Advanced Dotplot Generator

Generate a dotplot that supports score-based filters along with alignment filters. In addition, this version supports AJAX-friendly JSON output for found alignments

Filters

There are two types of filters:

• Alignment filters
• Score filters A score filter may represent a conservation value ranging from 0 to 1 and an alignment filter specifies the minimum match length for a non-gapped alignment. The alignment filter is first generated through the function find_alignments and then applied through apply_alignments. A value filter can be imported as a text file or given as an array.

Generator Program

Builds a configurable dotplot

Usage: genplot [OPTIONS] <sequence1> <sequence2> <output_file>

Options

• x file to use as the first score filter for sequence1
• y file to use as the first score filter for sequence2
• p file to use as the second score filter for sequence1
• q file to use as the second score filter for sequence2
• n minimum alignment length
• w width (in pixels) of the resulting file
• h height (in pixels) of the resulting file

API

dotplot *create_dotplot(char *seq1, char *seq2)

Creates an unfiltered dotplot from two sequence strings

dotplot *create_dotplot_from_fasta(char *file1, char *file2) (UNIX only)

Creates an unfiltered dotplot from two files containing sequences. Currently, only sequence files are supported without the fasta header because text processing in C is a pain

dotplot *zero_dotplot(dotplot *dp)

Creates one dotplot from another with all the cells cleared (values set to 0.0)

dotplot *clone_dotlot(dotplot *dp)

Creates a clone of a dotplot

void destroy_dotplot(dotplot *dp)

Frees allocated memory for a dotplot

list_t *find_alignments(dotplot *dp, int length)

Find alignments of minimum length length and return them as a list to be applied in a later step

dotplot *apply_alignments(dotplot *dp, list_t *alignments)

Apply alignments to a dotplot, returning a new dotplot with the filter applied

void destroy_alignments(list_t *alignments)

Free allocated memory for a list of alignments created through find_alignments

void print_alignments(list_t *alignments, char *seq1, char *seq2)

Print JSON output describing the list of alignments in the format

[
  {
    "sequence": "ACTG",
    "position": {
      "x": 1,
      "y": 1
    }
  }
]

filter *create_filter(int width, int, height, float **vals)

Create a filter with vals associating to each cell in the dotplot with each cell in the array as a value between 0 and 1

filter *create_filter_from_values(char *file1, char *file2) (UNIX only)

Create a filter as above but with the values coming from a filemask for seq1 and seq2

dotplot *apply_filter(dotplot *dp, filter *f)

Apply a score filter generated by create_filter and return the resulting dotplot

dotplot *apply_filter_safe(dotplot *dp, filter *f)

Same as apply_filter, but asserts dotplot and filter dimensions are the same

void destroy_filter(filter *f)

Free allocated memory for a filter

int set_value(dotplot *dp, int x, int y, float value)

Set the value at a cell in the dotplot. Returns 1 or 0 depending on whether or not the operation succeeded (ie., not out of bounds)

gdImagePtr render_dotplot(dotplot *dp, int width, int height)

Render the dotplot to an internal image representation with image dimensions of (width, height)

color_chooser *create_color_chooser(color default_color)

Create a color chooser to be used for rendering a continuous dotplot with a score filter (color is a struct with properties red, green, and blue)

destroy_color_chooser(color_chooser *cc)

Free allocated memory for a color chooser

int add_color(color_chooser *cc, float start, float end, color c)

Add a color to be chosen for a range between start and end when rendering a dotplot with a score filter. Returns 1 or 0 depending on whether or not the operation succeeded (ie., not out of bounds)

color color_for(color_chooser *cc, float value)

Find the color to be chosen for a color_chooser cc given value value

gdImagePtr render_dotplot_continuous(dotplot *dp, color_chooser *cc, int width, int height)

Render a multicolored dotplot where each color relates to a value from the applied score filter