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sbslee / dokdo

A Python package for microbiome sequencing analysis with QIIME 2
https://dokdo.readthedocs.io
MIT License
42 stars 12 forks source link

Problem with taxa_abundance_bar_plot #30

Closed RayanaFeltrin closed 2 years ago

RayanaFeltrin commented 3 years ago

Hey there!

Firstly, congrats on dokdo... I'm in love with the plots it can make and very excited to generate my first one!

Well, I'm working on Jupyter Notebook... I am with the qiime2 environment already activated, but after running the following code...

import dokdo

import matplotlib.pyplot as plt
%matplotlib inline

import numpy as np
np.random.seed(1)

qzv_file = '/home/rayana/Documents/MiSeq_16S/taxonomy.qzv'

dokdo.taxa_abundance_bar_plot(
    qzv_file,
    level=2,
    count=8,
    figsize=(9, 7)
)

plt.tight_layout()

... I've got the following error:

AttributeError Traceback (most recent call last) in _----> 1 dokdo.taxa_abundance_barplot( _2 qzvfile, 3 level=2, 4 count=8, 5 figsize=(9, 7)

_AttributeError: module 'dokdo' has no attribute 'taxa_abundance_barplot'

Could you please help me on what I should do?

Thank you in advance!

Best regards, Rayana

sbslee commented 3 years ago

@RayanaFeltrin,

I'm happy to hear you like dokdo's plots :) As for your problem, it looks like something went wrong during installation. Can you tell me how you installed dokdo? Did you follow the steps described in README:

$ git clone https://github.com/sbslee/dokdo
$ cd dokdo
$ pip install .

Also, can you show me the output of this command in your terminal?

$ dokdo -v
RayanaFeltrin commented 3 years ago

Thank you for the quick response!

Yeah, I've followed these steps... inclusively, I ran them inside the envs/qiime2-2021.4 folder to ensure dokdo was inside my environment (don't know if the way I did it makes sense).

The output of dokdo -v in my terminal is:

_Traceback (most recent call last):
  File "/home/rayana/anaconda3/bin/dokdo", line 5, in <module>
    from dokdo.__main__ import main
  File "/home/rayana/anaconda3/lib/python3.8/site-packages/dokdo/__init__.py", line 1, in <module>
    from .api import *
  File "/home/rayana/anaconda3/lib/python3.8/site-packages/dokdo/api/__init__.py", line 1, in <module>
    from .common import get_mf, pname
  File "/home/rayana/anaconda3/lib/python3.8/site-packages/dokdo/api/common.py", line 22, in <module>
    import qiime2
ModuleNotFoundError: No module named 'qiime2'_

... which for me is strange, because I'm actually running it inside the qiime2 environment!

sbslee commented 3 years ago

@RayanaFeltrin,

Can you print me the output of this command?

$ conda list
RayanaFeltrin commented 3 years ago

Here it is!

Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge alsa-lib 1.2.3 h516909a_0 conda-forge argon2-cffi 20.1.0 py38h497a2fe_2 conda-forge async_generator 1.10 py_0 conda-forge attrs 20.3.0 pyhd3deb0d_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge bibtexparser 1.1.0 py_0 conda-forge binutils_impl_linux-64 2.35.1 h193b22a_2 conda-forge binutils_linux-64 2.35 h67ddf6f_30 conda-forge bioconductor-biobase 2.50.0 r40hd029910_1 bioconda bioconductor-biocgenerics 0.36.0 r40hdfd78af_1 bioconda bioconductor-biocparallel 1.24.1 r40h399db7b_0 bioconda bioconductor-biostrings 2.58.0 r40hd029910_1 bioconda bioconductor-dada2 1.18.0 r40h399db7b_1 bioconda bioconductor-delayedarray 0.16.3 r40hd029910_0 bioconda bioconductor-genomeinfodb 1.26.4 r40hdfd78af_0 bioconda bioconductor-genomeinfodbdata 1.2.4 r40hdfd78af_2 bioconda bioconductor-genomicalignments 1.26.0 r40hd029910_1 bioconda bioconductor-genomicranges 1.42.0 r40hd029910_1 bioconda bioconductor-iranges 2.24.1 r40hd029910_0 bioconda bioconductor-matrixgenerics 1.2.1 r40hdfd78af_0 bioconda bioconductor-rhtslib 1.22.0 r40hd029910_1 bioconda bioconductor-rsamtools 2.6.0 r40h399db7b_1 bioconda bioconductor-s4vectors 0.28.1 r40hd029910_0 bioconda bioconductor-shortread 1.48.0 r40h399db7b_1 bioconda bioconductor-summarizedexperiment 1.20.0 r40hdfd78af_1 bioconda bioconductor-xvector 0.30.0 r40hd029910_1 bioconda bioconductor-zlibbioc 1.36.0 r40hd029910_1 bioconda biom-format 2.1.10 py38h0b5ebd8_0 conda-forge blas 1.1 openblas conda-forge blast 2.11.0 pl526he19e7b1_0 bioconda bleach 3.3.0 pyh44b312d_0 conda-forge bokeh 2.3.1 py38h578d9bd_0 conda-forge bowtie2 2.4.2 py38hc2f83ea_2 bioconda brotlipy 0.7.0 py38h497a2fe_1001 conda-forge bwidget 1.9.14 ha770c72_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h7f98852_1 conda-forge ca-certificates 2021.7.5 h06a4308_1
cachecontrol 0.12.6 py_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 h6cf1ce9_1008 conda-forge certifi 2021.5.30 py38h06a4308_0
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font-ttf-inconsolata 2.001 hcb22688_0
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font-ttf-ubuntu 0.83 h8b1ccd4_0
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pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-file-listing 6.04 pl526_1 bioconda perl-file-path 2.16 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-html-parser 3.72 pl526h6bb024c_5 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-html-tree 5.07 pl526_1 bioconda perl-http-cookies 6.04 pl526_0 bioconda perl-http-daemon 6.01 pl526_1 bioconda perl-http-date 6.02 pl526_3 bioconda perl-http-message 6.18 pl526_0 bioconda perl-http-negotiate 6.01 pl526_3 bioconda perl-io-compress 2.087 pl526he1b5a44_0 bioconda perl-io-html 1.001 pl526_2 bioconda perl-io-socket-ssl 2.066 pl526_0 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-libwww-perl 6.39 pl526_0 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-lwp-mediatypes 6.04 pl526_0 bioconda perl-lwp-protocol-https 6.07 pl526_4 bioconda 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py_1003 conda-forge pigz 2.6 h27826a3_0 conda-forge pillow 8.1.2 py38ha0e1e83_1 conda-forge pip 21.0.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pluggy 0.13.1 py38h578d9bd_4 conda-forge prometheus_client 0.10.1 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.18 pyha770c72_0 conda-forge psutil 5.8.0 py38h497a2fe_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge py 1.10.0 pyhd3deb0d_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygments 2.8.1 pyhd8ed1ab_0 conda-forge pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.12.3 py38h578d9bd_7 conda-forge pyqt-impl 5.12.3 py38h7400c14_7 conda-forge pyqt5-sip 4.19.18 py38h709712a_7 conda-forge pyqtchart 5.12 py38h7400c14_7 conda-forge pyqtwebengine 5.12.1 py38h7400c14_7 conda-forge pyrsistent 0.17.3 py38h497a2fe_2 conda-forge pysocks 1.7.1 py38h578d9bd_3 conda-forge pytest 6.2.3 py38h578d9bd_0 conda-forge python 3.8.8 hffdb5ce_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python-isal 0.10.0 py38h497a2fe_0 conda-forge python_abi 3.8 2_cp38 conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py38h497a2fe_0 conda-forge pyzmq 22.0.3 py38h2035c66_1 conda-forge q2-alignment 2021.4.0 py38_0 qiime2/label/r2021.4 q2-composition 2021.4.0 py38_0 qiime2/label/r2021.4 q2-cutadapt 2021.4.0 py38_0 qiime2/label/r2021.4 q2-dada2 2021.4.0 py38_0 qiime2/label/r2021.4 q2-deblur 2021.4.0 py38_0 qiime2/label/r2021.4 q2-demux 2021.4.0 py38_0 qiime2/label/r2021.4 q2-diversity 2021.4.0 py38_0 qiime2/label/r2021.4 q2-diversity-lib 2021.4.0 0 qiime2/label/r2021.4 q2-emperor 2021.4.0 py38_0 qiime2/label/r2021.4 q2-feature-classifier 2021.4.0 py38_0 qiime2/label/r2021.4 q2-feature-table 2021.4.0 py38_0 qiime2/label/r2021.4 q2-fragment-insertion 2021.4.0 py38_0 qiime2/label/r2021.4 q2-gneiss 2021.4.0 py38_0 qiime2/label/r2021.4 q2-longitudinal 2021.4.0 py38_0 qiime2/label/r2021.4 q2-metadata 2021.4.0 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sbslee commented 3 years ago

I think you cut off the metadata lines. Can you add those as well?

