RNAlib-2.5.1
Plotting

Create Plots of Secondary Structures, Feature Motifs, and Sequence Alignments

Producing secondary structure graphs

int PS_rna_plot ( char *string,
                  char *structure,
                  char *file)

Produce a secondary structure graph in PostScript and write it to 'filename'.

int PS_rna_plot_a (
            char *string,
            char *structure,
            char *file,
            char *pre,
            char *post)

Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'.

int gmlRNA (char *string,
            char *structure,
            char *ssfile,
            char option)

Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file.

int ssv_rna_plot (char *string,
                  char *structure,
                  char *ssfile)

Produce a secondary structure graph in SStructView format.

int svg_rna_plot (char *string,
                  char *structure,
                  char *ssfile)

Produce a secondary structure plot in SVG format and write it to a file.

int xrna_plot ( char *string,
                char *structure,
                char *ssfile)

Produce a secondary structure plot for further editing in XRNA.

int rna_plot_type

Switch for changing the secondary structure layout algorithm.

Two low-level functions provide direct access to the graph lauyouting algorithms:

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

Calculate nucleotide coordinates for secondary structure plot the Simple way

int naview_xy_coordinates ( short *pair_table,
                            float *X,
                            float *Y)
See also
PS_dot.h and naview.h for more detailed descriptions.


Table of Contents

Producing (colored) dot plots for base pair probabilities

int PS_color_dot_plot ( char *string,
                        cpair *pi,
                        char *filename)
int PS_color_dot_plot_turn (char *seq,
                            cpair *pi,
                            char *filename,
                            int winSize)
int PS_dot_plot_list (char *seq,
                      char *filename,
                      plist *pl,
                      plist *mf,
                      char *comment)

Produce a postscript dot-plot from two pair lists.

int PS_dot_plot_turn (char *seq,
                      struct plist *pl,
                      char *filename,
                      int winSize)
See also
PS_dot.h for more detailed descriptions.

Producing (colored) alignments

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.