How to modify dot plot in MUMmer 3 for bacteria comparative genomics?
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12 weeks ago
Manuela ▴ 30

I was trying to make a dotplot to visualize genome-genome sequence alignment by using the MUMmer 3 software. I runned the same command lines that I wrote in this question post What is the file .mums created by mummer ?

I obtain a plot that is consistent with what I expected but I do not understand why it does not show the axis scales (or labels ? I do not know how to explain but I report below my plot vs the plot made in the MUMmer page example 2.1. mummer so that you can understand what I mean). There could be two solutions:

1. Since my command lines that I use to make the plot are the same as the one of the example that I found on web, I think that I should modify the mummerplot code to fix this problem.

However, the code is written in C/C++, so not really easy for me. I tried to modify some lines of code but with no success. If you want to have a look at the code and give me some suggestions, it is available on Github.

2.But I wonder also if it is the only way to adjust the mummerplot plot. I found in the MUMmer 3 manual this:

The mummerplot script outputs three files, .gp .fplot .rplot, when run with standard parameters. The first of which is the gnuplot script. This script contains the commands necessary to generate the plot, and refers to the two data files which contain the forward and reverse matches respectively. [...] Line thickness, color, and many other options can be added or removed from the plot by hand editing the gnuplot script.

Indeed I noticed that my .gp file has some differences with respect to the .gp file of the example that I linked above (the one here). So I could simply modify my .gp file writing it as the one of the example and obtain the plot as I want it, as also the manual suggests. But how can I do it if running mummerplot to generate my plot I obtain the .ps image of the plot and the .gp file at the same time ? The .gp file is not something that I can create before running the mummerplot command...

Below I report, respectively, my plot and the plot of the example (whose aesthetics I would like to imitate): myplot niceplot

Thus, I ask if you can give me any hint by answering to one of the two questions or even both or even if there is a third way to solve that I ignore. Thank you in advance !

mummerplot • 437 views
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I haven't done this in a while, but my recollection is that gnuplot file is a simple text with commands, which you should be able to modify. Gnuplot has an extensive documentation.

Also, you could check with Mummer authors to find out the exact commands they used to make the second plot.

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As said in the question post:1. I do not understand how I can modify the gnuplot file since it is generated together with the plot; 2. the commands are the same (I also reported them). Mensur Dlakic

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You can open the .gp file in any text editor and modify it. If you learn what Gnuplot commands mean by consulting documentation, you may be able to modify them to suit your needs. Then you run Gnuplot and create a modified plot.

If the commands are identical, maybe figure 2 was made by a different program version that used to render the images differently.

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12 weeks ago

I would recommend using a different dot-plot visualizer for mummer output, one that is interactive and navigable

my favorite:

https://dnanexus.github.io/dot/

see also:

https://github.com/topics/dotplot

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