(fuc) sbslee@Seung-beens-Mac-mini getrm-tutorial % conda list
# packages in environment at /Users/sbslee/opt/anaconda3/envs/fuc:
#
# Name                    Version                   Build  Channel
alabaster                 0.7.12                     py_0    conda-forge
appnope                   0.1.2            py39h6e9494a_1    conda-forge
...
sbslee commented 3 years ago

Never mind. I found the problem. It looks like you somehow downloaded dokdo from PyPI:

...
dokdo 1.0.0 pypi_0 pypi
...

There is another package named dokdo that just got published to PyPI a couple months ago (I'm currently trying to communicate with its author to see if he or she is willing to remove it from PyPI so I can upload mine -- their project seems like a toy project with only 4 commits). Anyways, that's why I asked if you followed the installation steps in the README file.

You can remove the other dokdo with:

$ pip uninstall dokdo

And then install my dokdo as described in README. It should solve the problem.

RayanaFeltrin commented 3 years ago

Well, now it recognized the _taxa_abundance_barplot module... but should I have a level-6.csv file?

Because when I ran the same dokdo.taxa_abundance_bar_plot command that I mentioned in the beginning, I got the following error:

FileNotFoundError Traceback (most recent call last)

in ----> 1 dokdo.taxa_abundance_bar_plot( 2 qzv_file, 3 figsize=(10, 7), 4 level=6, 5 count=8, ~/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/dokdo/api/taxa_abundance.py in taxa_abundance_bar_plot(visualization, metadata, level, group, group_order, by, ax, figsize, width, count, exclude_samples, include_samples, exclude_taxa, sort_by_names, colors, label_columns, orders, sample_names, csv_file, taxa_names, sort_by_mean1, sort_by_mean2, sort_by_mean3, show_others, cmap_name, legend_short, pname_kws, legend) 510 with tempfile.TemporaryDirectory() as t: 511 common.export(visualization, t) --> 512 df = pd.read_csv(f'{t}/level-{level}.csv', index_col=0) 513 514 if sort_by_mean1: ~/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/io/parsers.py in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options) 608 kwds.update(kwds_defaults) 609 --> 610 return _read(filepath_or_buffer, kwds) 611 612 ~/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds) 460 461 # Create the parser. --> 462 parser = TextFileReader(filepath_or_buffer, **kwds) 463 464 if chunksize or iterator: ~/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/io/parsers.py in __init__(self, f, engine, **kwds) 817 self.options["has_index_names"] = kwds["has_index_names"] 818 --> 819 self._engine = self._make_engine(self.engine) 820 821 def close(self): ~/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/io/parsers.py in _make_engine(self, engine) 1048 ) 1049 # error: Too many arguments for "ParserBase" -> 1050 return mapping[engine](self.f, **self.options) # type: ignore[call-arg] 1051 1052 def _failover_to_python(self): ~/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/io/parsers.py in __init__(self, src, **kwds) 1865 1866 # open handles -> 1867 self._open_handles(src, kwds) 1868 assert self.handles is not None 1869 for key in ("storage_options", "encoding", "memory_map", "compression"): ~/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/io/parsers.py in _open_handles(self, src, kwds) 1360 Let the readers open IOHanldes after they are done with their potential raises. 1361 """ -> 1362 self.handles = get_handle( 1363 src, 1364 "r", ~/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/io/common.py in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options) 640 errors = "replace" 641 # Encoding --> 642 handle = open( 643 handle, 644 ioargs.mode, FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpgc2npuwu/level-6.csv'
RayanaFeltrin commented 2 years ago

I've just realized that I put the wrong .qzv file... now I put the taxa-bar-plots.qzv and it worked.

Thank you so much for your help!

Best, Rayana