>

Compute nucleotide coordinates for secondary structure plot.

Same as vrna_plot_coords() but takes a pair table with the structure information as input.

Note

On success, this function allocates memory for X and Y coordinates and assigns the pointers at addressess x and y to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

pt – The pair table that holds the secondary structure
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)
plot_type – The layout algorithm to be used

Returns:

The length of the structure on success, 0 otherwise

int vrna_plot_coords_simple(const char *structure, float **x, float **y)

#include <ViennaRNA/plotting/layouts.h>

Compute nucleotide coordinates for secondary structure plot the Simple way

This function basically is a wrapper to vrna_plot_coords() that passes the plot_type VRNA_PLOT_TYPE_SIMPLE.

Here is a simple example how to use this function, assuming variable structure contains a valid dot-bracket string:

float *x, *y;

if (vrna_plot_coords_simple(structure, &x, &y)) {
  printf("all fine");
} else {
  printf("some failure occured!");
}

free(x);
free(y);

Note

On success, this function allocates memory for X and Y coordinates and assigns the pointers at addressess x and y to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

structure – The secondary structure in dot-bracket notation
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)

Returns:

The length of the structure on success, 0 otherwise

int vrna_plot_coords_simple_pt(const short *pt, float **x, float **y)

#include <ViennaRNA/plotting/layouts.h>

Compute nucleotide coordinates for secondary structure plot the Simple way

Same as vrna_plot_coords_simple() but takes a pair table with the structure information as input.

Note

On success, this function allocates memory for X and Y coordinates and assigns the pointers at addressess x and y to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

pt – The pair table that holds the secondary structure
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)

Returns:

The length of the structure on success, 0 otherwise

int vrna_plot_coords_circular(const char *structure, float **x, float **y)

#include <ViennaRNA/plotting/layouts.h>

Compute coordinates of nucleotides mapped in equal distancies onto a unit circle.

This function basically is a wrapper to vrna_plot_coords() that passes the plot_type VRNA_PLOT_TYPE_CIRCULAR.

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

\[ P^{t}_y[i] = Y[i] * rs \]

.

Note

On success, this function allocates memory for X and Y coordinates and assigns the pointers at addressess x and y to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

structure – The secondary structure in dot-bracket notation
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)

Returns:

The length of the structure on success, 0 otherwise

int vrna_plot_coords_circular_pt(const short *pt, float **x, float **y)

#include <ViennaRNA/plotting/layouts.h>

Compute nucleotide coordinates for a Circular Plot

Same as vrna_plot_coords_circular() but takes a pair table with the structure information as input.

Note

On success, this function allocates memory for X and Y coordinates and assigns the pointers at addressess x and y to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

pt – The pair table that holds the secondary structure
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)

Returns:

The length of the structure on success, 0 otherwise

int vrna_plot_coords_puzzler(const char *structure, float **x, float **y, double **arc_coords, vrna_plot_options_puzzler_t *options)

#include <ViennaRNA/plotting/RNApuzzler/RNApuzzler.h>

Compute nucleotide coordinates for secondary structure plot using the RNApuzzler algorithm [Wiegreffe et al., 2019] .

This function basically is a wrapper to vrna_plot_coords() that passes the plot_type VRNA_PLOT_TYPE_PUZZLER.

Here is a simple example how to use this function, assuming variable structure contains a valid dot-bracket string and using the default options (options = NULL):

float  *x, *y;
double *arcs;

if (vrna_plot_coords_puzzler(structure, &x, &y, &arcs, NULL)) {
  printf("all fine");
} else {
  printf("some failure occured!");
}

free(x);
free(y);
free(arcs);

Note

On success, this function allocates memory for X, Y and arc coordinates and assigns the pointers at addressess x, y and arc_coords to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

structure – The secondary structure in dot-bracket notation
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)
arc_coords – [inout] The address of a pointer that will hold arc coordinates (pointer will point to memory, or NULL on failure)
options – The options for the RNApuzzler algorithm (or NULL)

Returns:

The length of the structure on success, 0 otherwise

int vrna_plot_coords_puzzler_pt(short const *const pair_table, float **x, float **y, double **arc_coords, vrna_plot_options_puzzler_t *puzzler)

#include <ViennaRNA/plotting/RNApuzzler/RNApuzzler.h>

Compute nucleotide coordinates for secondary structure plot using the RNApuzzler algorithm [Wiegreffe et al., 2019] .

