Add biplots to make_emperor.py -- fixes #12 #54
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This controller function will let you process the raw data i. e. otu table and coordinates file and will let you retrieve the scores and N most prevalent taxons.
Script is now capable of writting the biplots coordinates file.
This module currently aids with the sorting that should take place when operating otu tables from the script interface. The all variable in the __init__.py file is now updated.
This bug caused the biplot information to be placed in the exact coordinates where samples were positioned. This function now makes use of emperor.sort to make sure that the sample identifiers match between coordinates files and otu tables. The script interface was updated accordingly since the filtering of the otu table is now performed using the header in the coordinates data.
A new function has been added to the format module, this function is responsible for presenting the appropriate GUI elements on screen.
The following functions were added to the javascript file:
- Callback to respond to the controller in the user interface
to show or hide the labels with the taxonomic lineages.
- Scaling of the biplots when they appear on screen
- Presentation of the labels when for each frame
Minor updates took place in the emperor.css file to reflec the changes
in format.py and in emperor.js.
The main script now supports biplots and jackknifed plots. Test data was added for the new examples that have been added to the script interface. This closes biocore#12
preprocess_otu_table is now capable of handling empty inputs for the otu table related values. This will generate empty outputs. This change allows the script interface to follow the same structure as preprocess_mapping_file and preprocess_coodinates. This change also now allows using a custom axis and biplots.
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This works nicely but it will be good to be able to hide all the |
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Sounds good to me, will work on this. |
The color of the biplots on screen can now be changed to any color. The biplots can now be turned-off.
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Ok, two new controllers have been added addressing your suggestions. |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/emperor-github-pr/7/ |
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@jrrideout, do you know if this failure could be related to #69? |
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I don't think so, as I was able to find a workaround (by not running setup.py). Since the other pull requests have the script usage tests passing, these are probably real failures. |
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Also, note that only two of the script usage test commands are failing- the other five are passing. Emperor is using QIIME 1.6.0, biom-format 1.1.1, PyCogent 1.5.3, and NumPy 1.5.1 (the same setup that's in the latest QIIME 1.6.0 AMI). |
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Thanks for the info, I'll look into this, specifically with those versions. El 06/05/2013, a las 12:18, Jai Ram Rideout notifications@github.com escribió:
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Ok, I just looked into this and this is the thing that's causing the problem: qiime@qiime-VirtualBox:~/qiime_software/emperor/tests/scripts_test_data/make_emperor$ /home/qiime/qiime_software/emperor/scripts//make_emperor.py -i unweighted_unifrac_pc.txt -m Fasting_Map.txt -t otu_table_L3.txt -o _biplot
Traceback (most recent call last):
File "/home/qiime/qiime_software/emperor/scripts//make_emperor.py", line 400, in <module>
main()
File "/home/qiime/qiime_software/emperor/scripts//make_emperor.py", line 261, in main
taxa_fp, 'U'), count_map_f=float, remove_empty_rows=True)
TypeError: parse_classic_otu_table() got an unexpected keyword argument 'remove_empty_rows'It seems that the You were right @jrrideout 👍 this was specific to those versions. |
This change will allow the tests to pass for 1.6.0 and 1.6.0-dev.
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Sounds good- thanks @ElDeveloper! |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/emperor-github-pr/13/ |
Conflicts: emperor/format.py scripts/make_emperor.py
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/emperor-github-pr/15/ |
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Just solved the conflicts in this pull request. |
Add biplots to make_emperor.py -- fixes #12
A summary of the new features included in this pull request:
This pull request also includes two new command calls in the script usage examples.