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dendrogram-heatmap: Dendrogram heatmap.ΒΆ

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.

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).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.gneiss.visualizers import dendrogram_heatmap

Docstring:

Dendrogram heatmap.

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

Parameters
----------
table : FeatureTable[Frequency]
    The feature table that will be plotted as a heatmap. This table is
    assumed to have strictly positive values.
tree : Hierarchy
    A hierarchy of feature identifiers where each 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.
metadata : MetadataColumn[Categorical]
    Categorical metadata column to group the samples.
pseudocount : Float, optional
    The pseudocount to add to avoid division by zero.
ndim : Int, optional
    Number of dimensions to highlight.
method : Str % Choices('clr', 'log'), optional
    Specifies how the data should be normalized for display.Options include
    'log' or 'clr' (default='clr').
color_map : Str % 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'), optional
    Specifies the color map for plotting the heatmap. See
    https://matplotlib.org/examples/color/colormaps_reference.html for more
    details.

Returns
-------
visualization : Visualization