Same as vrna_plot_coords_puzzler() but takes a pair table with the structure information as input.

Note

On success, this function allocates memory for X, Y and arc coordinates and assigns the pointers at addressess x, y and arc_coords to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

pt – The pair table that holds the secondary structure
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)
arc_coords – [inout] The address of a pointer that will hold arc coordinates (pointer will point to memory, or NULL on failure)
options – The options for the RNApuzzler algorithm (or NULL)

Returns:

The length of the structure on success, 0 otherwise

vrna_plot_options_puzzler_t *vrna_plot_options_puzzler(void)

#include <ViennaRNA/plotting/RNApuzzler/RNApuzzler.h>

Create an RNApuzzler options data structure.

Returns:: An RNApuzzler options data structure with default settings

void vrna_plot_options_puzzler_free(vrna_plot_options_puzzler_t *options)

#include <ViennaRNA/plotting/RNApuzzler/RNApuzzler.h>

Free memory occupied by an RNApuzzler options data structure.

Parameters:

options – A pointer to the options data structure to free

int vrna_plot_coords_turtle(const char *structure, float **x, float **y, double **arc_coords)

#include <ViennaRNA/plotting/RNApuzzler/RNAturtle.h>

Compute nucleotide coordinates for secondary structure plot using the RNAturtle algorithm [Wiegreffe et al., 2019] .

This function basically is a wrapper to vrna_plot_coords() that passes the plot_type VRNA_PLOT_TYPE_TURTLE.

Here is a simple example how to use this function, assuming variable structure contains a valid dot-bracket string:

float  *x, *y;
double *arcs;

if (vrna_plot_coords_turtle(structure, &x, &y, &arcs)) {
  printf("all fine");
} else {
  printf("some failure occured!");
}

free(x);
free(y);
free(arcs);

Note

On success, this function allocates memory for X, Y and arc coordinates and assigns the pointers at addressess x, y and arc_coords to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

structure – The secondary structure in dot-bracket notation
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)
arc_coords – [inout] The address of a pointer that will hold arc coordinates (pointer will point to memory, or NULL on failure)

Returns:

The length of the structure on success, 0 otherwise

int vrna_plot_coords_turtle_pt(short const *const pair_table, float **x, float **y, double **arc_coords)

#include <ViennaRNA/plotting/RNApuzzler/RNAturtle.h>

Compute nucleotide coordinates for secondary structure plot using the RNAturtle algorithm [Wiegreffe et al., 2019] .

Same as vrna_plot_coords_turtle() but takes a pair table with the structure information as input.

Note

On success, this function allocates memory for X, Y and arc coordinates and assigns the pointers at addressess x, y and arc_coords to the corresponding memory locations. It’s the users responsibility to cleanup this memory after usage!

Parameters:

pt – The pair table that holds the secondary structure
x – [inout] The address of a pointer of X coordinates (pointer will point to memory, or NULL on failure)
y – [inout] The address of a pointer of Y coordinates (pointer will point to memory, or NULL on failure)
arc_coords – [inout] The address of a pointer that will hold arc coordinates (pointer will point to memory, or NULL on failure)

Returns:

The length of the structure on success, 0 otherwise

struct vrna_plot_layout_s

Public Members

unsigned int length

float *x

float *y

double *arcs

int bbox[4]

struct vrna_plot_options_puzzler_t

#include <ViennaRNA/plotting/RNApuzzler/RNApuzzler.h>

Options data structure for RNApuzzler algorithm implementation.

Public Members

short drawArcs

double paired

double unpaired

short checkAncestorIntersections

short checkSiblingIntersections

short checkExteriorIntersections

short allowFlipping

short optimize

int maximumNumberOfConfigChangesAllowed

char *config

const char *filename

int numberOfChangesAppliedToConfig

int psNumber