dendrogram-heatmap: Dendrogram heatmap.¶

Docstring:

Usage: qiime gneiss dendrogram-heatmap [OPTIONS]

  Visualize the feature table as a heatmap, with samples sorted along a
  specified categorical metadata column and features clustered together
  specified by the tree.

  WARNING:

  This command is deprecated and will be removed in a future version of this
  plugin.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          The feature table that will be plotted as a
                          heatmap. This table is assumed to have strictly
                          positive values.                          [required]
  --i-tree ARTIFACT       A hierarchy of feature identifiers where each
    Hierarchy             tipcorresponds to the feature identifiers in the
                          table. This tree can contain tip ids that are not
                          present in the table, but all feature ids in the
                          table must be present in this tree.       [required]
Parameters:
  --m-metadata-file METADATA
  --m-metadata-column COLUMN  MetadataColumn[Categorical]
                          Categorical metadata column to group the samples.
                                                                    [required]
  --p-pseudocount NUMBER  The pseudocount to add to avoid division by zero.
                                                                [default: 0.5]
  --p-ndim INTEGER        Number of dimensions to highlight.     [default: 10]
  --p-method TEXT Choices('clr', 'log')
                          Specifies how the data should be normalized for
                          display.Options include 'log' or 'clr'
                          (default='clr').                    [default: 'clr']
  --p-color-map TEXT Choices('viridis', 'inferno', 'plasma', 'magma',
    'Blues', 'BuGn', 'BuPu', 'GnBu', 'Greens', 'Greys', 'Oranges', 'OrRd',
    'PuBu', 'PuBuGn', 'PuRd', 'Purples', 'RdPu', 'Reds', 'YlGn', 'YlGnBu',
    'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'cool', 'copper',
    'gist_heat', 'gray', 'hot', 'pink', 'spring', 'summer', 'winter', 'BrBG',
    'bwr', 'coolwarm', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu',
    'RdYlGn', 'Spectral', 'seismic', 'Accent', 'Dark2', 'Paired', 'Pastel1',
    'Pastel2', 'Set1', 'Set2', 'Set3', 'Vega10', 'Vega20', 'Vega20b',
    'Vega20c', 'gist_earth', 'terrain', 'ocean', 'gist_stern', 'brg',
    'CMRmap', 'cubehelix', 'gnuplot', 'gnuplot2', 'gist_ncar',
    'nipy_spectral', 'jet', 'rainbow', 'gist_rainbow', 'hsv', 'flag', 'prism')
                          Specifies the color map for plotting the heatmap.
                          See
                          https://matplotlib.org/examples/color/colormaps_refe
                          rence.html for more details.    [default: 'viridis']
Outputs:
  --o-visualization VISUALIZATION
                                                                    [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).
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.