RNAlib-2.6.3
 
Loading...
Searching...
No Matches
Probabilities

Functions related to plotting of probabilities, such as dot-plots. More...

Detailed Description

Functions related to plotting of probabilities, such as dot-plots.

+ Collaboration diagram for Probabilities:

Data Structures

struct  vrna_dotplot_auxdata_t
 

Macros

#define VRNA_PLOT_PROBABILITIES_BP   1U
 Option flag for base pair probabilities in probability plot output functions.
 
#define VRNA_PLOT_PROBABILITIES_ACC   2U
 Option flag for accessibilities in probability plot output functions.
 
#define VRNA_PLOT_PROBABILITIES_UD   4U
 Option flag for unstructured domain probabilities in probability plot output functions.
 
#define VRNA_PLOT_PROBABILITIES_UD_LIN   8U
 Option flag for unstructured domain probabilities (linear representation) in probability plot output functions.
 
#define VRNA_PLOT_PROBABILITIES_SD   16U
 Option flag for structured domain probabilities (such as G-quadruplexes) in probability plot output functions.
 
#define VRNA_PLOT_PROBABILITIES_SC_MOTIF   32U
 Option flag for soft-constraint motif probabilities in probability plot output functions.
 
#define VRNA_PLOT_PROBABILITIES_DEFAULT
 Default option flag for probability plot output functions.
 

Functions

int vrna_plot_dp_EPS (const char *filename, const char *sequence, vrna_ep_t *upper, vrna_ep_t *lower, vrna_dotplot_auxdata_t *auxdata, unsigned int options)
 Produce an encapsulate PostScript (EPS) dot-plot from one or two lists of base pair probabilities.
 
int vrna_plot_dp_PS_list (char *seq, int cp, char *filename, vrna_ep_t *pl, vrna_ep_t *mf, char *comment)
 Produce a postscript dot-plot from two pair lists.
 

Data Structure Documentation

◆ vrna_dotplot_auxdata_t

struct vrna_dotplot_auxdata_t
+ Collaboration diagram for vrna_dotplot_auxdata_t:

Macro Definition Documentation

◆ VRNA_PLOT_PROBABILITIES_DEFAULT

#define VRNA_PLOT_PROBABILITIES_DEFAULT

#include <ViennaRNA/plotting/probabilities.h>

Value:
#define VRNA_PLOT_PROBABILITIES_SC_MOTIF
Option flag for soft-constraint motif probabilities in probability plot output functions.
Definition probabilities.h:67
#define VRNA_PLOT_PROBABILITIES_UD_LIN
Option flag for unstructured domain probabilities (linear representation) in probability plot output ...
Definition probabilities.h:55
#define VRNA_PLOT_PROBABILITIES_SD
Option flag for structured domain probabilities (such as G-quadruplexes) in probability plot output f...
Definition probabilities.h:61
#define VRNA_PLOT_PROBABILITIES_BP
Option flag for base pair probabilities in probability plot output functions.
Definition probabilities.h:37

Default option flag for probability plot output functions.

Default output includes actual base pair probabilties (VRNA_PLOT_PROBABILITIES_BP), structured domain probabilities such as G-quadruplexes (VRNA_PLOT_PROBABILITIES_SD), probabilities obtained from soft-constraint motif implementation (VRNA_PLOT_PROBABILITIES_SC_MOTIF), and unstructured domain probabilities (VRNA_PLOT_PROBABILITIES_UD_LIN).

See also
vrna_plot_dp_EPS()

Function Documentation

◆ vrna_plot_dp_EPS()

int vrna_plot_dp_EPS ( const char *  filename,
const char *  sequence,
vrna_ep_t upper,
vrna_ep_t lower,
vrna_dotplot_auxdata_t auxdata,
unsigned int  options 
)

#include <ViennaRNA/plotting/probabilities.h>

Produce an encapsulate PostScript (EPS) dot-plot from one or two lists of base pair probabilities.

This function reads two vrna_ep_t lists upper and lower (e.g. base pair probabilities and a secondary structure) and produces an EPS "dot plot" with filename 'filename' where data from upper is placed in the upper-triangular and data from lower is placed in the lower triangular part of the matrix.
For default output, provide the flag VRNA_PLOT_PROBABILITIES_DEFAULT as options parameter.

See also
vrna_plist(), vrna_plist_from_probs(), VRNA_PLOT_PROBABILITIES_DEFAULT
Parameters
filenameA filename for the EPS output
sequenceThe RNA sequence
upperThe base pair probabilities for the upper triangular part
lowerThe base pair probabilities for the lower triangular part
optionsOptions indicating which of the input data should be included in the dot-plot
Returns
1 if EPS file was successfully written, 0 otherwise
SWIG Wrapper Notes:
This function is available as overloaded function plot_dp_EPS() where the last three parameters may be omitted. The default values for these parameters are lower = NULL, auxdata = NULL, options = VRNA_PLOT_PROBABILITIES_DEFAULT

◆ vrna_plot_dp_PS_list()

int vrna_plot_dp_PS_list ( char *  seq,
int  cp,
char *  filename,
vrna_ep_t pl,
vrna_ep_t 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 vrna_plist_from_probs() and vrna_plist() 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
vrna_plist_from_probs(), vrna_plist()
Parameters
seqThe RNA sequence
filenameA filename for the postscript output
plThe base pair probability pairlist
mfThe mfe secondary structure pairlist
commentA comment
Returns
1 if postscript was successfully written, 0 otherwise