Fix for issue #18 (add .svg and .pdf support)

[lonelyjoeparker]

…dotPlotly/issues/18)

Issue raised by @Sven-Winter and @Jwindler suggested altering ggsave() argument to .pdf.

I implemented this including adding CLI options to the parser: --pdf-plot-on and --svg-plot-on. Defaults for both args are set to to FALSE to be consistent with existing behaviour. I chose long-form arguments as the obvious single letter (-f -v -g -p) forms were either already taken or ambiguous in meaning.

Consistent with the existing README.md but I also added a simpler example (MPA01-vs-PA01.minimap2.paf) at master...lonelyjoeparker:dotPlotly-issue-18:master#diff-cbccb4caeac8ae21fecaaabaab0b3548186ceeb961b37d23a167beeaf7d2dfb4 that executes more quickly, to facilitate testing; and a .gitignore file to exclude the various outputs from the repo (again, so users/coders can verify example below is working).

Fix and testing:

This now has the following behaviour which I believe validates this PR as working:

DEFAULT CASE: No .pdf or .svg enabled:

joe$ ./pafCoordsDotPlotly.R -i example/MPA01-vs-PA01.minimap2.paf -o out -s -t -m 500 -q 500000 -k 7 -l
PARAMETERS:
input (-i): example/MPA01-vs-PA01.minimap2.paf
output (-o): out
minimum query aggregate alignment length (-q): 5e+05
minimum alignment length (-m): 500
plot size (-p): 15
show horizontal lines (-l): TRUE
number of reference chromosomes to keep (-k): 7
show % identity (-s): TRUE
show % identity for on-target alignments only (-t): TRUE
produce interactive plot (-x): TRUE
produce .pdf plot (--pdf-plot-on): FALSE
produce .svg plot (--svg-plot-on): FALSE
reference IDs to keep (-r): 

Number of alignments: 5
Number of query sequences: 1

After filtering... Number of alignments: 4
After filtering... Number of query sequences: 1

joe$ ls -laht
total 4.0M
drwxrwxr-x  8 joe joe 4.0K Jan 17 13:27 .git
drwxrwxr-x  5 joe joe 4.0K Jan 17 13:27 .
-rw-rw-r--  1 joe joe 3.7M Jan 17 13:27 out.html
-rw-rw-r--  1 joe joe 166K Jan 17 13:27 out.png
drwxrwxr-x  2 joe joe 4.0K Jan 17 13:27 example
-rwxrwxr-x  1 joe joe  17K Jan 17 13:00 pafCoordsDotPlotly.R
-rwxrwxr-x  1 joe joe  15K Jan 17 13:00 mummerCoordsDotPlotly.R
drwxrwxr-x  2 joe joe 4.0K Jan 17 13:00 dotPlotly_shiny
-rw-rw-r--  1 joe joe 1.1K Jan 17 13:00 LICENSE.md
-rw-rw-r--  1 joe joe 2.3K Jan 17 13:00 README.md
drwxr-xr-x 34 joe joe 4.0K Jan 17 12:59 ..

POSITIVE case: .pdf and .svg both enabled:

joe$ ./pafCoordsDotPlotly.R -i example/MPA01-vs-PA01.minimap2.paf -o out -s -t -m 500 -q 500000 -k 7 -l --pdf-plot-on --svg-plot-on
PARAMETERS:
input (-i): example/MPA01-vs-PA01.minimap2.paf
output (-o): out
minimum query aggregate alignment length (-q): 5e+05
minimum alignment length (-m): 500
plot size (-p): 15
show horizontal lines (-l): TRUE
number of reference chromosomes to keep (-k): 7
show % identity (-s): TRUE
show % identity for on-target alignments only (-t): TRUE
produce interactive plot (-x): TRUE
produce .pdf plot (--pdf-plot-on): TRUE
produce .svg plot (--svg-plot-on): TRUE
reference IDs to keep (-r): 

Number of alignments: 5
Number of query sequences: 1

After filtering... Number of alignments: 4
After filtering... Number of query sequences: 1

 joe$ ls -laht
total 4.0M
drwxrwxr-x  8 joe joe 4.0K Jan 17 13:34 .git
drwxrwxr-x  5 joe joe 4.0K Jan 17 13:34 .
-rw-rw-r--  1 joe joe 3.7M Jan 17 13:34 out.html
-rw-rw-r--  1 joe joe 5.3K Jan 17 13:34 out.svg
-rw-rw-r--  1 joe joe 5.1K Jan 17 13:34 out.pdf
-rw-rw-r--  1 joe joe 166K Jan 17 13:34 out.png
-rw-rw-r--  1 joe joe    5 Jan 17 13:28 .gitignore
drwxrwxr-x  2 joe joe 4.0K Jan 17 13:27 example
-rwxrwxr-x  1 joe joe  17K Jan 17 13:00 pafCoordsDotPlotly.R
-rwxrwxr-x  1 joe joe  15K Jan 17 13:00 mummerCoordsDotPlotly.R
drwxrwxr-x  2 joe joe 4.0K Jan 17 13:00 dotPlotly_shiny
-rw-rw-r--  1 joe joe 1.1K Jan 17 13:00 LICENSE.md
-rw-rw-r--  1 joe joe 2.3K Jan 17 13:00 README.md
drwxr-xr-x 34 joe joe 4.0K Jan 17 12:59 ..

(NB, tested but not shown - alternately toggling .pdf OR .svg behaviour works as expected too)

HELP -h behaviour:

joe$ ./pafCoordsDotPlotly.R -h
Usage: ./pafCoordsDotPlotly.R -i alignments.coords -o out [options]


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, --identity
		turn on color alignments by % identity [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]

	--pdf-plot-on
		turn on production of .PDF format plotly [default FALSE]

	--svg-plot-on
		turn on production of .SVG format plotly [default FALSE]

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