NMDS plots in 2D format

[Becky]

Hi, 

I am working on creating NMDS plots for my data set. The script is working fine and I can then use emperor to view a 3D plot but I wanted to know if there is a way to view it in 2D like other platforms. This is easier to view in publications, etc. 

Thanks, 

Becky

[Luke Ursell]

Hi Becky,

The make_2d_plots.py script might be helpful for you.

Luke

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[Becky]

Thanks Luke I will give it a try

[Becky]

Its taken me a while to get back to this but when I tried to use the make_2d_plots.py I am getting this error

qiime@qiime-VirtualBox:~$ make_2d_plots.py -i weighted_unifrac_nmds -m xesto_UKY_all_mapC.txt -o weighted_unifrac_nmds_2d_plot

Traceback (most recent call last):

  File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/make_2d_plots.py", line 224, in <module>

    main()

  File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/make_2d_plots.py", line 175, in main

    data['coord'] = get_coord(opts.coord_fname)

  File "/home/qiime/qiime_software/qiime-1.8.0-release/lib/qiime/make_3d_plots.py", line 856, in get_coord

    coord_header, coords, eigvals, pct_var = parse_coords(coord_f)

  File "/home/qiime/qiime_software/qiime-1.8.0-release/lib/qiime/parse.py", line 361, in parse_coords

    raise QiimeParseError("The line with the vector number was not "

qiime.parse.QiimeParseError: The line with the vector number was not found, this information is required in coordinates files

[Tony Walters]

Becky, can you try specifying the principle coordinates file (usually _pc.txt) for the input?

[Becky]

HI, 

My overall goal is the create a graph for the nmds.py script. So I ran that script first using a distance matrix and then used the output created for my input for teh make_2d_plots.py. Is there another way to visualize the nmds plots in 2d?

Becky

 

qiime@qiime-VirtualBox:~$ nmds.py -i weighted_unifrac_dm.txt -o weighted_unifrac_nmds

[Tony Walters]

Becky, I don't think you can feed the nmds output into make_2d_plots.py. You might want to add a comment/request on this issue: https://github.com/qiime/qiime/issues/1341 to see about getting the output formatted in a such a way that it can be processed correctly with make_2d_plots as well as the 3d plots option.

You might want to check out the R package for this: http://jonlefcheck.net/2012/10/24/nmds-tutorial-in-r/