Interpretation of gnuplot

[HTaekOppa]

Dear MashMap,

Thank you for the great program. It was really easy to use.
I have a quick questions about the outcome of gun plot (plot dot graph).

If you look at the png file, it shows a different colours (light blue and purple) and and direction (vertically and/or inverted).

Could you please provide me a bit more explanation about this?

Many thanks in advance!

Cheers,

Taek

[cjain7]

Hi, each color dot/line indicates match between your ref. and query. We use two different colors to differentiate the strands (+ve/ -ve). Inverted lines indicate inversions.
You can also use the interactive terminal output format to zoom into various locations...

[HTaekOppa]

Hi,

Thank you for the answer.
Re interactive terminal output format to zoom, could you please tell me more about this? Is it required any specific mode and/or output file format? I used "png" mode to generate the plot.

Re other modes, I also used "x11" and "postscript" but did not work. It failed generating plot. What is the difference (output file/format) between "png" and "x11 & postscrpt"?

Rendering plot out
gnuplot -geometry 700x700+0+0 -title mashmap-dotplot out.gp
WARNING: Unable to query clipboard with xclip
unrecognized option -geometry
"700x700+0+0", line 0: Cannot open script file '700x700+0+0'

Can't find PostScript prologue file prologue.ps
loadpath is empty
gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/5.0
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"out.gp", line 909: Plot failed!

Apart from this, is there any chance I could generate a circulus plot using the current output from MashMap?

Cheers,

Taek

[cjain7]

Can you retry the "x11" option with the most recent version of generateDotPlot script ? I made a minor update to the script to work with gnuplot 5+.

We don't have support for circular visualization. You can try the popular circos tool; however the output of mashmap will need to be modified into its format.

[macarima]

In my case, same problem was happened.

ArimaMini:Genome_assembly_comparsion_mashmap

macarima$ ./generateDotPlot.pl postscript medium mashmap.out
gnuplot 5.2 patchlevel 6
Reading mashmap file mashmap.out
Writing plot files out.fplot, out.rplot
Writing gnuplot script out.gp
Rendering plot out.ps
gnuplot out.gp

set terminal postscript color solid "Courier" 8 enhanced font 'Courier,8'
^
"out.gp" line 1: extraneous argument in set terminal postscript

WARNING: Unable to run 'gnuplot out.gp', Inappropriate ioctl for device

I cannot use postscript or x11 mode, too.
I use gnuplot 5.2 patchlevel 6 on osx and linux.

[cjain7]

@macarima, after you run the script, can you remove the text enhanced font 'Courier,8' from the file out.gp , and try running gnuplot out.gp ?
Please try with three modes and let me know if it helps.

[cjain7]

I wonder if your gnuplot installation supports png. You can check by opening your terminal, and typing gnuplot, followed by set terminal to see all available options.

It seems like gnuplot needs to be installed properly to enable png support. This is a useful link on how to do it...