heatmap: Generate heatmap of important features.¶

Docstring:

Usage: qiime sample-classifier heatmap [OPTIONS]

  Generate a heatmap of important features. Features are filtered based on
  importance scores; samples are optionally grouped by sample metadata; and a
  heatmap is generated that displays (normalized) feature abundances per
  sample.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence | Composition]
                          Feature table containing all features that should
                          be used for target prediction.            [required]
  --i-importance ARTIFACT FeatureData[Importance]
                          Feature importances.                      [required]
Parameters:
  --m-sample-metadata-file METADATA
  --m-sample-metadata-column COLUMN  MetadataColumn[Categorical]
                          Sample metadata column to use for sample labeling
                          or grouping.                              [optional]
  --m-feature-metadata-file METADATA
  --m-feature-metadata-column COLUMN  MetadataColumn[Categorical]
                          Feature metadata (e.g., taxonomy) to use for
                          labeling features in the heatmap.         [optional]
  --p-feature-count INTEGER
    Range(0, None)        Filter feature table to include top N most
                          important features. Set to zero to include all
                          features.                              [default: 50]
  --p-importance-threshold NUMBER
    Range(0, None)        Filter feature table to exclude any features with
                          an importance score less than this threshold. Set to
                          zero to include all features.           [default: 0]
  --p-group-samples / --p-no-group-samples
                          Group samples by sample metadata.   [default: False]
  --p-normalize / --p-no-normalize
                          Normalize the feature table by adding a psuedocount
                          of 1 and then taking the log10 of the table.
                                                               [default: True]
  --p-missing-samples TEXT Choices('error', 'ignore')
                          How to handle missing samples in metadata. "error"
                          will fail if missing samples are detected. "ignore"
                          will cause the feature table and metadata to be
                          filtered, so that only samples found in both files
                          are retained.                    [default: 'ignore']
  --p-metric TEXT Choices('braycurtis', 'canberra', 'chebyshev',
    'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming',
    'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'minkowski',
    'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener',
    'sokalsneath', 'sqeuclidean', 'yule')
                          Metrics exposed by seaborn (see
                          http://seaborn.pydata.org/generated/seaborn.clusterm
                          ap.html#seaborn.clustermap for more detail).
                                                       [default: 'braycurtis']
  --p-method TEXT Choices('average', 'centroid', 'complete', 'median',
    'single', 'ward', 'weighted')
                          Clustering methods exposed by seaborn (see
                          http://seaborn.pydata.org/generated/seaborn.clusterm
                          ap.html#seaborn.clustermap for more detail).
                                                          [default: 'average']
  --p-cluster TEXT Choices('both', 'features', 'none', 'samples')
                          Specify which axes to cluster. [default: 'features']
  --p-color-scheme TEXT Choices('Accent', 'Accent_r', 'Blues', 'Blues_r',
    'BrBG', 'BrBG_r', 'BuGn', 'BuGn_r', 'BuPu', 'BuPu_r', 'CMRmap',
    'CMRmap_r', 'Dark2', 'Dark2_r', 'GnBu', 'GnBu_r', 'Greens', 'Greens_r',
    'Greys', 'Greys_r', 'OrRd', 'OrRd_r', 'Oranges', 'Oranges_r', 'PRGn',
    'PRGn_r', 'Paired', 'Paired_r', 'Pastel1', 'Pastel1_r', 'Pastel2',
    'Pastel2_r', 'PiYG', 'PiYG_r', 'PuBu', 'PuBuGn', 'PuBuGn_r', 'PuBu_r',
    'PuOr', 'PuOr_r', 'PuRd', 'PuRd_r', 'Purples', 'Purples_r', 'RdBu',
    'RdBu_r', 'RdGy', 'RdGy_r', 'RdPu', 'RdPu_r', 'RdYlBu', 'RdYlBu_r',
    'RdYlGn', 'RdYlGn_r', 'Reds', 'Reds_r', 'Set1', 'Set1_r', 'Set2',
    'Set2_r', 'Set3', 'Set3_r', 'Spectral', 'Spectral_r', 'Vega10',
    'Vega10_r', 'Vega20', 'Vega20_r', 'Vega20b', 'Vega20b_r', 'Vega20c',
    'Vega20c_r', 'Wistia', 'Wistia_r', 'YlGn', 'YlGnBu', 'YlGnBu_r', 'YlGn_r',
    'YlOrBr', 'YlOrBr_r', 'YlOrRd', 'YlOrRd_r', 'afmhot', 'afmhot_r',
    'autumn', 'autumn_r', 'binary', 'binary_r', 'bone', 'bone_r', 'brg',
    'brg_r', 'bwr', 'bwr_r', 'cividis', 'cividis_r', 'cool', 'cool_r',
    'coolwarm', 'coolwarm_r', 'copper', 'copper_r', 'cubehelix',
    'cubehelix_r', 'flag', 'flag_r', 'gist_earth', 'gist_earth_r',
    'gist_gray', 'gist_gray_r', 'gist_heat', 'gist_heat_r', 'gist_ncar',
    'gist_ncar_r', 'gist_rainbow', 'gist_rainbow_r', 'gist_stern',
    'gist_stern_r', 'gist_yarg', 'gist_yarg_r', 'gnuplot', 'gnuplot2',
    'gnuplot2_r', 'gnuplot_r', 'gray', 'gray_r', 'hot', 'hot_r', 'hsv',
    'hsv_r', 'icefire', 'icefire_r', 'inferno', 'inferno_r', 'jet', 'jet_r',
    'magma', 'magma_r', 'mako', 'mako_r', 'nipy_spectral', 'nipy_spectral_r',
    'ocean', 'ocean_r', 'pink', 'pink_r', 'plasma', 'plasma_r', 'prism',
    'prism_r', 'rainbow', 'rainbow_r', 'rocket', 'rocket_r', 'seismic',
    'seismic_r', 'spectral', 'spectral_r', 'spring', 'spring_r', 'summer',
    'summer_r', 'tab10', 'tab10_r', 'tab20', 'tab20_r', 'tab20b', 'tab20b_r',
    'tab20c', 'tab20c_r', 'terrain', 'terrain_r', 'viridis', 'viridis_r',
    'vlag', 'vlag_r', 'winter', 'winter_r')
                          Color scheme for heatmap.        [default: 'rocket']
Outputs:
  --o-heatmap VISUALIZATION
                          Heatmap of important features.            [required]
  --o-filtered-table ARTIFACT FeatureTable[Frequency]
                          Filtered feature table containing data displayed in
                          heatmap.                                  [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this pipeline. If not provided, the default
                          cache under $TMP/qiime2/ will be used.
                          IMPORTANT FOR HPC USERS: If you are on an HPC system
                          and are using parallel execution it is important to
                          set this to a location that is globally accessible
                          to all nodes in the cluster.
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.