Functions related to plotting of probabilities, such as dot-plots. More...
Functions related to plotting of probabilities, such as dot-plots.
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. | |
struct vrna_dotplot_auxdata_t |
#define VRNA_PLOT_PROBABILITIES_DEFAULT |
#include <ViennaRNA/plotting/probabilities.h>
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).
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.
filename | A filename for the EPS output |
sequence | The RNA sequence |
upper | The base pair probabilities for the upper triangular part |
lower | The base pair probabilities for the lower triangular part |
options | Options indicating which of the input data should be included in the dot-plot |
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 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.
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 |