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
- Added script for PAF format
- Fixes for Mummer format script: add -t param, add handling of one ref chrom
The script requires three R packages: install.packages(c("optparse", "ggplot2", "plotly")).
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