dotPlotly

Create an interactive dot plot from mummer output OR PAF format

R script that makes a plotly interactive and/or static (png/pdf) dot plot.

Shiny app available for testing

Example (more here)

For mummer (nucmer -> show-coords) output:

show-coords -c example.delta > example.coords
./mummerCoordsDotPlotly.R -i example.coords -o out -s -t -m 500 -q 500000 -k 7 -l

For PAF format (e.g. minimap2):

./pafCoordsDotPlotly.R -i example.paf -o out -s -t -m 500 -q 500000 -k 7 -l

Updates (10/29/17)

• Added script for PAF format
• Fixes for Mummer format script: add -t param, add handling of one ref chrom

Dependencies

The script requires three R packages: install.packages(c("optparse", "ggplot2", "plotly")).

Script parameters

Use ./mummerCoordsDotPlotly.R -h to see options.

    -i INPUT, --input=INPUT
        coords file from mummer program 'show.coords' [default NULL]

    -o OUTPUT, --output=OUTPUT
        output filename prefix [default out]

    -v, --verbose
        Print out all parameter settings [default]

    -q MIN-QUERY-LENGTH, --min-query-length=MIN-QUERY-LENGTH
        filter queries with total alignments less than cutoff X bp [default 4e+05]

    -m MIN-ALIGNMENT-LENGTH, --min-alignment-length=MIN-ALIGNMENT-LENGTH
        filter alignments less than cutoff X bp [default 10000]

    -p PLOT-SIZE, --plot-size=PLOT-SIZE
        plot size X by X inches [default 15]

    -l, --show-horizontal-lines
        turn on horizontal lines on plot for separating scaffolds  [default FALSE]

    -k NUMBER-REF-CHROMOSOMES, --number-ref-chromosomes=NUMBER-REF-CHROMOSOMES
        number of sorted reference chromosomes to keep [default all chromosmes]

    -s, --similarity
        turn on color alignments by percent similarity [default FALSE]

    -t, --identity-on-target
        turn on calculation of % identity for on-target alignments only [default FALSE]

    -x, --interactive-plot-off
        turn off production of interactive plotly [default TRUE]

    -r REFERENCE-IDS, --reference-ids=REFERENCE-IDS
        comma-separated list of reference IDs to keep [default NULL]

    -h, --help
        Show this help message and exit